SRX3404498 NTM.0106.BAL.R.untouched.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698204 SAMN08033294 NTM.0106.BAL.R.untouched.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404499 NTM.0072.N.S.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698206 SAMN08033219 NTM.0072.N.S.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404500 NTM.0106.BAL.L.untouched.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698205 SAMN08033293 NTM.0106.BAL.L.untouched.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404501 NTM.0148.BAL.L1.untouched.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698207 SAMN08033296 NTM.0148.BAL.L1.untouched.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404502 NTM.0148.BAL.L.untouched.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698208 SAMN08033295 NTM.0148.BAL.L.untouched.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404503 NTM.0057.Sputum.4 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698210 SAMN08033012 NTM.0057.Sputum.4 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404504 NTM.0057.Sputum.3 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698209 SAMN08033011 NTM.0057.Sputum.3 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404505 NTM.0033.Sputum.2 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698211 SAMN08033008 NTM.0033.Sputum.2 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404506 NTM.0027.Sputum.3 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698212 SAMN08033007 NTM.0027.Sputum.3 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404507 NTM.0045.Sputum.3 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698213 SAMN08033010 NTM.0045.Sputum.3 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404508 NTM.0038.Sputum.2 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698214 SAMN08033009 NTM.0038.Sputum.2 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404509 NTM.0018.Sputum.4 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698216 SAMN08033004 NTM.0018.Sputum.4 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404510 NTM.0018.Sputum.3 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698215 SAMN08033003 NTM.0018.Sputum.3 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404511 NTM.0026.Sputum.2 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698217 SAMN08033006 NTM.0026.Sputum.2 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404512 NTM.0025.Sputum.2 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698218 SAMN08033005 NTM.0025.Sputum.2 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404513 NTM.0040.2.Oral SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698219 SAMN08032887 NTM.0040.2.Oral AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404514 NTM.0087.Bronch.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698220 SAMN08033220 NTM.0087.Bronch.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404515 NTM.0106.Bronch.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698221 SAMN08033300 NTM.0106.Bronch.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404516 NTM.0179.BAL.RUL.untouched.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698222 SAMN08033299 NTM.0179.BAL.RUL.untouched.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404517 NTM.0006.1.Oral SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698223 SAMN08032801 NTM.0006.1.Oral AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404518 NTM.0007.1.Oral SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698224 SAMN08032802 NTM.0007.1.Oral AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404519 NTM.0003.2.Oral SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698225 SAMN08032799 NTM.0003.2.Oral AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404520 NTM.0004.1.Oral SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698226 SAMN08032800 NTM.0004.1.Oral AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404521 NTM.0002.5.Oral SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698227 SAMN08032797 NTM.0002.5.Oral AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404522 NTM.0003.1.Oral SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698228 SAMN08032798 NTM.0003.1.Oral AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404523 NTM.0002.2.Oral SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698229 SAMN08032795 NTM.0002.2.Oral AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404524 NTM.0002.4.Oral SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698230 SAMN08032796 NTM.0002.4.Oral AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404525 NTM.0001.1.Oral SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698244 SAMN08032793 NTM.0001.1.Oral AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404526 NTM.0002.1.Oral SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698231 SAMN08032794 NTM.0002.1.Oral AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404527 NTM.0072.Bronch.Yan.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698232 SAMN08033218 NTM.0072.Bronch.Yan.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404528 NTM.0067.Bronch.Yan.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698233 SAMN08033215 NTM.0067.Bronch.Yan.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404529 NTM.0053.1.Sputum SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698234 SAMN08032923 NTM.0053.1.Sputum AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404530 NTM.0031.1.Oral SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698235 SAMN08032924 NTM.0031.1.Oral AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404531 NTM.0049.1.Oral SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698236 SAMN08032925 NTM.0049.1.Oral AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404532 NTM.0050.1.Oral SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698237 SAMN08032926 NTM.0050.1.Oral AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404533 NTM.0050.1.Sputum SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698238 SAMN08032927 NTM.0050.1.Sputum AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404534 NTM.0002.Oral.Rinse.5 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698239 SAMN08032928 NTM.0002.Oral.Rinse.5 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404535 NTM.0002.Oral.Rinse.6 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698240 SAMN08032929 NTM.0002.Oral.Rinse.6 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404536 NTM.0002.Oral.Rinse.7 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698241 SAMN08032930 NTM.0002.Oral.Rinse.7 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404537 NTM.0002.Oral.Rinse.8 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698242 SAMN08032931 NTM.0002.Oral.Rinse.8 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404538 NTM.0003.Oral.Rinse.3 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698243 SAMN08032932 NTM.0003.Oral.Rinse.3 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404539 NTM.0067.N.S.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698261 SAMN08033216 NTM.0067.N.S.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404540 NTM.0050.N.S.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698245 SAMN08033213 NTM.0050.N.S.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404541 NTM.0049.N.S.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698246 SAMN08033210 NTM.0049.N.S.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404542 NTM.0049.Bronch.Yan.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698247 SAMN08033209 NTM.0049.Bronch.Yan.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404543 NTM.0049.Bronch.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698248 SAMN08033208 NTM.0049.Bronch.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404544 NTM.0031.N.S.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698249 SAMN08033207 NTM.0031.N.S.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404545 NTM.0031.Bronch.Yan.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698250 SAMN08033206 NTM.0031.Bronch.Yan.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404546 NTM.0031.Bronch.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698251 SAMN08033205 NTM.0031.Bronch.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404547 NTM.0009.N.S.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698252 SAMN08033204 NTM.0009.N.S.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404548 NTM.0009.Bronch.Yan.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698253 SAMN08033203 NTM.0009.Bronch.Yan.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404549 NTM.0050.Bronch.Yan.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698254 SAMN08033212 NTM.0050.Bronch.Yan.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404550 NTM.0050.Bronch.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698255 SAMN08033211 NTM.0050.Bronch.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404551 NTM.0067.Bronch.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698256 SAMN08033214 NTM.0067.Bronch.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404552 NTM.0107.BAL.LUL.untouched.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698257 SAMN08033273 NTM.0107.BAL.LUL.untouched.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404553 NTM.0086.Bronch.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698258 SAMN08033274 NTM.0086.Bronch.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404554 NTM.0086.Bronch.Yan.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698259 SAMN08033275 NTM.0086.Bronch.Yan.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404555 NTM.0086.N.S.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698262 SAMN08033276 NTM.0086.N.S.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404556 NTM.0107.Bronch.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698260 SAMN08033277 NTM.0107.Bronch.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404557 NTM.0107.Bronch.Yan.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698264 SAMN08033278 NTM.0107.Bronch.Yan.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404558 NTM.0107.N.S.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698263 SAMN08033279 NTM.0107.N.S.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404559 M.Fortuium.71 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698265 SAMN08033280 M.Fortuium.71 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404560 Strep.M.Fortuium.1.1.71 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698266 SAMN08033281 Strep.M.Fortuium.1.1.71 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404561 NTM.0036.Oral.Rinse.2 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698267 SAMN08033122 NTM.0036.Oral.Rinse.2 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404562 NTM.0148.Trach.Aspirate.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698268 SAMN08033313 NTM.0148.Trach.Aspirate.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404563 NTM.0017.Oral.Rinse.2 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698269 SAMN08033121 NTM.0017.Oral.Rinse.2 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404564 NTM.0109.Sputum.