SRX3551114 CP5781 SRP128846 PRJNA419744 Stool samples were homogenized in 1 mL of RNAlater. The NucliSens Magnetic Extraction kit and the QIAamp Stool DNA Miniprep Kit were used to extract nucleic acids from samples total nucleic acids and DNA respectively. Total nucleic acids were initially treated with the TURBO DNA-free kit and purified using the RNeasy MinElute Cleanup kit. For removal of ribosomal RNA from plant bacteria and mammalian host prior to RNA library preparation the total purified RNA was subjected to the ScriptSeq Complete Gold Kit: Epidemiology. The MiniElute PCR Purification Kit and the Agencourt AMPure XP System: PCR Purification kit were used to purify the PCR-amplified products whenever requested by the ScriptSeq kit protocol. DNA libraries were constructed using the DNA directly in Nextera DNA Sample Preparation kit. SRS2824503 SAMN08143631 CP5781 WGS METAGENOMIC other Illumina HiSeq 2500 SRX3551115 CP5819 SRP128846 PRJNA419744 Stool samples were homogenized in 1 mL of RNAlater. The NucliSens Magnetic Extraction kit and the QIAamp Stool DNA Miniprep Kit were used to extract nucleic acids from samples total nucleic acids and DNA respectively. Total nucleic acids were initially treated with the TURBO DNA-free kit and purified using the RNeasy MinElute Cleanup kit. For removal of ribosomal RNA from plant bacteria and mammalian host prior to RNA library preparation the total purified RNA was subjected to the ScriptSeq Complete Gold Kit: Epidemiology. The MiniElute PCR Purification Kit and the Agencourt AMPure XP System: PCR Purification kit were used to purify the PCR-amplified products whenever requested by the ScriptSeq kit protocol. DNA libraries were constructed using the DNA directly in Nextera DNA Sample Preparation kit. SRS2824508 SAMN08143632 CP5819 WGS METAGENOMIC other Illumina HiSeq 2500 SRX3551116 CP3453 SRP128846 PRJNA419744 Stool samples were homogenized in 1 mL of RNAlater. The NucliSens Magnetic Extraction kit and the QIAamp Stool DNA Miniprep Kit were used to extract nucleic acids from samples total nucleic acids and DNA respectively. Total nucleic acids were initially treated with the TURBO DNA-free kit and purified using the RNeasy MinElute Cleanup kit. For removal of ribosomal RNA from plant bacteria and mammalian host prior to RNA library preparation the total purified RNA was subjected to the ScriptSeq Complete Gold Kit: Epidemiology. The MiniElute PCR Purification Kit and the Agencourt AMPure XP System: PCR Purification kit were used to purify the PCR-amplified products whenever requested by the ScriptSeq kit protocol. DNA libraries were constructed using the DNA directly in Nextera DNA Sample Preparation kit. SRS2824504 SAMN08143629 CP3453 WGS METAGENOMIC other Illumina HiSeq 2500 SRX3551117 CP3469 SRP128846 PRJNA419744 Stool samples were homogenized in 1 mL of RNAlater. The NucliSens Magnetic Extraction kit and the QIAamp Stool DNA Miniprep Kit were used to extract nucleic acids from samples total nucleic acids and DNA respectively. Total nucleic acids were initially treated with the TURBO DNA-free kit and purified using the RNeasy MinElute Cleanup kit. For removal of ribosomal RNA from plant bacteria and mammalian host prior to RNA library preparation the total purified RNA was subjected to the ScriptSeq Complete Gold Kit: Epidemiology. The MiniElute PCR Purification Kit and the Agencourt AMPure XP System: PCR Purification kit were used to purify the PCR-amplified products whenever requested by the ScriptSeq kit protocol. DNA libraries were constructed using the DNA directly in Nextera DNA Sample Preparation kit. SRS2824505 SAMN08143630 CP3469 WGS METAGENOMIC other Illumina HiSeq 2500 SRX3551118 CP3403 SRP128846 PRJNA419744 Stool samples were homogenized in 1 mL of RNAlater. The NucliSens Magnetic Extraction kit and the QIAamp Stool DNA Miniprep Kit were used to extract nucleic acids from samples total nucleic acids and DNA respectively. Total nucleic acids were initially treated with the TURBO DNA-free kit and purified using the RNeasy MinElute Cleanup kit. For removal of ribosomal RNA from plant bacteria and mammalian host prior to RNA library preparation the total purified RNA was subjected to the ScriptSeq Complete Gold Kit: