SRX3203427 BC4_13_13236_9F_CCTAAGACAAGGCTAT_L001 SRP145069 PRJNA392687 Microbiota composition was determined in the colonic luminal content of 8-10 mice per diet group at the age of 6 and 28 months, resulting in a total of 68 samples. Genomic DNA was extracted from the colonic luminal content using the ZR Fecal DNA MicroPrep kit (ZYMO Research, Irvine, CA, USA) according to the instructions of the manufacturer. Subsequently, the V3-V4 region of the 16S rRNA gene was amplified using a 2-step PCR. First, 10-25 ng of DNA was amplified using the 341F (5'-CCTACGGGNGGCWGCAG-3') and 785R (5'-GACTACHVGGGTATCTAATCC-3') primers appended with Illumina adaptor sequences. Amplicons were purified using the ZR-96 DNA Clean and Concentrator-5 Kit (ZYMO Research, Irvine, CA, USA). To quantify DNA content of the resulting amplicon, the Qubit Fluorometric Quantitation device (ThermoFisher Scientific, Waltham, MA, USA) was used. Besides, the amplicons were run on a 2%-agarose gel to confirm amplicon size and amount. Purified PCR products were used for the second PCR in combination with sample-specific barcoded primers (Nextera XT index kit, Illumina, San Diego, CA, USA). Purified PCR products with an amplicon length of 550 base pairs (bp) (including adaptors) were submitted for sequencing in the paired-end (2x) modus (300 bp) on the MiSeq platform (Illumina, San Diego, CA, USA) at the BaseClear service laboratory (BaseClear BV, Leiden, The Netherlands). FASTQ files were generated and de-multiplexed based on sample-specific barcodes using the Casava pipeline (version 1.8.3, Illumina, San Diego, CA, USA). Sequence reads of low quality (only "passing filter" reads were selected) or containing the adapters or PhiX control signals were removed and the FASTQC pipeline (version 0.10.0, (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was applied for the initial quality control. One sample was excluded (old mouse on MF diet) because the coverage was below the threshold (50% of the median number of reads). SRS2529791 BC4_13 BC4_13_13236_9F_CCTAAGACAAGGCTAT_L001 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3203428 A4_9_13235_8F_CGAGGCTGAAGGCTAT_L001 SRP145069 PRJNA392687 Microbiota composition was determined in the colonic luminal content of 8-10 mice per diet group at the age of 6 and 28 months, resulting in a total of 68 samples. Genomic DNA was extracted from the colonic luminal content using the ZR Fecal DNA MicroPrep kit (ZYMO Research, Irvine, CA, USA) according to the instructions of the manufacturer. Subsequently, the V3-V4 region of the 16S rRNA gene was amplified using a 2-step PCR. First, 10-25 ng of DNA was amplified using the 341F (5'-CCTACGGGNGGCWGCAG-3') and 785R (5'-GACTACHVGGGTATCTAATCC-3') primers appended with Illumina adaptor sequences. Amplicons were purified using the ZR-96 DNA Clean and Concentrator-5 Kit (ZYMO Research, Irvine, CA, USA). To quantify DNA content of the resulting amplicon, the Qubit Fluorometric Quantitation device (ThermoFisher Scientific, Waltham, MA, USA) was used. Besides, the amplicons were run on a 2%-agarose gel to confirm amplicon size and amount. Purified PCR products were used for the second PCR in combination with sample-specific barcoded primers (Nextera XT index kit, Illumina, San Diego, CA, USA). Purified PCR products with an amplicon length of 550 base pairs (bp) (including adaptors) were submitted for sequencing in the paired-end (2x) modus (300 bp) on the MiSeq platform (Illumina, San Diego, CA, USA) at the BaseClear service laboratory (BaseClear BV, Leiden, The Netherlands). FASTQ files were generated and de-multiplexed based on sample-specific barcodes using the Casava pipeline (version 1.8.3, Illumina, San Diego, CA, USA). Sequence reads of low quality (only "passing filter" reads were selected) or containing the adapters or PhiX control signals were removed and the FASTQC pipeline (version 0.10.0, (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was applied for the initial quality control. One sample was excluded (old mouse on MF diet) because the coverage was below the threshold (50% of the median number of reads). SRS2529790 A4_9 A4_9_13235_8F_CGAGGCTGAAGGCTAT_L001 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3203429 A4_7_13234_11G_TGCAGCTACGTCTAAT_L001 SRP145069 PRJNA392687 Microbiota composition was determined in the colonic luminal content of 8-10 mice per diet group at the age of 6 and 28 months, resulting in a total of 68 samples. Genomic DNA was extracted from the colonic luminal content using the ZR Fecal DNA MicroPrep kit (ZYMO Research, Irvine, CA, USA) according to the instructions of the manufacturer. Subsequently, the V3-V4 region of the 16S rRNA gene was amplified using a 2-step PCR. First, 10-25 ng of DNA was amplified using the 341F (5'-CCTACGGGNGGCWGCAG-3') and 785R (5'-GACTACHVGGGTATCTAATCC-3') primers appended with Illumina adaptor sequences. Amplicons were purified using the ZR-96 DNA Clean and Concentrator-5 Kit (ZYMO Research, Irvine, CA, USA). To quantify DNA content of the resulting amplicon, the Qubit Fluorometric Quantitation device (ThermoFisher Scientific, Waltham, MA, USA) was used. Besides, the amplicons were run on a 2%-agarose gel to confirm amplicon size and amount. Purified PCR products were used for the second PCR in combination with sample-specific barcoded primers (Nextera XT index kit, Illumina, San Diego, CA, USA). Purified PCR products with an amplicon length of 550 base pairs (bp) (including adaptors) were submitted for sequencing in the paired-end (2x) modus (300 bp) on the MiSeq platform (Illumina, San Diego, CA, USA) at the BaseClear service laboratory (BaseClear BV, Leiden, The Netherlands). FASTQ files were generated and de-multiplexed based on sample-specific barcodes using the Casava pipeline (version 1.8.3, Illumina, San Diego, CA, USA). Sequence reads of low quality (only "passing filter" reads were selected) or containing the adapters or PhiX control signals were removed and the FASTQC pipeline (version 0.10.0, (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was applied for the initial quality control. One sample was excluded (old mouse on MF diet) because the coverage was below the threshold (50% of the median number of reads). SRS2529792 A4_7 A4_7_13234_11G_TGCAGCTACGTCTAAT_L001 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3203430 A4_5_13234_11F_TGCAGCTACTAAGCCT_L001 SRP145069 PRJNA392687 Microbiota composition was determined in the colonic luminal content of 8-10 mice per diet group at the age of 6 and 28 months, resulting in a total of 68 samples. Genomic DNA was extracted from the colonic luminal content using the ZR Fecal DNA MicroPrep kit (ZYMO Research, Irvine, CA, USA) according to the instructions of the manufacturer. Subsequently, the V3-V4 region of the 16S rRNA gene was amplified using a 2-step PCR. First, 10-25 ng of DNA was amplified using the 341F (5'-CCTACGGGNGGCWGCAG-3') and 785R (5'-GACTACHVGGGTATCTAATCC-3') primers appended with Illumina adaptor sequences. Amplicons were purified using the ZR-96 DNA Clean and Concentrator-5 Kit (ZYMO Research, Irvine, CA, USA). To quantify DNA content of the resulting amplicon, the Qubit Fluorometric Quantitation device (ThermoFisher Scientific, Waltham, MA, USA) was used. Besides, the amplicons were run on a 2%-agarose gel to confirm amplicon size and amount. Purified PCR products were used for the second PCR in combination with sample-specific barcoded primers (Nextera XT index kit, Illumina, San Diego, CA, USA). Purified PCR products with an amplicon length of 550 base pairs (bp) (including adaptors) were submitted for sequencing in the paired-end (2x) modus (300 bp) on the MiSeq platform (Illumina, San Diego, CA, USA) at the BaseClear service laboratory (BaseClear BV, Leiden, The Netherlands). FASTQ files were generated and de-multiplexed based on sample-specific barcodes using the Casava pipeline (version 1.8.3, Illumina, San Diego, CA, USA). Sequence reads of low quality (only "passing filter" reads were selected) or containing the adapters or PhiX control signals were removed and the FASTQC pipeline (version 0.10.0, (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was applied for