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698270 SAMN08033111 NTM.0109.Sputum.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404565 NTM.0022.2.Sputum SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698271 SAMN08032839 NTM.0022.2.Sputum AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404566 NTM.0110.Sputum.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698272 SAMN08033112 NTM.0110.Sputum.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404567 NTM.0101.Sputum.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698289 SAMN08033046 NTM.0101.Sputum.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404568 NTM.0098.Sputum.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698273 SAMN08033045 NTM.0098.Sputum.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404569 NTM.0104.Sputum.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698274 SAMN08033048 NTM.0104.Sputum.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404570 NTM.0103.Sputum.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698275 SAMN08033047 NTM.0103.Sputum.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404571 NTM.0105.Sputum.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698276 SAMN08033049 NTM.0105.Sputum.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404572 NTM.0106.Sputum.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698277 SAMN08033050 NTM.0106.Sputum.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404573 NTM.0005.Oral.Rinse.2 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698278 SAMN08033052 NTM.0005.Oral.Rinse.2 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404574 NTM.0112.Sputum.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698279 SAMN08033051 NTM.0112.Sputum.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404575 NTM.0110.Oral.Rinse.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698293 SAMN08033105 NTM.0110.Oral.Rinse.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404576 NTM.0082.Sputum.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698280 SAMN08033106 NTM.0082.Sputum.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404577 NTM.0083.Sputum.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698281 SAMN08033107 NTM.0083.Sputum.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404578 NTM.0096.Sputum.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698282 SAMN08033109 NTM.0096.Sputum.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404579 NTM.0085.Sputum.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698283 SAMN08033041 NTM.0085.Sputum.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404580 NTM.0099.Sputum.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698284 SAMN08033110 NTM.0099.Sputum.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404581 DFW.69 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698285 SAMN08033119 DFW.69 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404582 NTM.0017.Sputum.2 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698286 SAMN08033144 NTM.0017.Sputum.2 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404583 NTM.0095.Bronch.Yan.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698287 SAMN08033228 NTM.0095.Bronch.Yan.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404584 NTM.0095.Bronch.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698288 SAMN08033227 NTM.0095.Bronch.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404585 NTM.0100.Bronch.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698316 SAMN08033230 NTM.0100.Bronch.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404586 NTM.0179.Bronch.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698290 SAMN08033305 NTM.0179.Bronch.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404587 NTM.0148.Bronch.Yan.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698291 SAMN08033303 NTM.0148.Bronch.Yan.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404588 NTM.0179.Bronch.Yan.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698292 SAMN08033306 NTM.0179.Bronch.Yan.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404589 NTM.0095.N.S.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698294 SAMN08033229 NTM.0095.N.S.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404590 NTM.0148.OralRinse.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698306 SAMN08033309 NTM.0148.OralRinse.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404591 NTM.0148.Sputum.Pre.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698295 SAMN08033310 NTM.0148.Sputum.Pre.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404592 NTM.0179.N.S.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698308 SAMN08033307 NTM.0179.N.S.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404593 NTM.0148.Nasal.Swab.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698296 SAMN08033308 NTM.0148.Nasal.Swab.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404594 NTM.0091.Bronch.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698297 SAMN08033224 NTM.0091.Bronch.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404595 NTM.0106.Bronch.Sup.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698298 SAMN08033311 NTM.0106.Bronch.Sup.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404596 NTM.0148.Bronch.Sup.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698299 SAMN08033312 NTM.0148.Bronch.Sup.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404597 NTM.0090.N.S.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698300 SAMN08033223 NTM.0090.N.S.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404598 NTM.0091.N.S.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698301 SAMN08033226 NTM.0091.N.S.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404599 NTM.0091.Bronch.Yan.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698302 SAMN08033225 NTM.0091.Bronch.Yan.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404600 NTM.0068.Oral.Rinse.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698303 SAMN08032967 NTM.0068.Oral.Rinse.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404601 NTM.0068.Oral.Rinse.2 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698304 SAMN08032968 NTM.0068.Oral.Rinse.2 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404602 NTM.0069.Oral.Rinse.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698335 SAMN08032969 NTM.0069.Oral.Rinse.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404603 NTM.0069.Oral.Rinse.2 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698305 SAMN08032970 NTM.0069.Oral.Rinse.2 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404604 NTM.0065.Oral.Rinse.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698338 SAMN08032963 NTM.0065.Oral.Rinse.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404605 NTM.0065.Oral.Rinse.2 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698307 SAMN08032964 NTM.0065.Oral.Rinse.2 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404606 NTM.0066.Oral.Rinse.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698399 SAMN08032965 NTM.0066.Oral.Rinse.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404607 NTM.0066.Oral.Rinse.2 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698309 SAMN08032966 NTM.0066.Oral.Rinse.2 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404608 NTM.0070.Oral.Rinse.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698310 SAMN08032971 NTM.0070.Oral.Rinse.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404609 NTM.0071.Oral.Rinse.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698311 SAMN08032972 NTM.0071.Oral.Rinse.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404610 NTM.0067.Bronch.Sup.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698312 SAMN08033088 NTM.0067.Bronch.Sup.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404611 NTM.0050.Bronch.sup.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698313 SAMN08033087 NTM.0050.Bronch.sup.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404612 NTM.0087.Bronch.Sup.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698314 SAMN08033090 NTM.0087.Bronch.Sup.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404613 NTM.0072.Bronch.Sup.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698315 SAMN08033089 NTM.0072.Bronch.Sup.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404614 NTM.0009.Bronch.Sup.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698317 SAMN08033084 NTM.0009.Bronch.Sup.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404615 NTM.0108.Sputum.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698318 SAMN08033083 NTM.0108.Sputum.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404616 NTM.0049.Bronch.Sup.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698319 SAMN08033086 NTM.0049.Bronch.Sup.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404617 NTM.0031.Bronch.Sup.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698320 SAMN08033085 NTM.0031.Bronch.Sup.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404618 NTM.0052.1.Sputum.71 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698321 SAMN08033147 NTM.0052.1.Sputum.71 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404619 NTM.0052.2.Sputum.71 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698322 SAMN08033148 NTM.0052.2.Sputum.71 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404620 NTM.0053.1.Sputum.71 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698323 SAMN08033149 NTM.0053.1.Sputum.71 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404621 NTM.0076.Sputum.2 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698324 SAMN08033150 NTM.0076.Sputum.2 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404622 NTM.0091.Bronch.Sup.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698325 SAMN08033092 NTM.0091.Bronch.Sup.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404623 NTM.0090.Bronch.Sup.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698326 SAMN08033091 NTM.0090.Bronch.Sup.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404624 NTM.0036.Sputum.2 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698327 SAMN08033145 NTM.0036.Sputum.2 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404625 NTM.0051.1.Sputum.71 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698328 SAMN08033146 NTM.0051.1.Sputum.71 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404626 NTM.0024.2.Sputum SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698329 SAMN08032843 NTM.0024.2.Sputum AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404627 NTM.0072.Nasal.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698330 SAMN08033254 NTM.0072.Nasal.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404628 NTM.0105.Oral.Rinse.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698331 SAMN08032991 NTM.0105.Oral.Rinse.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404629 NTM.0106.Oral.Rinse.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698332 SAMN08032992 NTM.0106.Oral.Rinse.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404630 NTM.0101.Oral.Rinse.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698333 SAMN08032989 NTM.0101.Oral.Rinse.