Epidemiology. The MiniElute PCR Purification Kit and the Agencourt AMPure XP System: PCR Purification kit were used to purify the PCR-amplified products whenever requested by the ScriptSeq kit protocol. DNA libraries were constructed using the DNA directly in Nextera DNA Sample Preparation kit. SRS2824507 SAMN08143627 CP3403 WGS METAGENOMIC other Illumina HiSeq 2500 SRX3551119 CP3409 SRP128846 PRJNA419744 Stool samples were homogenized in 1 mL of RNAlater. The NucliSens Magnetic Extraction kit and the QIAamp Stool DNA Miniprep Kit were used to extract nucleic acids from samples total nucleic acids and DNA respectively. Total nucleic acids were initially treated with the TURBO DNA-free kit and purified using the RNeasy MinElute Cleanup kit. For removal of ribosomal RNA from plant bacteria and mammalian host prior to RNA library preparation the total purified RNA was subjected to the ScriptSeq Complete Gold Kit: Epidemiology. The MiniElute PCR Purification Kit and the Agencourt AMPure XP System: PCR Purification kit were used to purify the PCR-amplified products whenever requested by the ScriptSeq kit protocol. DNA libraries were constructed using the DNA directly in Nextera DNA Sample Preparation kit. SRS2824506 SAMN08143628 CP3409 WGS METAGENOMIC other Illumina HiSeq 2500 SRX3551120 CP3376 SRP128846 PRJNA419744 Stool samples were homogenized in 1 mL of RNAlater. The NucliSens Magnetic Extraction kit and the QIAamp Stool DNA Miniprep Kit were used to extract nucleic acids from samples total nucleic acids and DNA respectively. Total nucleic acids were initially treated with the TURBO DNA-free kit and purified using the RNeasy MinElute Cleanup kit. For removal of ribosomal RNA from plant bacteria and mammalian host prior to RNA library preparation the total purified RNA was subjected to the ScriptSeq Complete Gold Kit: Epidemiology. The MiniElute PCR Purification Kit and the Agencourt AMPure XP System: PCR Purification kit were used to purify the PCR-amplified products whenever requested by the ScriptSeq kit protocol. DNA libraries were constructed using the DNA directly in Nextera DNA Sample Preparation kit. SRS2824509 SAMN08143625 CP3376 WGS METAGENOMIC other Illumina HiSeq 2500 SRX3551121 CP3385 SRP128846 PRJNA419744 Stool samples were homogenized in 1 mL of RNAlater. The NucliSens Magnetic Extraction kit and the QIAamp Stool DNA Miniprep Kit were used to extract nucleic acids from samples total nucleic acids and DNA respectively. Total nucleic acids were initially treated with the TURBO DNA-free kit and purified using the RNeasy MinElute Cleanup kit. For removal of ribosomal RNA from plant bacteria and mammalian host prior to RNA library preparation the total purified RNA was subjected to the ScriptSeq Complete Gold Kit: Epidemiology. The MiniElute PCR Purification Kit and the Agencourt AMPure XP System: PCR Purification kit were used to purify the PCR-amplified products whenever requested by the ScriptSeq kit protocol. DNA libraries were constructed using the DNA directly in Nextera DNA Sample Preparation kit. SRS2824510 SAMN08143626 CP3385 WGS METAGENOMIC other Illumina HiSeq 2500 SRX3551122 CP6535 SRP128846 PRJNA419744 Stool samples were homogenized in 1 mL of RNAlater. The NucliSens Magnetic Extraction kit and the QIAamp Stool DNA Miniprep Kit were used to extract nucleic acids from samples total nucleic acids and DNA respectively. Total nucleic acids were initially treated with the TURBO DNA-free kit and purified using the RNeasy MinElute Cleanup kit. For removal of ribosomal RNA from plant bacteria and mammalian host prior to RNA library preparation the total purified RNA was subjected to the ScriptSeq Complete Gold Kit: Epidemiology. The MiniElute PCR Purification Kit and the Agencourt AMPure XP System: PCR Purification kit were used to purify the PCR-amplified products whenever requested by the ScriptSeq kit protocol. DNA libraries were constructed using the DNA directly in Nextera DNA Sample Preparation kit. SRS2824511 SAMN08143633 CP6535 WGS METAGENOMIC other Illumina HiSeq 2500 SRX3551123 CP7880 SRP128846 PRJNA419744 Stool samples were homogenized in 1 mL of RNAlater. The NucliSens Magnetic Extraction kit and the QIAamp Stool DNA Miniprep Kit were used to