the initial quality control. One sample was excluded (old mouse on MF diet) because the coverage was below the threshold (50% of the median number of reads). SRS2529793 A4_5 A4_5_13234_11F_TGCAGCTACTAAGCCT_L001 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3203431 A4_3_13234_8C_ACTGAGCGGTAAGGAG_L001 SRP145069 PRJNA392687 Microbiota composition was determined in the colonic luminal content of 8-10 mice per diet group at the age of 6 and 28 months, resulting in a total of 68 samples. Genomic DNA was extracted from the colonic luminal content using the ZR Fecal DNA MicroPrep kit (ZYMO Research, Irvine, CA, USA) according to the instructions of the manufacturer. Subsequently, the V3-V4 region of the 16S rRNA gene was amplified using a 2-step PCR. First, 10-25 ng of DNA was amplified using the 341F (5'-CCTACGGGNGGCWGCAG-3') and 785R (5'-GACTACHVGGGTATCTAATCC-3') primers appended with Illumina adaptor sequences. Amplicons were purified using the ZR-96 DNA Clean and Concentrator-5 Kit (ZYMO Research, Irvine, CA, USA). To quantify DNA content of the resulting amplicon, the Qubit Fluorometric Quantitation device (ThermoFisher Scientific, Waltham, MA, USA) was used. Besides, the amplicons were run on a 2%-agarose gel to confirm amplicon size and amount. Purified PCR products were used for the second PCR in combination with sample-specific barcoded primers (Nextera XT index kit, Illumina, San Diego, CA, USA). Purified PCR products with an amplicon length of 550 base pairs (bp) (including adaptors) were submitted for sequencing in the paired-end (2x) modus (300 bp) on the MiSeq platform (Illumina, San Diego, CA, USA) at the BaseClear service laboratory (BaseClear BV, Leiden, The Netherlands). FASTQ files were generated and de-multiplexed based on sample-specific barcodes using the Casava pipeline (version 1.8.3, Illumina, San Diego, CA, USA). Sequence reads of low quality (only "passing filter" reads were selected) or containing the adapters or PhiX control signals were removed and the FASTQC pipeline (version 0.10.0, (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was applied for the initial quality control. One sample was excluded (old mouse on MF diet) because the coverage was below the threshold (50% of the median number of reads). SRS2529794 A4_3 A4_3_13234_8C_ACTGAGCGGTAAGGAG_L001 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3203432 A4_21_13236_8E_ACTGAGCGCTATTAAG_L001 SRP145069 PRJNA392687 Microbiota composition was determined in the colonic luminal content of 8-10 mice per diet group at the age of 6 and 28 months, resulting in a total of 68 samples. Genomic DNA was extracted from the colonic luminal content using the ZR Fecal DNA MicroPrep kit (ZYMO Research, Irvine, CA, USA) according to the instructions of the manufacturer. Subsequently, the V3-V4 region of the 16S rRNA gene was amplified using a 2-step PCR. First, 10-25 ng of DNA was amplified using the 341F (5'-CCTACGGGNGGCWGCAG-3') and 785R (5'-GACTACHVGGGTATCTAATCC-3') primers appended with Illumina adaptor sequences. Amplicons were purified using the ZR-96 DNA Clean and Concentrator-5 Kit (ZYMO Research, Irvine, CA, USA). To quantify DNA content of the resulting amplicon, the Qubit Fluorometric Quantitation device (ThermoFisher Scientific, Waltham, MA, USA) was used. Besides, the amplicons were run on a 2%-agarose gel to confirm amplicon size and amount. Purified PCR products were used for the second PCR in combination with sample-specific barcoded primers (Nextera XT index kit, Illumina, San Diego, CA, USA). Purified PCR products with an amplicon length of 550 base pairs (bp) (including adaptors) were submitted for sequencing in the paired-end (2x) modus (300 bp) on the MiSeq platform (Illumina, San Diego, CA, USA) at the BaseClear service laboratory (BaseClear BV, Leiden, The Netherlands). FASTQ files were generated and de-multiplexed based on sample-specific barcodes using the Casava pipeline (version 1.8.3, Illumina, San Diego, CA, USA). Sequence reads of low quality (only "passing filter" reads were selected) or containing the adapters or PhiX control signals were removed and the FASTQC pipeline (version 0.10.0, (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was applied for the initial quality control. One sample was excluded (old mouse on MF diet) because the coverage was below the threshold (50% of the median number of reads). SRS2529795 A4_21 A4_21_13236_8E_ACTGAGCGCTATTAAG_L001 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3203433 A4_1_13234_8B_ACTGAGCGTATCCTCT_L001 SRP145069 PRJNA392687 Microbiota composition was determined in the colonic luminal content of 8-10 mice per diet group at the age of 6 and 28 months, resulting in a total of 68 samples. Genomic DNA was extracted from the colonic luminal content using the ZR Fecal DNA MicroPrep kit (ZYMO Research, Irvine, CA, USA) according to the instructions of the manufacturer. Subsequently, the V3-V4 region of the 16S rRNA gene was amplified using a 2-step PCR. First, 10-25 ng of DNA was amplified using the 341F (5'-CCTACGGGNGGCWGCAG-3') and 785R (5'-GACTACHVGGGTATCTAATCC-3') primers appended with Illumina adaptor sequences. Amplicons were purified using the ZR-96 DNA Clean and Concentrator-5 Kit (ZYMO Research, Irvine, CA, USA). To quantify DNA content of the resulting amplicon, the Qubit Fluorometric Quantitation device (ThermoFisher Scientific, Waltham, MA, USA) was used. Besides, the amplicons were run on a 2%-agarose gel to confirm amplicon size and amount. Purified PCR products were used for the second PCR in combination with sample-specific barcoded primers (Nextera XT index kit, Illumina, San Diego, CA, USA). Purified PCR products with an amplicon length of 550 base pairs (bp) (including adaptors) were submitted for sequencing in the paired-end (2x) modus (300 bp) on the MiSeq platform (Illumina, San Diego, CA, USA) at the BaseClear service laboratory (BaseClear BV, Leiden, The Netherlands). FASTQ files were generated and de-multiplexed based on sample-specific barcodes using the Casava pipeline (version 1.8.3, Illumina, San Diego, CA, USA). Sequence reads of low quality (only "passing filter" reads were selected) or containing the adapters or PhiX control signals were removed and the FASTQC pipeline (version 0.10.0, (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was applied for the initial quality control. One sample was excluded (old mouse on MF diet) because the coverage was below the threshold (50% of the median number of reads). SRS2529796 A4_1 A4_1_13234_8B_ACTGAGCGTATCCTCT_L001 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3203434 A4_19_13236_8D_ACTGAGCGGCGTAAGA_L001 SRP145069 PRJNA392687 Microbiota composition was determined in the colonic luminal content of 8-10 mice per diet group at the age of 6 and 28 months, resulting in a total of 68 samples. Genomic DNA was extracted from the colonic luminal content using the ZR Fecal DNA MicroPrep kit (ZYMO Research, Irvine, CA, USA) according to the instructions of the manufacturer. Subsequently, the V3-V4 region of the 16S rRNA gene was amplified using a 2-step PCR. First, 10-25 ng of DNA was amplified using the 341F (5'-CCTACGGGNGGCWGCAG-3') and 785R (5'-GACTACHVGGGTATCTAATCC-3') primers appended with Illumina adaptor sequences. Amplicons were purified using the ZR-96 DNA Clean and Concentrator-5 Kit (ZYMO Research, Irvine, CA, USA). To quantify DNA content of the resulting amplicon, the Qubit Fluorometric Quantitation device (ThermoFisher Scientific, Waltham, MA, USA) was used. Besides, the amplicons were run on a 2%-agarose gel to confirm amplicon size and amount. Purified PCR products were used for the second PCR in combination with sample-specific barcoded primers (Nextera XT index kit, Illumina, San Diego, CA, USA). Purified PCR products with an amplicon length of 550 base pairs (bp) (including adaptors) were submitted for sequencing in the paired-end (2x) modus (300 bp) on the MiSeq platform (Illumina, San Diego, CA, USA) at the BaseClear service laboratory (BaseClear BV, Leiden, The Netherlands). FASTQ files were generated and de-multiplexed based on sample-specific barcodes using the Casava pipeline (version 1.8.3, Illumina, San