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404631 NTM.0103.Oral.Rinse.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698334 SAMN08032990 NTM.0103.Oral.Rinse.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404632 NTM.0097.Oral.Rinse.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698337 SAMN08032987 NTM.0097.Oral.Rinse.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404633 NTM.0098.Oral.Rinse.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698336 SAMN08032988 NTM.0098.Oral.Rinse.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404634 NTM.0089.Oral.Rinse.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698339 SAMN08032985 NTM.0089.Oral.Rinse.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404635 NTM.0092.Oral.Rinse.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698340 SAMN08032986 NTM.0092.Oral.Rinse.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404636 NTM.0084.Oral.Rinse.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698341 SAMN08032983 NTM.0084.Oral.Rinse.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404637 NTM.0085.Oral.Rinse.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698342 SAMN08032984 NTM.0085.Oral.Rinse.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404638 NTM.0026.1.Sputum SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698343 SAMN08032846 NTM.0026.1.Sputum AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404639 NTM.0067.Oral.Rinse.2 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698344 SAMN08033257 NTM.0067.Oral.Rinse.2 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404640 NTM.0027.2.Sputum SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698345 SAMN08032847 NTM.0027.2.Sputum AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404641 NTM.0115.Oral.Rinse.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698346 SAMN08033258 NTM.0115.Oral.Rinse.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404642 NTM.0028.1.Sputum SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698348 SAMN08032848 NTM.0028.1.Sputum AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404643 NTM.0049.Nasal.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698347 SAMN08033252 NTM.0049.Nasal.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404644 NTM.0009.Nasal.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698349 SAMN08033251 NTM.0009.Nasal.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404645 NTM.0030.1.Sputum SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698350 SAMN08032849 NTM.0030.1.Sputum AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404646 NTM.0123.Bronch.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698351 SAMN08033245 NTM.0123.Bronch.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404647 NTM.0123.Bronch.Yan.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698352 SAMN08033246 NTM.0123.Bronch.Yan.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404648 NTM.0115.N.S.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698353 SAMN08033244 NTM.0115.N.S.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404649 NTM.0115.Bronch.Yan.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698354 SAMN08033243 NTM.0115.Bronch.Yan.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404650 NTM.0005.B.Nasal.71 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698355 SAMN08033250 NTM.0005.B.Nasal.71 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404651 NTM.0031.LungTissue.L.uninvoled.P SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698356 SAMN08033249 NTM.0031.LungTissue.L.uninvoled.P AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404652 NTM.0031.LungTissue.L.invoved.P SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698357 SAMN08033248 NTM.0031.LungTissue.L.invoved.P AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404653 NTM.0123.Oral.Wash.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698495 SAMN08033259 NTM.0123.Oral.Wash.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404654 NTM.0123.N.S.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698358 SAMN08033247 NTM.0123.N.S.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404655 NTM.0050.1.Oral.71 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698359 SAMN08033256 NTM.0050.1.Oral.71 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404656 NTM.0065.Sputum.2 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698360 SAMN08033021 NTM.0065.Sputum.2 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404657 NTM.0066.Sputum.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698361 SAMN08033022 NTM.0066.Sputum.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404658 NTM.0057.Sputum.5 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698362 SAMN08033013 NTM.0057.Sputum.5 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404659 NTM.0059.Sputum.2 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698363 SAMN08033014 NTM.0059.Sputum.2 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404660 NTM.0061.Sputum.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698366 SAMN08033016 NTM.0061.Sputum.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404661 NTM.0060.Sputum.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698365 SAMN08033015 NTM.0060.Sputum.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404662 NTM.0062.Sputum.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698364 SAMN08033017 NTM.0062.Sputum.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404663 NTM.0063.Sputum.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698369 SAMN08033018 NTM.0063.Sputum.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404664 NTM.0064.Sputum.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698367 SAMN08033019 NTM.0064.Sputum.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404665 NTM.0065.Sputum.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698368 SAMN08033020 NTM.0065.Sputum.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404666 NTM.0148.N.S.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698370 SAMN08033304 NTM.0148.N.S.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404667 NTM.0090.BAL.L.untouched.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698372 SAMN08033184 NTM.0090.BAL.L.untouched.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404668 NTM.0087.BAL.L.untouched.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698371 SAMN08033183 NTM.0087.BAL.L.untouched.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404669 NTM.0090.BAL.R.untouched.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698375 SAMN08033185 NTM.0090.BAL.R.untouched.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404670 NTM.0091.BAL.L.untouched.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698374 SAMN08033186 NTM.0091.BAL.L.untouched.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404671 NTM.0091.BAL.R.untouched.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698373 SAMN08033187 NTM.0091.BAL.R.untouched.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404672 NTM.0095.BAL.L.untouched.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698377 SAMN08033188 NTM.0095.BAL.L.untouched.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404673 NTM.0095.BAL.R.untouched.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698376 SAMN08033189 NTM.0095.BAL.R.untouched.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404674 NTM.0100.BAL.RUL1.Untouche.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698378 SAMN08033191 NTM.0100.BAL.RUL1.Untouche.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404675 NTM.0100.BAL.RML.Untouched.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698379 SAMN08033190 NTM.0100.BAL.RML.Untouched.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404676 NTM.0102.BAL.RML.untouched.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698380 SAMN08033192 NTM.0102.BAL.RML.untouched.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404677 NTM.0067.Sputum.2 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698381 SAMN08033261 NTM.0067.Sputum.2 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404678 NTM.0115.Sputum.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698382 SAMN08033262 NTM.0115.Sputum.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404679 NTM.0009.2.Sputum SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698383 SAMN08032876 NTM.0009.2.Sputum AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404680 NTM.0009.2.Oral SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698384 SAMN08032875 NTM.0009.2.Oral AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404681 NTM.0005.B.Yan SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698385 SAMN08032873 NTM.0005.B.Yan AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404682 NTM.0005.B.Nasal SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698386 SAMN08032874 NTM.0005.B.Nasal AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404683 NTM.0035.1.Oral SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698387 SAMN08032880 NTM.0035.1.Oral AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404684 NTM.0033.1.Oral SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698388 SAMN08032879 NTM.0033.1.Oral AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404685 NTM.0032.1.Oral SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698389 SAMN08032878 NTM.0032.1.Oral AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404686 NTM.0005.B.Sup SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698390 SAMN08032877 NTM.0005.B.Sup AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404687 NTM.0036.1.Oral SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698391 SAMN08032882 NTM.0036.1.Oral AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404688 NTM.0035.2.Oral SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698392 SAMN08032881 NTM.0035.2.Oral AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404689 DWF.2.72 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698393 SAMN08033292 DWF.2.72 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404690 DWF.1.72 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698395 SAMN08033291 DWF.1.72 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404691 DFW.71 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698394 SAMN08033290 DFW.71 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404692 Strep.M.Fortuium.1.10000000.71 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698397 SAMN08033288 Strep.M.Fortuium.1.10000000.71 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404693 Streptococcus.71 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698396 SAMN08033289 Streptococcus.71 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404694 Strep.M.Fortuium.1.1000000.71 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698398 SAMN08033287 Strep.M.Fortuium.1.1000000.71 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404695 Strep.M.Fortuium.1.100000.71 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698401 SAMN08033286 Strep.M.Fortuium.1.100000.71 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404696 Strep.M.Fortuium.1.10000.71 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698400 