extract nucleic acids from samples total nucleic acids and DNA respectively. Total nucleic acids were initially treated with the TURBO DNA-free kit and purified using the RNeasy MinElute Cleanup kit. For removal of ribosomal RNA from plant bacteria and mammalian host prior to RNA library preparation the total purified RNA was subjected to the ScriptSeq Complete Gold Kit: Epidemiology. The MiniElute PCR Purification Kit and the Agencourt AMPure XP System: PCR Purification kit were used to purify the PCR-amplified products whenever requested by the ScriptSeq kit protocol. DNA libraries were constructed using the DNA directly in Nextera DNA Sample Preparation kit. SRS2824512 SAMN08143634 CP7880 WGS METAGENOMIC other Illumina HiSeq 2500 SRX3551124 CP9852 SRP128846 PRJNA419744 Stool samples were homogenized in 1 mL of RNAlater. The NucliSens Magnetic Extraction kit and the QIAamp Stool DNA Miniprep Kit were used to extract nucleic acids from samples total nucleic acids and DNA respectively. Total nucleic acids were initially treated with the TURBO DNA-free kit and purified using the RNeasy MinElute Cleanup kit. For removal of ribosomal RNA from plant bacteria and mammalian host prior to RNA library preparation the total purified RNA was subjected to the ScriptSeq Complete Gold Kit: Epidemiology. The MiniElute PCR Purification Kit and the Agencourt AMPure XP System: PCR Purification kit were used to purify the PCR-amplified products whenever requested by the ScriptSeq kit protocol. DNA libraries were constructed using the DNA directly in Nextera DNA Sample Preparation kit. SRS2824513 SAMN08143646 CP9852 WGS METAGENOMIC other Illumina HiSeq 2500 SRX3551125 CP9725 SRP128846 PRJNA419744 Stool samples were homogenized in 1 mL of RNAlater. The NucliSens Magnetic Extraction kit and the QIAamp Stool DNA Miniprep Kit were used to extract nucleic acids from samples total nucleic acids and DNA respectively. Total nucleic acids were initially treated with the TURBO DNA-free kit and purified using the RNeasy MinElute Cleanup kit. For removal of ribosomal RNA from plant bacteria and mammalian host prior to RNA library preparation the total purified RNA was subjected to the ScriptSeq Complete Gold Kit: Epidemiology. The MiniElute PCR Purification Kit and the Agencourt AMPure XP System: PCR Purification kit were used to purify the PCR-amplified products whenever requested by the ScriptSeq kit protocol. DNA libraries were constructed using the DNA directly in Nextera DNA Sample Preparation kit. SRS2824514 SAMN08143645 CP9725 WGS METAGENOMIC other Illumina HiSeq 2500 SRX3551126 CP9854 SRP128846 PRJNA419744 Stool samples were homogenized in 1 mL of RNAlater. The NucliSens Magnetic Extraction kit and the QIAamp Stool DNA Miniprep Kit were used to extract nucleic acids from samples total nucleic acids and DNA respectively. Total nucleic acids were initially treated with the TURBO DNA-free kit and purified using the RNeasy MinElute Cleanup kit. For removal of ribosomal RNA from plant bacteria and mammalian host prior to RNA library preparation the total purified RNA was subjected to the ScriptSeq Complete Gold Kit: Epidemiology. The MiniElute PCR Purification Kit and the Agencourt AMPure XP System: PCR Purification kit were used to purify the PCR-amplified products whenever requested by the ScriptSeq kit protocol. DNA libraries were constructed using the DNA directly in Nextera DNA Sample Preparation kit. SRS2824515 SAMN08143647 CP9854 WGS METAGENOMIC other Illumina HiSeq 2500 SRX3551127 CP9683 SRP128846 PRJNA419744 Stool samples were homogenized in 1 mL of RNAlater. The NucliSens Magnetic Extraction kit and the QIAamp Stool DNA Miniprep Kit were used to extract nucleic acids from samples total nucleic acids and DNA respectively. Total nucleic acids were initially treated with the TURBO DNA-free kit and purified using the RNeasy MinElute Cleanup kit. For removal of ribosomal RNA from plant bacteria and mammalian host prior to RNA library preparation the total purified RNA was subjected to the ScriptSeq Complete Gold Kit: Epidemiology. The MiniElute PCR Purification Kit and the Agencourt AMPure XP System: PCR Purification kit were used to purify the PCR-amplified products whenever requested by the