Diego, CA, USA). Sequence reads of low quality (only "passing filter" reads were selected) or containing the adapters or PhiX control signals were removed and the FASTQC pipeline (version 0.10.0, (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was applied for the initial quality control. One sample was excluded (old mouse on MF diet) because the coverage was below the threshold (50% of the median number of reads). SRS2529797 A4_19 A4_19_13236_8D_ACTGAGCGGCGTAAGA_L001 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3203435 A4_17_13236_5G_TACGCTGCGAGCCTTA_L001 SRP145069 PRJNA392687 Microbiota composition was determined in the colonic luminal content of 8-10 mice per diet group at the age of 6 and 28 months, resulting in a total of 68 samples. Genomic DNA was extracted from the colonic luminal content using the ZR Fecal DNA MicroPrep kit (ZYMO Research, Irvine, CA, USA) according to the instructions of the manufacturer. Subsequently, the V3-V4 region of the 16S rRNA gene was amplified using a 2-step PCR. First, 10-25 ng of DNA was amplified using the 341F (5'-CCTACGGGNGGCWGCAG-3') and 785R (5'-GACTACHVGGGTATCTAATCC-3') primers appended with Illumina adaptor sequences. Amplicons were purified using the ZR-96 DNA Clean and Concentrator-5 Kit (ZYMO Research, Irvine, CA, USA). To quantify DNA content of the resulting amplicon, the Qubit Fluorometric Quantitation device (ThermoFisher Scientific, Waltham, MA, USA) was used. Besides, the amplicons were run on a 2%-agarose gel to confirm amplicon size and amount. Purified PCR products were used for the second PCR in combination with sample-specific barcoded primers (Nextera XT index kit, Illumina, San Diego, CA, USA). Purified PCR products with an amplicon length of 550 base pairs (bp) (including adaptors) were submitted for sequencing in the paired-end (2x) modus (300 bp) on the MiSeq platform (Illumina, San Diego, CA, USA) at the BaseClear service laboratory (BaseClear BV, Leiden, The Netherlands). FASTQ files were generated and de-multiplexed based on sample-specific barcodes using the Casava pipeline (version 1.8.3, Illumina, San Diego, CA, USA). Sequence reads of low quality (only "passing filter" reads were selected) or containing the adapters or PhiX control signals were removed and the FASTQC pipeline (version 0.10.0, (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was applied for the initial quality control. One sample was excluded (old mouse on MF diet) because the coverage was below the threshold (50% of the median number of reads). SRS2529798 A4_17 A4_17_13236_5G_TACGCTGCGAGCCTTA_L001 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3203436 A4_13_13236_5F_TACGCTGCAAGGCTAT_L001 SRP145069 PRJNA392687 Microbiota composition was determined in the colonic luminal content of 8-10 mice per diet group at the age of 6 and 28 months, resulting in a total of 68 samples. Genomic DNA was extracted from the colonic luminal content using the ZR Fecal DNA MicroPrep kit (ZYMO Research, Irvine, CA, USA) according to the instructions of the manufacturer. Subsequently, the V3-V4 region of the 16S rRNA gene was amplified using a 2-step PCR. First, 10-25 ng of DNA was amplified using the 341F (5'-CCTACGGGNGGCWGCAG-3') and 785R (5'-GACTACHVGGGTATCTAATCC-3') primers appended with Illumina adaptor sequences. Amplicons were purified using the ZR-96 DNA Clean and Concentrator-5 Kit (ZYMO Research, Irvine, CA, USA). To quantify DNA content of the resulting amplicon, the Qubit Fluorometric Quantitation device (ThermoFisher Scientific, Waltham, MA, USA) was used. Besides, the amplicons were run on a 2%-agarose gel to confirm amplicon size and amount. Purified PCR products were used for the second PCR in combination with sample-specific barcoded primers (Nextera XT index kit, Illumina, San Diego, CA, USA). Purified PCR products with an amplicon length of 550 base pairs (bp) (including adaptors) were submitted for sequencing in the paired-end (2x) modus (300 bp) on the MiSeq platform (Illumina, San Diego, CA, USA) at the BaseClear service laboratory (BaseClear BV, Leiden, The Netherlands). FASTQ files were generated and de-multiplexed based on sample-specific barcodes using the Casava pipeline (version 1.8.3, Illumina, San Diego, CA, USA). Sequence reads of low quality (only "passing filter" reads were selected) or containing the adapters or PhiX control signals were removed and the FASTQC pipeline (version 0.10.0, (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was applied for the initial quality control. One sample was excluded (old mouse on MF diet) because the coverage was below the threshold (50% of the median number of reads). SRS2529799 A4_13 A4_13_13236_5F_TACGCTGCAAGGCTAT_L001 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3203437 A4_11_13235_8G_CGAGGCTGGAGCCTTA_L001 SRP145069 PRJNA392687 Microbiota composition was determined in the colonic luminal content of 8-10 mice per diet group at the age of 6 and 28 months, resulting in a total of 68 samples. Genomic DNA was extracted from the colonic luminal content using the ZR Fecal DNA MicroPrep kit (ZYMO Research, Irvine, CA, USA) according to the instructions of the manufacturer. Subsequently, the V3-V4 region of the 16S rRNA gene was amplified using a 2-step PCR. First, 10-25 ng of DNA was amplified using the 341F (5'-CCTACGGGNGGCWGCAG-3') and 785R (5'-GACTACHVGGGTATCTAATCC-3') primers appended with Illumina adaptor sequences. Amplicons were purified using the ZR-96 DNA Clean and Concentrator-5 Kit (ZYMO Research, Irvine, CA, USA). To quantify DNA content of the resulting amplicon, the Qubit Fluorometric Quantitation device (ThermoFisher Scientific, Waltham, MA, USA) was used. Besides, the amplicons were run on a 2%-agarose gel to confirm amplicon size and amount. Purified PCR products were used for the second PCR in combination with sample-specific barcoded primers (Nextera XT index kit, Illumina, San Diego, CA, USA). Purified PCR products with an amplicon length of 550 base pairs (bp) (including adaptors) were submitted for sequencing in the paired-end (2x) modus (300 bp) on the MiSeq platform (Illumina, San Diego, CA, USA) at the BaseClear service laboratory (BaseClear BV, Leiden, The Netherlands). FASTQ files were generated and de-multiplexed based on sample-specific barcodes using the Casava pipeline (version 1.8.3, Illumina, San Diego, CA, USA). Sequence reads of low quality (only "passing filter" reads were selected) or containing the adapters or PhiX control signals were removed and the FASTQC pipeline (version 0.10.0, (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was applied for the initial quality control. One sample was excluded (old mouse on MF diet) because the coverage was below the threshold (50% of the median number of reads). SRS2529800 A4_11 A4_11_13235_8G_CGAGGCTGGAGCCTTA_L001 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3203438 B4_13_13236_10D_CGATCAGTGCGTAAGA_L001 SRP145069 PRJNA392687 Microbiota composition was determined in the colonic luminal content of 8-10 mice per diet group at the age of 6 and 28 months, resulting in a total of 68 samples. Genomic DNA was extracted from the colonic luminal content using the ZR Fecal DNA MicroPrep kit (ZYMO Research, Irvine, CA, USA) according to the instructions of the manufacturer. Subsequently, the V3-V4 region of the 16S rRNA gene was amplified using a 2-step PCR. First, 10-25 ng of DNA was amplified using the 341F (5'-CCTACGGGNGGCWGCAG-3') and 785R (5'-GACTACHVGGGTATCTAATCC-3') primers appended with Illumina adaptor sequences. Amplicons were purified using the ZR-96 DNA Clean and Concentrator-5 Kit (ZYMO Research, Irvine, CA, USA). To quantify DNA content of the resulting amplicon, the Qubit Fluorometric Quantitation device (ThermoFisher Scientific, Waltham, MA, USA) was used. Besides, the amplicons were run on a 2%-agarose gel to confirm amplicon size and amount. Purified PCR products were used for the second PCR in combination with sample-specific barcoded primers (Nextera XT index kit, Illumina, San Diego, CA, USA). Purified PCR products with an amplicon length of 550 base pairs (bp) (including adaptors) were submitted for sequencing in the paired-end (2x) modus (300 bp) on the