SAMN08033285 Strep.M.Fortuium.1.10000.71 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404697 Strep.M.Fortuium.1.1000.71 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698402 SAMN08033284 Strep.M.Fortuium.1.1000.71 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404698 Strep.M.Fortuium.1.100.71 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698403 SAMN08033283 Strep.M.Fortuium.1.100.71 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404699 NTM.0052.1.Sputum SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698404 SAMN08032921 NTM.0052.1.Sputum AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404700 NTM.0052.2.Sputum SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698405 SAMN08032922 NTM.0052.2.Sputum AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404701 NTM.0051.1.Sputum SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698406 SAMN08032920 NTM.0051.1.Sputum AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404702 NTM.0048.1.Sputum SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698407 SAMN08032919 NTM.0048.1.Sputum AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404703 NTM.0047.2.Sputum SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698408 SAMN08032918 NTM.0047.2.Sputum AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404704 NTM.0047.1.Sputum SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698409 SAMN08032917 NTM.0047.1.Sputum AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404705 NTM.0046.2.Sputum SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698411 SAMN08032916 NTM.0046.2.Sputum AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404706 NTM.0044.1.Sputum SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698410 SAMN08032914 NTM.0044.1.Sputum AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404707 NTM.0045.1.Sputum SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698412 SAMN08032915 NTM.0045.1.Sputum AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404708 NTM.0043.1.Sputum SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698413 SAMN08032913 NTM.0043.1.Sputum AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404709 NTM.0067.Oral.Rinse.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698414 SAMN08033061 NTM.0067.Oral.Rinse.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404710 NTM.0072.Oral.Rinse.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698415 SAMN08033062 NTM.0072.Oral.Rinse.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404711 NTM.0049.Oral.Rinse.2 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698418 SAMN08033057 NTM.0049.Oral.Rinse.2 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404712 NTM.0049.Oral.Rinse.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698416 SAMN08033058 NTM.0049.Oral.Rinse.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404713 NTM.0067.Oral.Rinse.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698417 SAMN08033060 NTM.0067.Oral.Rinse.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404714 NTM.0050.Oral.Rinse.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698419 SAMN08033059 NTM.0050.Oral.Rinse.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404715 NTM.0009.Oral.Rinse.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698420 SAMN08033053 NTM.0009.Oral.Rinse.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404716 NTM.0031.Oral.Rinse.2 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698422 SAMN08033054 NTM.0031.Oral.Rinse.2 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404717 NTM.0031.Oral.Rinse.3 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698421 SAMN08033055 NTM.0031.Oral.Rinse.3 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404718 NTM.0031.Oral.Rinse.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698425 SAMN08033056 NTM.0031.Oral.Rinse.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404719 NTM.0093.Oral.Rinse.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698423 SAMN08033100 NTM.0093.Oral.Rinse.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404720 NTM.0082.Oral.Rinse.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698424 SAMN08033098 NTM.0082.Oral.Rinse.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404721 NTM.0083.Oral.Rinse.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698427 SAMN08033099 NTM.0083.Oral.Rinse.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404722 NTM.0111.Bronch.Sup.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698426 SAMN08033097 NTM.0111.Bronch.Sup.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404723 NTM.0108.Bronch.Sup.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698428 SAMN08033096 NTM.0108.Bronch.Sup.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404724 NTM.0102.Bronch.Sup.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698429 SAMN08033095 NTM.0102.Bronch.Sup.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404725 NTM.0100.Bronch.Sup.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698431 SAMN08033094 NTM.0100.Bronch.Sup.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404726 NTM.0095.Bronch.Sup.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698430 SAMN08033093 NTM.0095.Bronch.Sup.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404727 NTM.0094.Oral.Rinse.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698432 SAMN08033101 NTM.0094.Oral.Rinse.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404728 NTM.0096.Oral.Rinse.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698433 SAMN08033102 NTM.0096.Oral.Rinse.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404729 NTM.0016.1.Oral SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698434 SAMN08032807 NTM.0016.1.Oral AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404730 NTM.0017.1.Oral SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698435 SAMN08032808 NTM.0017.1.Oral AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404731 NTM.0018.1.Oral SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698610 SAMN08032809 NTM.0018.1.Oral AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404732 NTM.0019.1.Oral SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698436 SAMN08032810 NTM.0019.1.Oral AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404733 NTM.0008.1.Oral SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698437 SAMN08032803 NTM.0008.1.Oral AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404734 NTM.0014.1.Oral SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698438 SAMN08032805 NTM.0014.1.Oral AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404735 NTM.0013.1.Oral SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698439 SAMN08032804 NTM.0013.1.Oral AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404736 NTM.0015.1.Oral SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698440 SAMN08032806 NTM.0015.1.Oral AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404737 NTM.0022.1.Oral SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698441 SAMN08032811 NTM.0022.1.Oral AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404738 NTM.0022.2.Oral SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698442 SAMN08032812 NTM.0022.2.Oral AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404739 NTM.0114.Oral.Rinse.3 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698443 SAMN08033131 NTM.0114.Oral.Rinse.3 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404740 NTM.0066.Sputum.2 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698444 SAMN08033023 NTM.0066.Sputum.2 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404741 NTM.0052.1.Oral.71 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698445 SAMN08033124 NTM.0052.1.Oral.71 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404742 NTM.0051.1.Oral.71 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698446 SAMN08033123 NTM.0051.1.Oral.71 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404743 NTM.0024.3.Sputum SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698447 SAMN08032844 NTM.0024.3.Sputum AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404744 NTM.0025.1.Sputum SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698448 SAMN08032845 NTM.0025.1.Sputum AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404745 NTM.0040.1.Sputum SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698449 SAMN08032909 NTM.0040.1.Sputum AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404746 NTM.0040.2.Sputum SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698450 SAMN08032910 NTM.0040.2.Sputum AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404747 NTM.0038.1.Sputum SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698451 SAMN08032907 NTM.0038.1.Sputum AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404748 NTM.0036.1.Sputum SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698452 SAMN08032905 NTM.0036.1.Sputum AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404749 NTM.0039.1.Sputum SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698453 SAMN08032908 NTM.0039.1.Sputum AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404750 NTM.0037.1.Sputum SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698454 SAMN08032906 NTM.0037.1.Sputum AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404751 NTM.0035.1.Sputum SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698455 SAMN08032903 NTM.0035.1.Sputum AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404752 NTM.0035.2.Sputum SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698457 SAMN08032904 NTM.0035.2.Sputum AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404753 NTM.0148.Bronch.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698456 SAMN08033302 NTM.0148.Bronch.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404754 NTM.0106.N.S.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698458 SAMN08033301 NTM.0106.N.S.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404755 NTM.0042.1.Sputum SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698459 SAMN08032912 NTM.0042.1.Sputum AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404756 NTM.0041.1.Sputum SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698460 SAMN08032911 NTM.0041.1.Sputum AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404757 NTM.0080.Sputum.3 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698463 SAMN08033151 NTM.0080.Sputum.3 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404758 NTM.0114.Sputum.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698462 SAMN08033152 NTM.0114.Sputum.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404759 NTM.0087.Bronch.Yan.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698461 SAMN08033221 NTM.0087.Bronch.Yan.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404760 NTM.0087.N.S.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698464 SAMN08033222 NTM.0087.N.S.