ScriptSeq kit protocol. DNA libraries were constructed using the DNA directly in Nextera DNA Sample Preparation kit. SRS2824517 SAMN08143643 CP9683 WGS METAGENOMIC other Illumina HiSeq 2500 SRX3551128 CP9686 SRP128846 PRJNA419744 Stool samples were homogenized in 1 mL of RNAlater. The NucliSens Magnetic Extraction kit and the QIAamp Stool DNA Miniprep Kit were used to extract nucleic acids from samples total nucleic acids and DNA respectively. Total nucleic acids were initially treated with the TURBO DNA-free kit and purified using the RNeasy MinElute Cleanup kit. For removal of ribosomal RNA from plant bacteria and mammalian host prior to RNA library preparation the total purified RNA was subjected to the ScriptSeq Complete Gold Kit: Epidemiology. The MiniElute PCR Purification Kit and the Agencourt AMPure XP System: PCR Purification kit were used to purify the PCR-amplified products whenever requested by the ScriptSeq kit protocol. DNA libraries were constructed using the DNA directly in Nextera DNA Sample Preparation kit. SRS2824516 SAMN08143644 CP9686 WGS METAGENOMIC other Illumina HiSeq 2500 SRX3551129 CP8797 SRP128846 PRJNA419744 Stool samples were homogenized in 1 mL of RNAlater. The NucliSens Magnetic Extraction kit and the QIAamp Stool DNA Miniprep Kit were used to extract nucleic acids from samples total nucleic acids and DNA respectively. Total nucleic acids were initially treated with the TURBO DNA-free kit and purified using the RNeasy MinElute Cleanup kit. For removal of ribosomal RNA from plant bacteria and mammalian host prior to RNA library preparation the total purified RNA was subjected to the ScriptSeq Complete Gold Kit: Epidemiology. The MiniElute PCR Purification Kit and the Agencourt AMPure XP System: PCR Purification kit were used to purify the PCR-amplified products whenever requested by the ScriptSeq kit protocol. DNA libraries were constructed using the DNA directly in Nextera DNA Sample Preparation kit. SRS2824518 SAMN08143639 CP8797 WGS METAGENOMIC other Illumina HiSeq 2500 SRX3551130 CP8804 SRP128846 PRJNA419744 Stool samples were homogenized in 1 mL of RNAlater. The NucliSens Magnetic Extraction kit and the QIAamp Stool DNA Miniprep Kit were used to extract nucleic acids from samples total nucleic acids and DNA respectively. Total nucleic acids were initially treated with the TURBO DNA-free kit and purified using the RNeasy MinElute Cleanup kit. For removal of ribosomal RNA from plant bacteria and mammalian host prior to RNA library preparation the total purified RNA was subjected to the ScriptSeq Complete Gold Kit: Epidemiology. The MiniElute PCR Purification Kit and the Agencourt AMPure XP System: PCR Purification kit were used to purify the PCR-amplified products whenever requested by the ScriptSeq kit protocol. DNA libraries were constructed using the DNA directly in Nextera DNA Sample Preparation kit. SRS2824520 SAMN08143640 CP8804 WGS METAGENOMIC other Illumina HiSeq 2500 SRX3551131 CP9667 SRP128846 PRJNA419744 Stool samples were homogenized in 1 mL of RNAlater. The NucliSens Magnetic Extraction kit and the QIAamp Stool DNA Miniprep Kit were used to extract nucleic acids from samples total nucleic acids and DNA respectively. Total nucleic acids were initially treated with the TURBO DNA-free kit and purified using the RNeasy MinElute Cleanup kit. For removal of ribosomal RNA from plant bacteria and mammalian host prior to RNA library preparation the total purified RNA was subjected to the ScriptSeq Complete Gold Kit: Epidemiology. The MiniElute PCR Purification Kit and the Agencourt AMPure XP System: PCR Purification kit were used to purify the PCR-amplified products whenever requested by the ScriptSeq kit protocol. DNA libraries were constructed using the DNA directly in Nextera DNA Sample Preparation kit. SRS2824519 SAMN08143641 CP9667 WGS METAGENOMIC other Illumina HiSeq 2500 SRX3551132 CP9679 SRP128846 PRJNA419744 Stool samples were homogenized in 1 mL of RNAlater. The NucliSens Magnetic Extraction kit and the QIAamp Stool DNA Miniprep Kit were used to extract nucleic acids from samples total nucleic acids and DNA respectively. Total nucleic acids were initially treated with the TURBO DNA-free kit and purified using the RNeasy MinElute