MiSeq platform (Illumina, San Diego, CA, USA) at the BaseClear service laboratory (BaseClear BV, Leiden, The Netherlands). FASTQ files were generated and de-multiplexed based on sample-specific barcodes using the Casava pipeline (version 1.8.3, Illumina, San Diego, CA, USA). Sequence reads of low quality (only "passing filter" reads were selected) or containing the adapters or PhiX control signals were removed and the FASTQC pipeline (version 0.10.0, (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was applied for the initial quality control. One sample was excluded (old mouse on MF diet) because the coverage was below the threshold (50% of the median number of reads). SRS2529801 B4_13 B4_13_13236_10D_CGATCAGTGCGTAAGA_L001 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3203439 B4_11_13235_12E_ATCTCAGGCTATTAAG_L001 SRP145069 PRJNA392687 Microbiota composition was determined in the colonic luminal content of 8-10 mice per diet group at the age of 6 and 28 months, resulting in a total of 68 samples. Genomic DNA was extracted from the colonic luminal content using the ZR Fecal DNA MicroPrep kit (ZYMO Research, Irvine, CA, USA) according to the instructions of the manufacturer. Subsequently, the V3-V4 region of the 16S rRNA gene was amplified using a 2-step PCR. First, 10-25 ng of DNA was amplified using the 341F (5'-CCTACGGGNGGCWGCAG-3') and 785R (5'-GACTACHVGGGTATCTAATCC-3') primers appended with Illumina adaptor sequences. Amplicons were purified using the ZR-96 DNA Clean and Concentrator-5 Kit (ZYMO Research, Irvine, CA, USA). To quantify DNA content of the resulting amplicon, the Qubit Fluorometric Quantitation device (ThermoFisher Scientific, Waltham, MA, USA) was used. Besides, the amplicons were run on a 2%-agarose gel to confirm amplicon size and amount. Purified PCR products were used for the second PCR in combination with sample-specific barcoded primers (Nextera XT index kit, Illumina, San Diego, CA, USA). Purified PCR products with an amplicon length of 550 base pairs (bp) (including adaptors) were submitted for sequencing in the paired-end (2x) modus (300 bp) on the MiSeq platform (Illumina, San Diego, CA, USA) at the BaseClear service laboratory (BaseClear BV, Leiden, The Netherlands). FASTQ files were generated and de-multiplexed based on sample-specific barcodes using the Casava pipeline (version 1.8.3, Illumina, San Diego, CA, USA). Sequence reads of low quality (only "passing filter" reads were selected) or containing the adapters or PhiX control signals were removed and the FASTQC pipeline (version 0.10.0, (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was applied for the initial quality control. One sample was excluded (old mouse on MF diet) because the coverage was below the threshold (50% of the median number of reads). SRS2529802 B4_11 B4_11_13235_12E_ATCTCAGGCTATTAAG_L001 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3203440 B4_1_13234_10B_CGATCAGTTATCCTCT_L001 SRP145069 PRJNA392687 Microbiota composition was determined in the colonic luminal content of 8-10 mice per diet group at the age of 6 and 28 months, resulting in a total of 68 samples. Genomic DNA was extracted from the colonic luminal content using the ZR Fecal DNA MicroPrep kit (ZYMO Research, Irvine, CA, USA) according to the instructions of the manufacturer. Subsequently, the V3-V4 region of the 16S rRNA gene was amplified using a 2-step PCR. First, 10-25 ng of DNA was amplified using the 341F (5'-CCTACGGGNGGCWGCAG-3') and 785R (5'-GACTACHVGGGTATCTAATCC-3') primers appended with Illumina adaptor sequences. Amplicons were purified using the ZR-96 DNA Clean and Concentrator-5 Kit (ZYMO Research, Irvine, CA, USA). To quantify DNA content of the resulting amplicon, the Qubit Fluorometric Quantitation device (ThermoFisher Scientific, Waltham, MA, USA) was used. Besides, the amplicons were run on a 2%-agarose gel to confirm amplicon size and amount. Purified PCR products were used for the second PCR in combination with sample-specific barcoded primers (Nextera XT index kit, Illumina, San Diego, CA, USA). Purified PCR products with an amplicon length of 550 base pairs (bp) (including adaptors) were submitted for sequencing in the paired-end (2x) modus (300 bp) on the MiSeq platform (Illumina, San Diego, CA, USA) at the BaseClear service laboratory (BaseClear BV, Leiden, The Netherlands). FASTQ files were generated and de-multiplexed based on sample-specific barcodes using the Casava pipeline (version 1.8.3, Illumina, San Diego, CA, USA). Sequence reads of low quality (only "passing filter" reads were selected) or containing the adapters or PhiX control signals were removed and the FASTQC pipeline (version 0.10.0, (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was applied for the initial quality control. One sample was excluded (old mouse on MF diet) because the coverage was below the threshold (50% of the median number of reads). SRS2529803 B4_1 B4_1_13234_10B_CGATCAGTTATCCTCT_L001 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3203441 B4_17_13236_10E_CGATCAGTCTATTAAG_L001 SRP145069 PRJNA392687 Microbiota composition was determined in the colonic luminal content of 8-10 mice per diet group at the age of 6 and 28 months, resulting in a total of 68 samples. Genomic DNA was extracted from the colonic luminal content using the ZR Fecal DNA MicroPrep kit (ZYMO Research, Irvine, CA, USA) according to the instructions of the manufacturer. Subsequently, the V3-V4 region of the 16S rRNA gene was amplified using a 2-step PCR. First, 10-25 ng of DNA was amplified using the 341F (5'-CCTACGGGNGGCWGCAG-3') and 785R (5'-GACTACHVGGGTATCTAATCC-3') primers appended with Illumina adaptor sequences. Amplicons were purified using the ZR-96 DNA Clean and Concentrator-5 Kit (ZYMO Research, Irvine, CA, USA). To quantify DNA content of the resulting amplicon, the Qubit Fluorometric Quantitation device (ThermoFisher Scientific, Waltham, MA, USA) was used. Besides, the amplicons were run on a 2%-agarose gel to confirm amplicon size and amount. Purified PCR products were used for the second PCR in combination with sample-specific barcoded primers (Nextera XT index kit, Illumina, San Diego, CA, USA). Purified PCR products with an amplicon length of 550 base pairs (bp) (including adaptors) were submitted for sequencing in the paired-end (2x) modus (300 bp) on the MiSeq platform (Illumina, San Diego, CA, USA) at the BaseClear service laboratory (BaseClear BV, Leiden, The Netherlands). FASTQ files were generated and de-multiplexed based on sample-specific barcodes using the Casava pipeline (version 1.8.3, Illumina, San Diego, CA, USA). Sequence reads of low quality (only "passing filter" reads were selected) or containing the adapters or PhiX control signals were removed and the FASTQC pipeline (version 0.10.0, (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was applied for the initial quality control. One sample was excluded (old mouse on MF diet) because the coverage was below the threshold (50% of the median number of reads). SRS2529804 B4_17 B4_17_13236_10E_CGATCAGTCTATTAAG_L001 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3203442 B4_3_13235_5D_GGACTCCTGCGTAAGA_L001 SRP145069 PRJNA392687 Microbiota composition was determined in the colonic luminal content of 8-10 mice per diet group at the age of 6 and 28 months, resulting in a total of 68 samples. Genomic DNA was extracted from the colonic luminal content using the ZR Fecal DNA MicroPrep kit (ZYMO Research, Irvine, CA, USA) according to the instructions of the manufacturer. Subsequently, the V3-V4 region of the 16S rRNA gene was amplified using a 2-step PCR. First, 10-25 ng of DNA was amplified using the 341F (5'-CCTACGGGNGGCWGCAG-3') and 785R (5'-GACTACHVGGGTATCTAATCC-3') primers appended with Illumina adaptor sequences. Amplicons were purified using the ZR-96 DNA Clean and Concentrator-5 Kit (ZYMO Research, Irvine, CA, USA). To quantify DNA content of the resulting amplicon, the Qubit Fluorometric Quantitation device (ThermoFisher Scientific, Waltham, MA, USA) was used. Besides, the amplicons were run on a 2%-agarose gel to confirm amplicon size and amount. Purified PCR products were used for the second PCR in