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404761 NTM.0057.Oral.Rinse.5 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698465 SAMN08032956 NTM.0057.Oral.Rinse.5 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404762 NTM.0057.Oral.Rinse.3 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698466 SAMN08032954 NTM.0057.Oral.Rinse.3 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404763 NTM.0057.Oral.Rinse.4 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698467 SAMN08032955 NTM.0057.Oral.Rinse.4 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404764 NTM.0057.Oral.Rinse.2 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698468 SAMN08032953 NTM.0057.Oral.Rinse.2 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404765 NTM.0062.Oral.Rinse.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698469 SAMN08032960 NTM.0062.Oral.Rinse.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404766 NTM.0061.Oral.Rinse.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698470 SAMN08032959 NTM.0061.Oral.Rinse.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404767 NTM.0060.Oral.Rinse.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698472 SAMN08032958 NTM.0060.Oral.Rinse.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404768 NTM.0059.Oral.Rinse.2 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698471 SAMN08032957 NTM.0059.Oral.Rinse.2 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404769 NTM.0063.Oral.Rinse.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698473 SAMN08032961 NTM.0063.Oral.Rinse.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404770 NTM.0064.Oral.Rinse.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698474 SAMN08032962 NTM.0064.Oral.Rinse.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404771 NTM.0072.Bronch.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698476 SAMN08033217 NTM.0072.Bronch.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404772 NTM.0004.Sputum.4 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698475 SAMN08033142 NTM.0004.Sputum.4 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404773 NTM.0122.Oral.Wash.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698477 SAMN08033141 NTM.0122.Oral.Wash.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404774 NTM.0100.N.S.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698478 SAMN08033232 NTM.0100.N.S.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404775 NTM.0100.Bronch.Yan.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698479 SAMN08033231 NTM.0100.Bronch.Yan.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404776 NTM.0120.Oral.Wash.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698480 SAMN08033135 NTM.0120.Oral.Wash.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404777 NTM.0120.Oral.Wash.2 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698481 SAMN08033136 NTM.0120.Oral.Wash.2 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404778 NTM.0118.Oral.Rinse.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698482 SAMN08033134 NTM.0118.Oral.Rinse.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404779 NTM.0117.Oral.Rinse.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698484 SAMN08033133 NTM.0117.Oral.Rinse.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404780 NTM.0121.Oral.Wash.3 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698483 SAMN08033140 NTM.0121.Oral.Wash.3 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404781 NTM.0121.Oral.Wash.2 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698485 SAMN08033139 NTM.0121.Oral.Wash.2 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404782 NTM.0121.Oral.Wash.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698486 SAMN08033138 NTM.0121.Oral.Wash.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404783 NTM.0005.1.Oral SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698487 SAMN08032851 NTM.0005.1.Oral AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404784 NTM.0120.Oral.Wash.3 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698488 SAMN08033137 NTM.0120.Oral.Wash.3 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404785 NTM.0009.1.Oral SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698490 SAMN08032852 NTM.0009.1.Oral AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404786 NTM.0081.Oral.Rinse.2 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698489 SAMN08032982 NTM.0081.Oral.Rinse.2 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404787 NTM.0081.Oral.Rinse.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698491 SAMN08032981 NTM.0081.Oral.Rinse.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404788 NTM.0078.Oral.Rinse.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698492 SAMN08032978 NTM.0078.Oral.Rinse.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404789 NTM.0077.Oral.Rinse.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698493 SAMN08032977 NTM.0077.Oral.Rinse.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404790 NTM.0080.Oral.Rinse.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698494 SAMN08032979 NTM.0080.Oral.Rinse.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404791 NTM.0080.Oral.Rinse.2 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698496 SAMN08032980 NTM.0080.Oral.Rinse.2 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404792 NTM.0074.Oral.Rinse.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698497 SAMN08032974 NTM.0074.Oral.Rinse.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404793 NTM.0073.Oral.Rinse.2 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698498 SAMN08032973 NTM.0073.Oral.Rinse.2 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404794 NTM.0076.Oral.Rinse.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698499 SAMN08032976 NTM.0076.Oral.Rinse.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404795 NTM.0075.Oral.Rinse.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698501 SAMN08032975 NTM.0075.Oral.Rinse.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404796 NTM.0008.Sputum.3 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698502 SAMN08033143 NTM.0008.Sputum.3 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404797 NTM.012.1.Sputum SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698500 SAMN08032850 NTM.012.1.Sputum AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404798 NTM.0024.1.Sputum SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698503 SAMN08032842 NTM.0024.1.Sputum AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404799 NTM.0023.1.Sputum SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698504 SAMN08032841 NTM.0023.1.Sputum AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404800 NTM.0073.Sputum.2 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698505 SAMN08033030 NTM.0073.Sputum.2 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404801 NTM.0071.Sputum.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698507 SAMN08033029 NTM.0071.Sputum.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404802 NTM.0070.Sputum.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698506 SAMN08033028 NTM.0070.Sputum.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404803 NTM.0069.Sputum.2 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698508 SAMN08033027 NTM.0069.Sputum.2 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404804 NTM.0068.Sputum.2 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698509 SAMN08033025 NTM.0068.Sputum.2 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404805 NTM.0069.Sputum.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698510 SAMN08033026 NTM.0069.Sputum.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404806 NTM.0068.Sputum.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698511 SAMN08033024 NTM.0068.Sputum.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404807 NTM.0116.Oral.Rinse.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698512 SAMN08033132 NTM.0116.Oral.Rinse.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404808 NTM.0114.Oral.Rinse.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698513 SAMN08033129 NTM.0114.Oral.Rinse.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404809 NTM.0114.Oral.Rinse.2 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698514 SAMN08033130 NTM.0114.Oral.Rinse.2 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404810 NTM.0076.Oral.Wash.2 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698515 SAMN08033127 NTM.0076.Oral.Wash.2 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404811 NTM.0052.2.Oral.71 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698516 SAMN08033125 NTM.0052.2.Oral.71 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404812 NTM.0080.Oral.Rinse.3 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698519 SAMN08033128 NTM.0080.Oral.Rinse.3 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404813 NTM.0053.1.Oral.71 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698517 SAMN08033126 NTM.0053.1.Oral.71 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404814 NTM.0075.Sputum.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698518 SAMN08033032 NTM.0075.Sputum.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404815 NTM.0074.Sputum.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698520 SAMN08033031 NTM.0074.Sputum.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404816 NTM.0019.1.Sputum SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698521 SAMN08032837 NTM.0019.1.Sputum AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404817 NTM.012.1.Oral SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698522 SAMN08032822 NTM.012.1.Oral AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404818 NTM.0025.1.Oral SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698523 SAMN08032818 NTM.0025.1.Oral AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404819 NTM.0028.1.Oral SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698524 SAMN08032821 NTM.0028.1.Oral AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404820 NTM.0024.3.Oral SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698525 SAMN08032817 NTM.0024.3.Oral AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404821 NTM.0027.2.Oral SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698526 SAMN08032820 NTM.0027.2.Oral AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404822 NTM.0026.1.Oral SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698527 SAMN08032819 NTM.0026.1.Oral AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404823 NTM.0023.1.Oral SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698528 SAMN08032814 NTM.0023.1.Oral AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404824 NTM.0022.3.Oral SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698530 SAMN08032813 NTM.0022.3.Oral AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404825 NTM.0024.1.Oral SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698529 SAMN08032815 NTM.0024.1.Oral AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404826 NTM.0024.2.Oral SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698531 SAMN08032816 NTM.0024.2.Oral AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404827 NTM.0015.1.Sputum SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698533 SAMN08032834 NTM.0015.1.Sputum AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404828 NTM.0179.BAL.LLL.untouched.