Cleanup kit. For removal of ribosomal RNA from plant bacteria and mammalian host prior to RNA library preparation the total purified RNA was subjected to the ScriptSeq Complete Gold Kit: Epidemiology. The MiniElute PCR Purification Kit and the Agencourt AMPure XP System: PCR Purification kit were used to purify the PCR-amplified products whenever requested by the ScriptSeq kit protocol. DNA libraries were constructed using the DNA directly in Nextera DNA Sample Preparation kit. SRS2824521 SAMN08143642 CP9679 WGS METAGENOMIC other Illumina HiSeq 2500 SRX3551133 CP7885 SRP128846 PRJNA419744 Stool samples were homogenized in 1 mL of RNAlater. The NucliSens Magnetic Extraction kit and the QIAamp Stool DNA Miniprep Kit were used to extract nucleic acids from samples total nucleic acids and DNA respectively. Total nucleic acids were initially treated with the TURBO DNA-free kit and purified using the RNeasy MinElute Cleanup kit. For removal of ribosomal RNA from plant bacteria and mammalian host prior to RNA library preparation the total purified RNA was subjected to the ScriptSeq Complete Gold Kit: Epidemiology. The MiniElute PCR Purification Kit and the Agencourt AMPure XP System: PCR Purification kit were used to purify the PCR-amplified products whenever requested by the ScriptSeq kit protocol. DNA libraries were constructed using the DNA directly in Nextera DNA Sample Preparation kit. SRS2824522 SAMN08143635 CP7885 WGS METAGENOMIC other Illumina HiSeq 2500 SRX3551134 CP7890 SRP128846 PRJNA419744 Stool samples were homogenized in 1 mL of RNAlater. The NucliSens Magnetic Extraction kit and the QIAamp Stool DNA Miniprep Kit were used to extract nucleic acids from samples total nucleic acids and DNA respectively. Total nucleic acids were initially treated with the TURBO DNA-free kit and purified using the RNeasy MinElute Cleanup kit. For removal of ribosomal RNA from plant bacteria and mammalian host prior to RNA library preparation the total purified RNA was subjected to the ScriptSeq Complete Gold Kit: Epidemiology. The MiniElute PCR Purification Kit and the Agencourt AMPure XP System: PCR Purification kit were used to purify the PCR-amplified products whenever requested by the ScriptSeq kit protocol. DNA libraries were constructed using the DNA directly in Nextera DNA Sample Preparation kit. SRS2824523 SAMN08143636 CP7890 WGS METAGENOMIC other Illumina HiSeq 2500 SRX3551135 CP8084 SRP128846 PRJNA419744 Stool samples were homogenized in 1 mL of RNAlater. The NucliSens Magnetic Extraction kit and the QIAamp Stool DNA Miniprep Kit were used to extract nucleic acids from samples total nucleic acids and DNA respectively. Total nucleic acids were initially treated with the TURBO DNA-free kit and purified using the RNeasy MinElute Cleanup kit. For removal of ribosomal RNA from plant bacteria and mammalian host prior to RNA library preparation the total purified RNA was subjected to the ScriptSeq Complete Gold Kit: Epidemiology. The MiniElute PCR Purification Kit and the Agencourt AMPure XP System: PCR Purification kit were used to purify the PCR-amplified products whenever requested by the ScriptSeq kit protocol. DNA libraries were constructed using the DNA directly in Nextera DNA Sample Preparation kit. SRS2824524 SAMN08143637 CP8084 WGS METAGENOMIC other Illumina HiSeq 2500 SRX3551136 CP8789 SRP128846 PRJNA419744 Stool samples were homogenized in 1 mL of RNAlater. The NucliSens Magnetic Extraction kit and the QIAamp Stool DNA Miniprep Kit were used to extract nucleic acids from samples total nucleic acids and DNA respectively. Total nucleic acids were initially treated with the TURBO DNA-free kit and purified using the RNeasy MinElute Cleanup kit. For removal of ribosomal RNA from plant bacteria and mammalian host prior to RNA library preparation the total purified RNA was subjected to the ScriptSeq Complete Gold Kit: Epidemiology. The MiniElute PCR Purification Kit and the Agencourt AMPure XP System: PCR Purification kit were used to purify the PCR-amplified products whenever requested by the ScriptSeq kit protocol. DNA libraries were constructed using the DNA directly in Nextera DNA Sample Preparation kit. SRS2824525 SAMN08143638 CP8789 WGS METAGENOMIC other Illumina HiSeq 2500