combination with sample-specific barcoded primers (Nextera XT index kit, Illumina, San Diego, CA, USA). Purified PCR products with an amplicon length of 550 base pairs (bp) (including adaptors) were submitted for sequencing in the paired-end (2x) modus (300 bp) on the MiSeq platform (Illumina, San Diego, CA, USA) at the BaseClear service laboratory (BaseClear BV, Leiden, The Netherlands). FASTQ files were generated and de-multiplexed based on sample-specific barcodes using the Casava pipeline (version 1.8.3, Illumina, San Diego, CA, USA). Sequence reads of low quality (only "passing filter" reads were selected) or containing the adapters or PhiX control signals were removed and the FASTQC pipeline (version 0.10.0, (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was applied for the initial quality control. One sample was excluded (old mouse on MF diet) because the coverage was below the threshold (50% of the median number of reads). SRS2529805 B4_3 B4_3_13235_5D_GGACTCCTGCGTAAGA_L001 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3203443 B4_2_13234_10C_CGATCAGTGTAAGGAG_L001 SRP145069 PRJNA392687 Microbiota composition was determined in the colonic luminal content of 8-10 mice per diet group at the age of 6 and 28 months, resulting in a total of 68 samples. Genomic DNA was extracted from the colonic luminal content using the ZR Fecal DNA MicroPrep kit (ZYMO Research, Irvine, CA, USA) according to the instructions of the manufacturer. Subsequently, the V3-V4 region of the 16S rRNA gene was amplified using a 2-step PCR. First, 10-25 ng of DNA was amplified using the 341F (5'-CCTACGGGNGGCWGCAG-3') and 785R (5'-GACTACHVGGGTATCTAATCC-3') primers appended with Illumina adaptor sequences. Amplicons were purified using the ZR-96 DNA Clean and Concentrator-5 Kit (ZYMO Research, Irvine, CA, USA). To quantify DNA content of the resulting amplicon, the Qubit Fluorometric Quantitation device (ThermoFisher Scientific, Waltham, MA, USA) was used. Besides, the amplicons were run on a 2%-agarose gel to confirm amplicon size and amount. Purified PCR products were used for the second PCR in combination with sample-specific barcoded primers (Nextera XT index kit, Illumina, San Diego, CA, USA). Purified PCR products with an amplicon length of 550 base pairs (bp) (including adaptors) were submitted for sequencing in the paired-end (2x) modus (300 bp) on the MiSeq platform (Illumina, San Diego, CA, USA) at the BaseClear service laboratory (BaseClear BV, Leiden, The Netherlands). FASTQ files were generated and de-multiplexed based on sample-specific barcodes using the Casava pipeline (version 1.8.3, Illumina, San Diego, CA, USA). Sequence reads of low quality (only "passing filter" reads were selected) or containing the adapters or PhiX control signals were removed and the FASTQC pipeline (version 0.10.0, (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was applied for the initial quality control. One sample was excluded (old mouse on MF diet) because the coverage was below the threshold (50% of the median number of reads). SRS2529806 B4_2 B4_2_13234_10C_CGATCAGTGTAAGGAG_L001 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3203444 B4_6_13235_7B_CTCTCTACTTCTAGCT_L001 SRP145069 PRJNA392687 Microbiota composition was determined in the colonic luminal content of 8-10 mice per diet group at the age of 6 and 28 months, resulting in a total of 68 samples. Genomic DNA was extracted from the colonic luminal content using the ZR Fecal DNA MicroPrep kit (ZYMO Research, Irvine, CA, USA) according to the instructions of the manufacturer. Subsequently, the V3-V4 region of the 16S rRNA gene was amplified using a 2-step PCR. First, 10-25 ng of DNA was amplified using the 341F (5'-CCTACGGGNGGCWGCAG-3') and 785R (5'-GACTACHVGGGTATCTAATCC-3') primers appended with Illumina adaptor sequences. Amplicons were purified using the ZR-96 DNA Clean and Concentrator-5 Kit (ZYMO Research, Irvine, CA, USA). To quantify DNA content of the resulting amplicon, the Qubit Fluorometric Quantitation device (ThermoFisher Scientific, Waltham, MA, USA) was used. Besides, the amplicons were run on a 2%-agarose gel to confirm amplicon size and amount. Purified PCR products were used for the second PCR in combination with sample-specific barcoded primers (Nextera XT index kit, Illumina, San Diego, CA, USA). Purified PCR products with an amplicon length of 550 base pairs (bp) (including adaptors) were submitted for sequencing in the paired-end (2x) modus (300 bp) on the MiSeq platform (Illumina, San Diego, CA, USA) at the BaseClear service laboratory (BaseClear BV, Leiden, The Netherlands). FASTQ files were generated and de-multiplexed based on sample-specific barcodes using the Casava pipeline (version 1.8.3, Illumina, San Diego, CA, USA). Sequence reads of low quality (only "passing filter" reads were selected) or containing the adapters or PhiX control signals were removed and the FASTQC pipeline (version 0.10.0, (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was applied for the initial quality control. One sample was excluded (old mouse on MF diet) because the coverage was below the threshold (50% of the median number of reads). SRS2529807 B4_6 B4_6_13235_7B_CTCTCTACTTCTAGCT_L001 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3203445 B4_5_13235_5E_GGACTCCTCTATTAAG_L001 SRP145069 PRJNA392687 Microbiota composition was determined in the colonic luminal content of 8-10 mice per diet group at the age of 6 and 28 months, resulting in a total of 68 samples. Genomic DNA was extracted from the colonic luminal content using the ZR Fecal DNA MicroPrep kit (ZYMO Research, Irvine, CA, USA) according to the instructions of the manufacturer. Subsequently, the V3-V4 region of the 16S rRNA gene was amplified using a 2-step PCR. First, 10-25 ng of DNA was amplified using the 341F (5'-CCTACGGGNGGCWGCAG-3') and 785R (5'-GACTACHVGGGTATCTAATCC-3') primers appended with Illumina adaptor sequences. Amplicons were purified using the ZR-96 DNA Clean and Concentrator-5 Kit (ZYMO Research, Irvine, CA, USA). To quantify DNA content of the resulting amplicon, the Qubit Fluorometric Quantitation device (ThermoFisher Scientific, Waltham, MA, USA) was used. Besides, the amplicons were run on a 2%-agarose gel to confirm amplicon size and amount. Purified PCR products were used for the second PCR in combination with sample-specific barcoded primers (Nextera XT index kit, Illumina, San Diego, CA, USA). Purified PCR products with an amplicon length of 550 base pairs (bp) (including adaptors) were submitted for sequencing in the paired-end (2x) modus (300 bp) on the MiSeq platform (Illumina, San Diego, CA, USA) at the BaseClear service laboratory (BaseClear BV, Leiden, The Netherlands). FASTQ files were generated and de-multiplexed based on sample-specific barcodes using the Casava pipeline (version 1.8.3, Illumina, San Diego, CA, USA). Sequence reads of low quality (only "passing filter" reads were selected) or containing the adapters or PhiX control signals were removed and the FASTQC pipeline (version 0.10.0, (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was applied for the initial quality control. One sample was excluded (old mouse on MF diet) because the coverage was below the threshold (50% of the median number of reads). SRS2529808 B4_5 B4_5_13235_5E_GGACTCCTCTATTAAG_L001 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3203446 B4_9_13235_12D_ATCTCAGGGCGTAAGA_L001 SRP145069 PRJNA392687 Microbiota composition was determined in the colonic luminal content of 8-10 mice per diet group at the age of 6 and 28 months, resulting in a total of 68 samples. Genomic DNA was extracted from the colonic luminal content using the ZR Fecal DNA MicroPrep kit (ZYMO Research, Irvine, CA, USA) according to the instructions of the manufacturer. Subsequently, the V3-V4 region of the 16S rRNA gene was amplified using a 2-step PCR. First, 10-25 ng of DNA was amplified using the 341F (5'-CCTACGGGNGGCWGCAG-3') and 785R (5'-GACTACHVGGGTATCTAATCC-3') primers appended with Illumina adaptor sequences. Amplicons were purified using the ZR-96 DNA Clean and Concentrator-5 Kit (ZYMO Research, Irvine, CA, USA). To quantify DNA content of the resulting