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698532 SAMN08033298 NTM.0179.BAL.LLL.untouched.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404829 NTM.0014.1.Sputum SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698534 SAMN08032833 NTM.0014.1.Sputum AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404830 NTM.0148.BAL.R.untouched.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698535 SAMN08033297 NTM.0148.BAL.R.untouched.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404831 Strep.M.Fortuium.1.10.71 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698536 SAMN08033282 Strep.M.Fortuium.1.10.71 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404832 NTM.0115.Bronch.Sup.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698537 SAMN08033264 NTM.0115.Bronch.Sup.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404833 NTM.0067.Nasal.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698538 SAMN08033253 NTM.0067.Nasal.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404834 NTM.0005.B.Sup.71 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698539 SAMN08033263 NTM.0005.B.Sup.71 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404835 NTM.0094.Oral.Rinse.2 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698540 SAMN08033266 NTM.0094.Oral.Rinse.2 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404836 NTM.0123.Bronch.Sup.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698543 SAMN08033265 NTM.0123.Bronch.Sup.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404837 NTM.0119.Oral.Rinse.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698541 SAMN08033268 NTM.0119.Oral.Rinse.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404838 NTM.0113.Oral.Rinse.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698542 SAMN08033267 NTM.0113.Oral.Rinse.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404839 NTM.0094.Sputum.2 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698544 SAMN08033269 NTM.0094.Sputum.2 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404840 NTM.0113.Sputum.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698545 SAMN08033270 NTM.0113.Sputum.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404841 NTM.0086.BAL.untouched.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698547 SAMN08033272 NTM.0086.BAL.untouched.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404842 NTM.0119.Sputum.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698546 SAMN08033271 NTM.0119.Sputum.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404843 NTM.0042.1.Oral SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698549 SAMN08032889 NTM.0042.1.Oral AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404844 NTM.0043.1.Oral SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698548 SAMN08032890 NTM.0043.1.Oral AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404845 NTM.0037.1.Oral SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698550 SAMN08032883 NTM.0037.1.Oral AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404846 NTM.0039.1.Oral SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698552 SAMN08032885 NTM.0039.1.Oral AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404847 NTM.0038.1.Oral SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698551 SAMN08032884 NTM.0038.1.Oral AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404848 NTM.0040.1.Oral SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698553 SAMN08032886 NTM.0040.1.Oral AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404849 NTM.0115.Nasal.Swab.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698555 SAMN08033255 NTM.0115.Nasal.Swab.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404850 NTM.0045.Oral.Rinse.2 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698554 SAMN08032951 NTM.0045.Oral.Rinse.2 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404851 NTM.0045.Oral.Rinse.3 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698556 SAMN08032952 NTM.0045.Oral.Rinse.3 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404852 NTM.0026.Oral.Rinse.2 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698557 SAMN08032945 NTM.0026.Oral.Rinse.2 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404853 NTM.0020.Oral.Rinse.2 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698558 SAMN08032943 NTM.0020.Oral.Rinse.2 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404854 NTM.0027.Oral.Rinse.3 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698559 SAMN08032946 NTM.0027.Oral.Rinse.3 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404855 NTM.0025.Oral.Rinse.2 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698561 SAMN08032944 NTM.0025.Oral.Rinse.2 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404856 NTM.0030.Oral.Rinse.2 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698560 SAMN08032949 NTM.0030.Oral.Rinse.2 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404857 NTM.0038.Oral.Rinse.2 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698562 SAMN08032950 NTM.0038.Oral.Rinse.2 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404858 NTM.0027.Oral.Rinse.4 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698563 SAMN08032947 NTM.0027.Oral.Rinse.4 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404859 NTM.0028.Oral.Rinse.2 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698564 SAMN08032948 NTM.0028.Oral.Rinse.2 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404860 NTM.0108.Oral.Rinse.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698565 SAMN08033071 NTM.0108.Oral.Rinse.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404861 NTM.0111.Oral.Rinse.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698567 SAMN08033072 NTM.0111.Oral.Rinse.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404862 NTM.0091.Oral.Rinse.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698566 SAMN08033066 NTM.0091.Oral.Rinse.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404863 NTM.0090.Oral.Rinse.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698568 SAMN08033065 NTM.0090.Oral.Rinse.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404864 NTM.0087.Oral.Rinse.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698569 SAMN08033064 NTM.0087.Oral.Rinse.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404865 NTM.0072.Oral.Rinse.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698570 SAMN08033063 NTM.0072.Oral.Rinse.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404866 NTM.0102.Oral.Rinse.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698571 SAMN08033070 NTM.0102.Oral.Rinse.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404867 NTM.0100.Oral.Rinse.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698572 SAMN08033068 NTM.0100.Oral.Rinse.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404868 NTM.0102.Oral.Rinse.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698573 SAMN08033069 NTM.0102.Oral.Rinse.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404869 NTM.0095.Oral.Rinse.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698574 SAMN08033067 NTM.0095.Oral.Rinse.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404870 NTM.0005.B.BAL.UnI.RUL.71 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698575 SAMN08033165 NTM.0005.B.BAL.UnI.RUL.71 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404871 NTM.0009.BAL.L.untouched.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698576 SAMN08033166 NTM.0009.BAL.L.untouched.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404872 NTM.0121.Sputum.3 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698578 SAMN08033163 NTM.0121.Sputum.3 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404873 NTM.0005.B.BAL.In.RML.71 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698577 SAMN08033164 NTM.0005.B.BAL.In.RML.71 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404874 NTM.0031.BAL.LUL.untouvhed.P SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698579 SAMN08033170 NTM.0031.BAL.LUL.untouvhed.P AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404875 NTM.0031.BAL.LUL.untouched.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698580 SAMN08033169 NTM.0031.BAL.LUL.untouched.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404876 NTM.0009.BAL.L1.untouched.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698581 SAMN08033167 NTM.0009.BAL.L1.untouched.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404877 NTM.0009.BAL.RUL.untouched.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698585 SAMN08033168 NTM.0009.BAL.RUL.untouched.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404878 NTM.0049.BAL.L.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698583 SAMN08033171 NTM.0049.BAL.L.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404879 NTM.0049.BAL.L1.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698582 SAMN08033172 NTM.0049.BAL.L1.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404880 NTM.0009.1.Sputum SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698584 SAMN08032854 NTM.0009.1.Sputum AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404881 NTM.0055.1.Oral SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698586 SAMN08032856 NTM.0055.1.Oral AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404882 NTM.0005.1.Sputum SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698587 SAMN08032853 NTM.0005.1.Sputum AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404883 NTM.0054.1.Oral SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698588 SAMN08032855 NTM.0054.1.Oral AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404884 NTM.0057.1.Oral SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698589 SAMN08032858 NTM.0057.1.Oral AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404885 NTM.0056.1.Oral SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698591 SAMN08032857 NTM.0056.1.Oral AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404886 NTM.0059.1.Oral SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698590 SAMN08032860 NTM.0059.1.Oral AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404887 NTM.0058.1.Oral SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698592 SAMN08032859 NTM.0058.1.Oral AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404888 NTM.0054.1.Sputum SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698748 SAMN08032861 NTM.0054.1.Sputum AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404889 NTM.0055.1.Sputum SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698594 SAMN08032862 NTM.0055.1.Sputum AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404890 NTM.0072.BAL.R.untouched.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698593 SAMN08033182 NTM.0072.BAL.R.untouched.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404891 NTM.0072.BAL.L1.untouched.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698595 SAMN08033181 NTM.0072.BAL.L1.untouched.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404892 NTM.0072.BAL.L.untouched.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698596 SAMN08033180 NTM.0072.BAL.L.untouched.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404893 NTM.0067.BAL.R.untouched.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698597 SAMN08033179 NTM.0067.BAL.R.untouched.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404894 NTM.0067.BAL.L.Untouched.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698598 SAMN08033178 NTM.0067.BAL.L.Untouched.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404895 NTM.0050.BAL.RUL1.untouched.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698599 SAMN08033176 NTM.0050.BAL.RUL1.untouched.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404896 NTM.0050.BAL.RUL2.untouched.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698600 SAMN08033177 NTM.0050.BAL.RUL2.untouched.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404897 NTM.0050.BAL.RML.untouched.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698601 SAMN08033175 NTM.0050.BAL.RML.untouched.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404898 NTM.0050.BAL.LLL.untouched.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698602 SAMN08033174 NTM.0050.BAL.LLL.untouched.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404899 NTM.0049.BAL.R.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698605 SAMN08033173 NTM.0049.BAL.R.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404900 NTM.0013.Sputum.4 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698603 SAMN08033001 NTM.0013.Sputum.4 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404901 NTM.0013.Sputum.5 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698604 SAMN08033002 NTM.0013.Sputum.5 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404902 NTM.0004.Sputum.3 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698606 SAMN08033000 NTM.0004.Sputum.3 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404903 NTM.0004.Sputum.2 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698607 SAMN08032999 NTM.0004.Sputum.2 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404904 NTM.0002.Sputum.8 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698608 SAMN08032997 NTM.0002.Sputum.8 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404905 NTM.0003.Sputum.3 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698609 SAMN08032998 NTM.0003.Sputum.3 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404906 NTM.0002.Sputum.6 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698611 SAMN08032995 NTM.0002.Sputum.6 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404907 NTM.0002.Sputum.7 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698612 SAMN08032996 NTM.0002.Sputum.7 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404908 NTM.0112.Oral.Rinse.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698613 SAMN08032993 NTM.0112.Oral.Rinse.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404909 NTM.0050.1.Sputum.71 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698614 SAMN08033260 NTM.0050.1.Sputum.71 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404910 NTM.0002.Sputum.5 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698615 SAMN08032994 NTM.0002.Sputum.5 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404911 NTM.0022.3.Sputum SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698616 SAMN08032840 NTM.0022.3.Sputum AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404912 NTM.0052.1.Oral SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698617 SAMN08032898 NTM.0052.1.Oral AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404913 NTM.0051.1.Oral SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698618 SAMN08032897 NTM.0051.1.Oral AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404914 NTM.0053.1.Oral SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698619 SAMN08032900 NTM.0053.1.Oral AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404915 NTM.0052.2.Oral SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698621 SAMN08032899 NTM.0052.2.Oral AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404916 NTM.0046.2.Oral SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698620 SAMN08032893 NTM.0046.2.Oral AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404917 NTM.0047.1.Oral SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698622 SAMN08032894 NTM.0047.1.Oral AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404918 NTM.0048.1.Oral SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698623 SAMN08032896 NTM.0048.1.Oral AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404919 NTM.0047.2.Oral SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698624 SAMN08032895 NTM.0047.2.Oral AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404920 NTM.0033.1.Sputum SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698626 SAMN08032902 NTM.0033.1.Sputum AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404921 NTM.0032.1.Sputum SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698625 SAMN08032901 NTM.0032.1.Sputum AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404922 NTM.0097.Sputum.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698627 SAMN08033044 NTM.0097.Sputum.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404923 NTM.0089.Sputum.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698629 SAMN08033043 NTM.0089.Sputum.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404924 NTM.0022.1.Sputum SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698628 SAMN08032838 NTM.0022.1.Sputum AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404925 NTM.0005.B.Yan.71 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698631 SAMN08033201 NTM.0005.B.Yan.71 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404926 NTM.0009.Bronch.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698630 SAMN08033202 NTM.0009.Bronch.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404927 NTM.0108.BAL.untouched.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698632 SAMN08033193 NTM.0108.BAL.untouched.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404928 NTM.0111.BAL.RML.untouched.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698634 SAMN08033194 NTM.0111.BAL.RML.untouched.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404929 NTM.0115.BAL.L.untouched.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698633 SAMN08033195 NTM.0115.BAL.L.untouched.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404930 NTM.0115.BAL.R.untouched.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698637 SAMN08033197 NTM.0115.BAL.R.untouched.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404931 NTM.0115.BAL.L1.untuoched.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698638 SAMN08033196 NTM.0115.BAL.L1.untuoched.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404932 NTM.0123.BAL.RML.untouched.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698635 SAMN08033198 NTM.0123.BAL.RML.untouched.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404933 NTM.0005.B.Bronch.71 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698636 SAMN08033199 NTM.0005.B.Bronch.71 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404934 NTM.0005.B.NS.71 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698639 SAMN08033200 NTM.0005.B.NS.71 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404935 NTM.0099.Oral.Rinse.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698640 SAMN08033103 NTM.0099.Oral.Rinse.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404936 NTM.0109.Oral.Rinse.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698641 SAMN08033104 NTM.0109.Oral.Rinse.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404937 NTM.0094.Sputum.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698643 SAMN08033108 NTM.0094.Sputum.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404938 NTM.0018.1.Sputum SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698644 SAMN08032836 NTM.0018.1.Sputum AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404939 NTM.0017.1.Sputum SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698642 SAMN08032835 NTM.0017.1.Sputum AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404940 NTM.0078.Sputum.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698645 SAMN08033035 NTM.0078.Sputum.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404941 NTM.0080.Sputum.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698646 SAMN08033036 NTM.0080.Sputum.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404942 NTM.0076.Sputum.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698647 SAMN08033033 NTM.0076.Sputum.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404943 NTM.0077.Sputum.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698648 SAMN08033034 NTM.0077.Sputum.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404944 NTM.0084.Sputum.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698649 SAMN08033040 NTM.0084.Sputum.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404945 NTM.0081.Sputum.2 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698651 SAMN08033039 NTM.0081.Sputum.2 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404946 NTM.0080.Sputum.2 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698650 SAMN08033037 NTM.0080.Sputum.2 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404947 NTM.0081.Sputum.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698652 SAMN08033038 NTM.0081.Sputum.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404948 DFW.70 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698653 SAMN08033118 DFW.70 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404949 NTM.0107.Bronch.Sup.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698654 SAMN08033117 NTM.0107.Bronch.Sup.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404950 NTM.0008.Oral.Rinse.3 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698655 SAMN08033120 NTM.0008.Oral.Rinse.3 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404951 NTM.0088.Sputum.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698656 SAMN08033042 NTM.0088.Sputum.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404952 NTM.0107.Oral.Rinse.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698657 SAMN08033114 NTM.0107.Oral.Rinse.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404953 NTM.0086.Bronch.Sup.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698658 SAMN08033116 NTM.0086.Bronch.Sup.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404954 NTM.0086.Oral.Rinse.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698659 SAMN08033113 NTM.0086.Oral.Rinse.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404955 NTM.0086.Sputum.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698660 SAMN08033115 NTM.0086.Sputum.