amplicon, the Qubit Fluorometric Quantitation device (ThermoFisher Scientific, Waltham, MA, USA) was used. Besides, the amplicons were run on a 2%-agarose gel to confirm amplicon size and amount. Purified PCR products were used for the second PCR in combination with sample-specific barcoded primers (Nextera XT index kit, Illumina, San Diego, CA, USA). Purified PCR products with an amplicon length of 550 base pairs (bp) (including adaptors) were submitted for sequencing in the paired-end (2x) modus (300 bp) on the MiSeq platform (Illumina, San Diego, CA, USA) at the BaseClear service laboratory (BaseClear BV, Leiden, The Netherlands). FASTQ files were generated and de-multiplexed based on sample-specific barcodes using the Casava pipeline (version 1.8.3, Illumina, San Diego, CA, USA). Sequence reads of low quality (only "passing filter" reads were selected) or containing the adapters or PhiX control signals were removed and the FASTQC pipeline (version 0.10.0, (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was applied for the initial quality control. One sample was excluded (old mouse on MF diet) because the coverage was below the threshold (50% of the median number of reads). SRS2529809 B4_9 B4_9_13235_12D_ATCTCAGGGCGTAAGA_L001 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3203447 B4_7_13235_7C_CTCTCTACCCTAGAGT_L001 SRP145069 PRJNA392687 Microbiota composition was determined in the colonic luminal content of 8-10 mice per diet group at the age of 6 and 28 months, resulting in a total of 68 samples. Genomic DNA was extracted from the colonic luminal content using the ZR Fecal DNA MicroPrep kit (ZYMO Research, Irvine, CA, USA) according to the instructions of the manufacturer. Subsequently, the V3-V4 region of the 16S rRNA gene was amplified using a 2-step PCR. First, 10-25 ng of DNA was amplified using the 341F (5'-CCTACGGGNGGCWGCAG-3') and 785R (5'-GACTACHVGGGTATCTAATCC-3') primers appended with Illumina adaptor sequences. Amplicons were purified using the ZR-96 DNA Clean and Concentrator-5 Kit (ZYMO Research, Irvine, CA, USA). To quantify DNA content of the resulting amplicon, the Qubit Fluorometric Quantitation device (ThermoFisher Scientific, Waltham, MA, USA) was used. Besides, the amplicons were run on a 2%-agarose gel to confirm amplicon size and amount. Purified PCR products were used for the second PCR in combination with sample-specific barcoded primers (Nextera XT index kit, Illumina, San Diego, CA, USA). Purified PCR products with an amplicon length of 550 base pairs (bp) (including adaptors) were submitted for sequencing in the paired-end (2x) modus (300 bp) on the MiSeq platform (Illumina, San Diego, CA, USA) at the BaseClear service laboratory (BaseClear BV, Leiden, The Netherlands). FASTQ files were generated and de-multiplexed based on sample-specific barcodes using the Casava pipeline (version 1.8.3, Illumina, San Diego, CA, USA). Sequence reads of low quality (only "passing filter" reads were selected) or containing the adapters or PhiX control signals were removed and the FASTQC pipeline (version 0.10.0, (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was applied for the initial quality control. One sample was excluded (old mouse on MF diet) because the coverage was below the threshold (50% of the median number of reads). SRS2529810 B4_7 B4_7_13235_7C_CTCTCTACCCTAGAGT_L001 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3203448 C1_11_13236_4F_CGGAGCCTAAGGCTAT_L001 SRP145069 PRJNA392687 Microbiota composition was determined in the colonic luminal content of 8-10 mice per diet group at the age of 6 and 28 months, resulting in a total of 68 samples. Genomic DNA was extracted from the colonic luminal content using the ZR Fecal DNA MicroPrep kit (ZYMO Research, Irvine, CA, USA) according to the instructions of the manufacturer. Subsequently, the V3-V4 region of the 16S rRNA gene was amplified using a 2-step PCR. First, 10-25 ng of DNA was amplified using the 341F (5'-CCTACGGGNGGCWGCAG-3') and 785R (5'-GACTACHVGGGTATCTAATCC-3') primers appended with Illumina adaptor sequences. Amplicons were purified using the ZR-96 DNA Clean and Concentrator-5 Kit (ZYMO Research, Irvine, CA, USA). To quantify DNA content of the resulting amplicon, the Qubit Fluorometric Quantitation device (ThermoFisher Scientific, Waltham, MA, USA) was used. Besides, the amplicons were run on a 2%-agarose gel to confirm amplicon size and amount. Purified PCR products were used for the second PCR in combination with sample-specific barcoded primers (Nextera XT index kit, Illumina, San Diego, CA, USA). Purified PCR products with an amplicon length of 550 base pairs (bp) (including adaptors) were submitted for sequencing in the paired-end (2x) modus (300 bp) on the MiSeq platform (Illumina, San Diego, CA, USA) at the BaseClear service laboratory (BaseClear BV, Leiden, The Netherlands). FASTQ files were generated and de-multiplexed based on sample-specific barcodes using the Casava pipeline (version 1.8.3, Illumina, San Diego, CA, USA). Sequence reads of low quality (only "passing filter" reads were selected) or containing the adapters or PhiX control signals were removed and the FASTQC pipeline (version 0.10.0, (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was applied for the initial quality control. One sample was excluded (old mouse on MF diet) because the coverage was below the threshold (50% of the median number of reads). SRS2529811 C1_11 C1_11_13236_4F_CGGAGCCTAAGGCTAT_L001 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3203449 C1_10_13235_7G_CTCTCTACGAGCCTTA_L001 SRP145069 PRJNA392687 Microbiota composition was determined in the colonic luminal content of 8-10 mice per diet group at the age of 6 and 28 months, resulting in a total of 68 samples. Genomic DNA was extracted from the colonic luminal content using the ZR Fecal DNA MicroPrep kit (ZYMO Research, Irvine, CA, USA) according to the instructions of the manufacturer. Subsequently, the V3-V4 region of the 16S rRNA gene was amplified using a 2-step PCR. First, 10-25 ng of DNA was amplified using the 341F (5'-CCTACGGGNGGCWGCAG-3') and 785R (5'-GACTACHVGGGTATCTAATCC-3') primers appended with Illumina adaptor sequences. Amplicons were purified using the ZR-96 DNA Clean and Concentrator-5 Kit (ZYMO Research, Irvine, CA, USA). To quantify DNA content of the resulting amplicon, the Qubit Fluorometric Quantitation device (ThermoFisher Scientific, Waltham, MA, USA) was used. Besides, the amplicons were run on a 2%-agarose gel to confirm amplicon size and amount. Purified PCR products were used for the second PCR in combination with sample-specific barcoded primers (Nextera XT index kit, Illumina, San Diego, CA, USA). Purified PCR products with an amplicon length of 550 base pairs (bp) (including adaptors) were submitted for sequencing in the paired-end (2x) modus (300 bp) on the MiSeq platform (Illumina, San Diego, CA, USA) at the BaseClear service laboratory (BaseClear BV, Leiden, The Netherlands). FASTQ files were generated and de-multiplexed based on sample-specific barcodes using the Casava pipeline (version 1.8.3, Illumina, San Diego, CA, USA). Sequence reads of low quality (only "passing filter" reads were selected) or containing the adapters or PhiX control signals were removed and the FASTQC pipeline (version 0.10.0, (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was applied for the initial quality control. One sample was excluded (old mouse on MF diet) because the coverage was below the threshold (50% of the median number of reads). SRS2529812 C1_10 C1_10_13235_7G_CTCTCTACGAGCCTTA_L001 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3203450 C1_6_13235_8E_CGAGGCTGCTATTAAG_L001 SRP145069 PRJNA392687 Microbiota composition was determined in the colonic luminal content of 8-10 mice per diet group at the age of 6 and 28 months, resulting in a total of 68 samples. Genomic DNA was extracted from the colonic luminal content using the ZR Fecal DNA MicroPrep kit (ZYMO Research, Irvine, CA, USA) according to the instructions of the manufacturer. Subsequently, the V3-V4 region of the 16S rRNA gene was amplified using a 2-step PCR. First, 10-25 ng of DNA was amplified using the 341F (5'-CCTACGGGNGGCWGCAG-3') and 785R (5'-GACTACHVGGGTATCTAATCC-3') primers appended with Illumina adaptor sequences. Amplicons were purified using the ZR-96 DNA Clean and Concentrator-5 Kit (ZYMO Research, Irvine, CA, USA). To quantify DNA content of the resulting amplicon, the Qubit Fluorometric Quantitation device (ThermoFisher Scientific, Waltham, MA, USA) was used. Besides, the amplicons were run on a 2%-agarose gel to confirm amplicon size and amount. Purified PCR products were used for the second PCR in combination with sample-specific barcoded primers (Nextera XT index kit, Illumina, San Diego, CA, USA). Purified PCR products with an amplicon length of 550 base pairs (bp) (including adaptors) were submitted for sequencing in the paired-end (2x) modus (300 bp) on the MiSeq platform (Illumina, San Diego, CA, USA) at the BaseClear service laboratory (BaseClear BV, Leiden, The Netherlands). FASTQ files were generated and de-multiplexed based on sample-specific barcodes using the Casava pipeline (version 1.8.3, Illumina, San Diego, CA, USA). Sequence reads of low quality (only "passing filter" reads were selected) or containing the adapters or PhiX control signals were removed and the FASTQC pipeline (version 0.10.0, (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was applied for the initial quality control. One sample was excluded (old mouse on MF diet) because the coverage was below the threshold (50% of the median number of reads). SRS2529813 C1_6 C1_6_13235_8E_CGAGGCTGCTATTAAG_L001 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3203451 C1_5_13235_8D_CGAGGCTGGCGTAAGA_L001 SRP145069 PRJNA392687 Microbiota composition was determined in the colonic luminal content of 8-10 mice per diet group at the age of 6 and 28 months, resulting in a total of 68 samples. Genomic DNA was extracted from the colonic luminal content using the ZR Fecal DNA MicroPrep kit (ZYMO Research, Irvine, CA, USA) according to the instructions of the manufacturer. Subsequently, the V3-V4 region of the 16S rRNA gene was amplified using a 2-step PCR. First, 10-25 ng of DNA was amplified using the 341F (5'-CCTACGGGNGGCWGCAG-3') and 785R (5'-GACTACHVGGGTATCTAATCC-3') primers appended with Illumina adaptor sequences. Amplicons were purified using the ZR-96 DNA Clean and Concentrator-5 Kit (ZYMO Research, Irvine, CA, USA). To quantify DNA content of the resulting amplicon, the Qubit Fluorometric Quantitation device (ThermoFisher Scientific, Waltham, MA, USA) was used. Besides, the amplicons were run on a 2%-agarose gel to confirm amplicon size and amount. Purified PCR products were used for the second PCR in combination with sample-specific barcoded primers (Nextera XT index kit, Illumina, San Diego, CA, USA). Purified PCR products with an amplicon length of 550 base pairs (bp) (including adaptors) were submitted for sequencing in the paired-end (2x) modus (300 bp) on the MiSeq platform (Illumina, San Diego, CA, USA) at the BaseClear service laboratory (BaseClear BV, Leiden, The Netherlands). FASTQ files were generated and de-multiplexed based on sample-specific barcodes using the Casava pipeline (version 1.8.3, Illumina, San Diego, CA, USA). Sequence reads of low quality (only "passing filter" reads were selected) or containing the adapters or PhiX control signals were removed and the FASTQC pipeline (version 0.10.0, (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was applied for the initial quality control. One sample was excluded (old mouse on MF diet) because the coverage was below the threshold (50% of the median number of reads). SRS2529814 C1_5 C1_5_13235_8D_CGAGGCTGGCGTAAGA_L001 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3203452 C1_3_13235_7F_CTCTCTACAAGGCTAT_L001 SRP145069 PRJNA392687 Microbiota composition was determined in the colonic luminal content of 8-10 mice per diet group at the age of 6 and 28 months, resulting in a total of 68 samples. Genomic DNA was extracted from the colonic luminal content using the ZR Fecal DNA MicroPrep kit (ZYMO Research, Irvine, CA, USA) according to the instructions of the manufacturer. Subsequently, the V3-V4 region of the 16S rRNA gene was amplified using a 2-step PCR. First, 10-25 ng of DNA was amplified using the 341F (5'-CCTACGGGNGGCWGCAG-3') and 785R (5'-GACTACHVGGGTATCTAATCC-3') primers appended with Illumina adaptor sequences. Amplicons were purified using the ZR-96 DNA Clean and Concentrator-5 Kit (ZYMO Research, Irvine, CA, USA). To quantify DNA content of the resulting amplicon, the Qubit Fluorometric Quantitation device (ThermoFisher Scientific, Waltham, MA, USA) was used. Besides, the amplicons were run on a 2%-agarose gel to confirm amplicon size and amount. Purified PCR products were used for the second PCR in combination with sample-specific barcoded primers (Nextera XT index kit, Illumina, San Diego, CA, USA). Purified PCR products with an amplicon length of 550 base pairs (bp) (including adaptors) were submitted for sequencing in the paired-end (2x) modus (300 bp) on the MiSeq platform (Illumina, San Diego, CA, USA) at the BaseClear service laboratory (BaseClear BV, Leiden, The Netherlands). FASTQ files were generated and de-multiplexed based on sample-specific barcodes using the Casava pipeline (version 1.8.3, Illumina, San Diego, CA, USA). Sequence reads of low quality (only "passing filter" reads were selected) or containing the adapters or PhiX control signals were removed and the FASTQC pipeline (version 0.10.0, (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was applied for the initial quality control. One sample was excluded (old mouse on MF diet) because the coverage was below the threshold (50% of the median number of reads). SRS2529815 C1_3 C1_3_13235_7F_CTCTCTACAAGGCTAT_L001 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3203453 C1_2_13235_5C_GGACTCCTCCTAGAGT_L001 SRP145069 PRJNA392687 Microbiota composition was determined in the colonic luminal content of 8-10 mice per diet group at the age of 6 and 28 months, resulting in a total of 68 samples. Genomic DNA was extracted from the colonic luminal content using the ZR Fecal DNA MicroPrep kit (ZYMO Research, Irvine, CA, USA) according to the instructions of the manufacturer. Subsequently, the V3-V4 region of the 16S rRNA gene was amplified using a 2-step PCR. First, 10-25 ng of DNA was amplified using the 341F (5'-CCTACGGGNGGCWGCAG-3') and 785R (5'-GACTACHVGGGTATCTAATCC-3') primers appended with Illumina adaptor sequences. Amplicons were purified using the ZR-96 DNA Clean and Concentrator-5 Kit (ZYMO Research, Irvine, CA, USA). To quantify DNA content of the resulting amplicon, the Qubit Fluorometric Quantitation device (ThermoFisher Scientific, Waltham, MA, USA) was used. Besides, the amplicons were run on a 2%-agarose gel to confirm amplicon size and amount. Purified PCR products were used for the second PCR in combination with sample-specific barcoded primers (Nextera XT index kit, Illumina, San Diego, CA, USA). Purified PCR products with an amplicon length of 550 base pairs (bp) (including adaptors) were submitted for sequencing in the paired-end (2x) modus (300 bp) on the MiSeq platform (Illumina, San Diego, CA, USA) at the BaseClear service laboratory (BaseClear BV, Leiden, The Netherlands). FASTQ files were generated and de-multiplexed based on sample-specific barcodes using the Casava pipeline (version 1.8.3, Illumina, San Diego, CA, USA). Sequence reads of low quality (only "passing filter" reads were selected) or containing the adapters or PhiX control signals were removed and the FASTQC pipeline (version 0.10.0, (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was applied for the initial quality control. One sample was excluded (old mouse on MF diet) because the coverage was below the threshold (50% of the median number of reads). SRS2529816 C1_2 C1_2_13235_5C_GGACTCCTCCTAGAGT_L001 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3203454 C1_9_13236_3E_GCGTAGTACTATTAAG_L001 SRP145069 PRJNA392687 Microbiota composition was determined in the colonic luminal content of 8-10 mice per diet group at the age of 6 and 28 months, resulting in a total of 68 samples. Genomic DNA was extracted from the colonic luminal content using