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404956 NTM.0007.1.Sputum SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698661 SAMN08032831 NTM.0007.1.Sputum AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404957 NTM.0013.1.Sputum SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698662 SAMN08032832 NTM.0013.1.Sputum AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404958 NTM.0004.1.Sputum SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698663 SAMN08032829 NTM.0004.1.Sputum AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404959 NTM.0006.1.Sputum SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698664 SAMN08032830 NTM.0006.1.Sputum AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404960 NTM.0003.2.Sputum SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698665 SAMN08032828 NTM.0003.2.Sputum AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404961 NTM.0003.1.Sputum SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698666 SAMN08032827 NTM.0003.1.Sputum AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404962 NTM.0002.2.Sputum SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698667 SAMN08032825 NTM.0002.2.Sputum AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404963 NTM.0002.5.Sputum SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698668 SAMN08032826 NTM.0002.5.Sputum AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404964 NTM.0001.1.Sputum SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698669 SAMN08032823 NTM.0001.1.Sputum AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404965 NTM.0002.1.Sputum SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698670 SAMN08032824 NTM.0002.1.Sputum AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404966 NTM.0044.1.Oral SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698671 SAMN08032891 NTM.0044.1.Oral AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404967 NTM.0018.Oral.Rinse.5 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698672 SAMN08032942 NTM.0018.Oral.Rinse.5 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404968 NTM.0045.1.Oral SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698673 SAMN08032892 NTM.0045.1.Oral AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404969 NTM.0018.Oral.Rinse.4 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698674 SAMN08032941 NTM.0018.Oral.Rinse.4 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404970 NTM.0041.1.Oral SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698675 SAMN08032888 NTM.0041.1.Oral AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404971 NTM.0008.Oral.Rinse.2 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698676 SAMN08032934 NTM.0008.Oral.Rinse.2 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404972 NTM.0004.Oral.Rinse.2 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698677 SAMN08032933 NTM.0004.Oral.Rinse.2 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404973 NTM.0013.Oral.Rinse.2 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698678 SAMN08032936 NTM.0013.Oral.Rinse.2 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404974 NTM.0013.Oral.Rinse.5 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698679 SAMN08032938 NTM.0013.Oral.Rinse.5 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404975 NTM.0010.Oral.Rinse.2 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698681 SAMN08032935 NTM.0010.Oral.Rinse.2 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404976 NTM.0013.Oral.Rinse.3 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698680 SAMN08032937 NTM.0013.Oral.Rinse.3 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404977 NTM.0018.Oral.Rinse.3 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698682 SAMN08032940 NTM.0018.Oral.Rinse.3 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404978 NTM.0014.Oral.Rinse.2 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698749 SAMN08032939 NTM.0014.Oral.Rinse.2 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404979 NTM.0091.Sputum.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698683 SAMN08033079 NTM.0091.Sputum.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404980 NTM.0100.Sputum.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698686 SAMN08033080 NTM.0100.Sputum.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404981 NTM.0072.Sputum.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698685 SAMN08033078 NTM.0072.Sputum.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404982 NTM.0067.Sputum.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698684 SAMN08033077 NTM.0067.Sputum.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404983 NTM.0049.Sputum.2 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698687 SAMN08033075 NTM.0049.Sputum.2 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404984 NTM.0050.Sputum.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698688 SAMN08033076 NTM.0050.Sputum.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404985 NTM.0009.Sputum.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698689 SAMN08033073 NTM.0009.Sputum.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404986 NTM.0031.Sputum.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698690 SAMN08033074 NTM.0031.Sputum.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404987 NTM.0102.Sputum.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698691 SAMN08033081 NTM.0102.Sputum.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404988 NTM.0114.Sputum.3 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698692 SAMN08033154 NTM.0114.Sputum.3 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404989 NTM.0102.Sputum.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698693 SAMN08033082 NTM.0102.Sputum.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404990 NTM.0114.Sputum.2 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698694 SAMN08033153 NTM.0114.Sputum.2 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404991 NTM.0117.Sputum.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698695 SAMN08033156 NTM.0117.Sputum.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404992 NTM.0116.Sputum.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698696 SAMN08033155 NTM.0116.Sputum.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404993 NTM.0120.Sputum.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698698 SAMN08033158 NTM.0120.Sputum.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404994 NTM.0118.Sputum.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698697 SAMN08033157 NTM.0118.Sputum.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404995 NTM.0120.Sputum.2 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698699 SAMN08033159 NTM.0120.Sputum.2 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404996 NTM.0120.Sputum.3 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698701 SAMN08033160 NTM.0120.Sputum.3 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404997 NTM.0121.Sputum.2 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698700 SAMN08033162 NTM.0121.Sputum.2 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404998 NTM.0121.Sputum.1 SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698702 SAMN08033161 NTM.0121.Sputum.1 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3404999 NTM.0058.1.Sputum SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698703 SAMN08032865 NTM.0058.1.Sputum AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3405000 NTM.0059.1.Sputum SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698705 SAMN08032866 NTM.0059.1.Sputum AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3405001 NTM.0056.1.Sputum SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698704 SAMN08032863 NTM.0056.1.Sputum AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3405002 NTM.0005.B.BALF.In.RML SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698706 SAMN08032869 NTM.0005.B.BALF.In.RML AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3405003 NTM.0057.1.Sputum SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698707 SAMN08032864 NTM.0057.1.Sputum AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3405004 NTM.0005.B.BALF.UnI.RUL SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698708 SAMN08032870 NTM.0005.B.BALF.UnI.RUL AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3405005 NTM.0005.B.BAL.In.RML SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698709 SAMN08032867 NTM.0005.B.BAL.In.RML AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3405006 NTM.0005.B.BAL.UnI.RUL SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698710 SAMN08032868 NTM.0005.B.BAL.UnI.RUL AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3405007 NTM.0005.B.Bronch SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698711 SAMN08032871 NTM.0005.B.Bronch AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3405008 NTM.0005.B.NS SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698712 SAMN08032872 NTM.0005.B.NS AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3405009 NTM.0115.Bronch.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698713 SAMN08033242 NTM.0115.Bronch.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3405010 NTM.0111.N.S.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698714 SAMN08033241 NTM.0111.N.S.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3405011 NTM.0108.Bronch.Yan.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698715 SAMN08033237 NTM.0108.Bronch.Yan.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3405012 NTM.0108.N.S.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698716 SAMN08033238 NTM.0108.N.S.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3405013 NTM.0111.Bronch.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698717 SAMN08033239 NTM.0111.Bronch.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3405014 NTM.0111.Bronch.Yan.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698719 SAMN08033240 NTM.0111.Bronch.Yan.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3405015 NTM.0102.Bronch.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698718 SAMN08033233 NTM.0102.Bronch.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3405016 NTM.0102.Bronch.Yan.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698720 SAMN08033234 NTM.0102.Bronch.Yan.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3405017 NTM.0102.N.S.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698750 SAMN08033235 NTM.0102.N.S.B AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3405018 NTM.0108.Bronch.B SRP125205 PRJNA418131 Amplicon library preparation was performed using an automated platform (Biomek 4000) using a custom liquid handling method. For each sample, the V4 region of the bacterial 16S rRNA gene was amplified in duplicate reactions, using primer set 515F/806R, which nearly universally amplifies bacterial and archaeal 16S rRNA genes.1,2 Each unique barcoded amplicon was generated in pairs of 25_l reactions with the following reaction conditions: 11_l PCR-grade H2O, 10_l Hot MasterMix (5 Prime Cat# 2200410), 2_l of forward and reversed barcoded primer (5_M) and 2_l template DNA. Reactions were run on a C1000 Touch Thermal Cycler (Bio-Rad) with the following cycling conditions: initial denaturing at 94çC for 3 min followed by 35 cycles of denaturation at 94çC for 45 seconds, annealing at 58çC for 1 minute, and extension at 72 C for 90 seconds, with a final extension of 10 min at 72çC. Amplicons were quantified using Agilent 2200 TapeStation system and pooled. Purification was then performed using Ampure XT (Beckman Coulter Cat# A63882) as per the manufacturer instructions SRS2698722 SAMN08033236 NTM.0108.Bronch.B AMPLICON METAGENOMIC PCR Illumina MiSeq