the ZR Fecal DNA MicroPrep kit (ZYMO Research, Irvine, CA, USA) according to the instructions of the manufacturer. Subsequently, the V3-V4 region of the 16S rRNA gene was amplified using a 2-step PCR. First, 10-25 ng of DNA was amplified using the 341F (5'-CCTACGGGNGGCWGCAG-3') and 785R (5'-GACTACHVGGGTATCTAATCC-3') primers appended with Illumina adaptor sequences. Amplicons were purified using the ZR-96 DNA Clean and Concentrator-5 Kit (ZYMO Research, Irvine, CA, USA). To quantify DNA content of the resulting amplicon, the Qubit Fluorometric Quantitation device (ThermoFisher Scientific, Waltham, MA, USA) was used. Besides, the amplicons were run on a 2%-agarose gel to confirm amplicon size and amount. Purified PCR products were used for the second PCR in combination with sample-specific barcoded primers (Nextera XT index kit, Illumina, San Diego, CA, USA). Purified PCR products with an amplicon length of 550 base pairs (bp) (including adaptors) were submitted for sequencing in the paired-end (2x) modus (300 bp) on the MiSeq platform (Illumina, San Diego, CA, USA) at the BaseClear service laboratory (BaseClear BV, Leiden, The Netherlands). FASTQ files were generated and de-multiplexed based on sample-specific barcodes using the Casava pipeline (version 1.8.3, Illumina, San Diego, CA, USA). Sequence reads of low quality (only "passing filter" reads were selected) or containing the adapters or PhiX control signals were removed and the FASTQC pipeline (version 0.10.0, (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was applied for the initial quality control. One sample was excluded (old mouse on MF diet) because the coverage was below the threshold (50% of the median number of reads). SRS2529817 C1_9 C1_9_13236_3E_GCGTAGTACTATTAAG_L001 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3203455 C4_7_13235_7E_CTCTCTACCTATTAAG_L001 SRP145069 PRJNA392687 Microbiota composition was determined in the colonic luminal content of 8-10 mice per diet group at the age of 6 and 28 months, resulting in a total of 68 samples. Genomic DNA was extracted from the colonic luminal content using the ZR Fecal DNA MicroPrep kit (ZYMO Research, Irvine, CA, USA) according to the instructions of the manufacturer. Subsequently, the V3-V4 region of the 16S rRNA gene was amplified using a 2-step PCR. First, 10-25 ng of DNA was amplified using the 341F (5'-CCTACGGGNGGCWGCAG-3') and 785R (5'-GACTACHVGGGTATCTAATCC-3') primers appended with Illumina adaptor sequences. Amplicons were purified using the ZR-96 DNA Clean and Concentrator-5 Kit (ZYMO Research, Irvine, CA, USA). To quantify DNA content of the resulting amplicon, the Qubit Fluorometric Quantitation device (ThermoFisher Scientific, Waltham, MA, USA) was used. Besides, the amplicons were run on a 2%-agarose gel to confirm amplicon size and amount. Purified PCR products were used for the second PCR in combination with sample-specific barcoded primers (Nextera XT index kit, Illumina, San Diego, CA, USA). Purified PCR products with an amplicon length of 550 base pairs (bp) (including adaptors) were submitted for sequencing in the paired-end (2x) modus (300 bp) on the MiSeq platform (Illumina, San Diego, CA, USA) at the BaseClear service laboratory (BaseClear BV, Leiden, The Netherlands). FASTQ files were generated and de-multiplexed based on sample-specific barcodes using the Casava pipeline (version 1.8.3, Illumina, San Diego, CA, USA). Sequence reads of low quality (only "passing filter" reads were selected) or containing the adapters or PhiX control signals were removed and the FASTQC pipeline (version 0.10.0, (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was applied for the initial quality control. One sample was excluded (old mouse on MF diet) because the coverage was below the threshold (50% of the median number of reads). SRS2529818 C4_7 C4_7_13235_7E_CTCTCTACCTATTAAG_L001 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3203456 A1_5_13234_6C_ATGCGCAGGTAAGGAG_L001 SRP145069 PRJNA392687 Microbiota composition was determined in the colonic luminal content of 8-10 mice per diet group at the age of 6 and 28 months, resulting in a total of 68 samples. Genomic DNA was extracted from the colonic luminal content using the ZR Fecal DNA MicroPrep kit (ZYMO Research, Irvine, CA, USA) according to the instructions of the manufacturer. Subsequently, the V3-V4 region of the 16S rRNA gene was amplified using a 2-step PCR. First, 10-25 ng of DNA was amplified using the 341F (5'-CCTACGGGNGGCWGCAG-3') and 785R (5'-GACTACHVGGGTATCTAATCC-3') primers appended with Illumina adaptor sequences. Amplicons were purified using the ZR-96 DNA Clean and Concentrator-5 Kit (ZYMO Research, Irvine, CA, USA). To quantify DNA content of the resulting amplicon, the Qubit Fluorometric Quantitation device (ThermoFisher Scientific, Waltham, MA, USA) was used. Besides, the amplicons were run on a 2%-agarose gel to confirm amplicon size and amount. Purified PCR products were used for the second PCR in combination with sample-specific barcoded primers (Nextera XT index kit, Illumina, San Diego, CA, USA). Purified PCR products with an amplicon length of 550 base pairs (bp) (including adaptors) were submitted for sequencing in the paired-end (2x) modus (300 bp) on the MiSeq platform (Illumina, San Diego, CA, USA) at the BaseClear service laboratory (BaseClear BV, Leiden, The Netherlands). FASTQ files were generated and de-multiplexed based on sample-specific barcodes using the Casava pipeline (version 1.8.3, Illumina, San Diego, CA, USA). Sequence reads of low quality (only "passing filter" reads were selected) or containing the adapters or PhiX control signals were removed and the FASTQC pipeline (version 0.10.0, (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was applied for the initial quality control. One sample was excluded (old mouse on MF diet) because the coverage was below the threshold (50% of the median number of reads). SRS2529819 A1_5 A1_5_13234_6C_ATGCGCAGGTAAGGAG_L001 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3203457 C4_1_13234_6F_ATGCGCAGCTAAGCCT_L001 SRP145069 PRJNA392687 Microbiota composition was determined in the colonic luminal content of 8-10 mice per diet group at the age of 6 and 28 months, resulting in a total of 68 samples. Genomic DNA was extracted from the colonic luminal content using the ZR Fecal DNA MicroPrep kit (ZYMO Research, Irvine, CA, USA) according to the instructions of the manufacturer. Subsequently, the V3-V4 region of the 16S rRNA gene was amplified using a 2-step PCR. First, 10-25 ng of DNA was amplified using the 341F (5'-CCTACGGGNGGCWGCAG-3') and 785R (5'-GACTACHVGGGTATCTAATCC-3') primers appended with Illumina adaptor sequences. Amplicons were purified using the ZR-96 DNA Clean and Concentrator-5 Kit (ZYMO Research, Irvine, CA, USA). To quantify DNA content of the resulting amplicon, the Qubit Fluorometric Quantitation device (ThermoFisher Scientific, Waltham, MA, USA) was used. Besides, the amplicons were run on a 2%-agarose gel to confirm amplicon size and amount. Purified PCR products were used for the second PCR in combination with sample-specific barcoded primers (Nextera XT index kit, Illumina, San Diego, CA, USA). Purified PCR products with an amplicon length of 550 base pairs (bp) (including adaptors) were submitted for sequencing in the paired-end (2x) modus (300 bp) on the MiSeq platform (Illumina, San Diego, CA, USA) at the BaseClear service laboratory (BaseClear BV, Leiden, The Netherlands). FASTQ files were generated and de-multiplexed based on sample-specific barcodes using the Casava pipeline (version 1.8.3, Illumina, San Diego, CA, USA). Sequence reads of low quality (only "passing filter" reads were selected) or containing the adapters or PhiX control signals were removed and the FASTQC pipeline (version 0.10.0, (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was applied for the initial quality control. One sample was excluded (old mouse on MF diet) because the coverage was below the threshold (50% of the median number of reads). SRS2529820 C4_1 C4_1_13234_6F_ATGCGCAGCTAAGCCT_L001 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3203458 C4_3_13234_6G_ATGCGCAGCGTCTAAT_L001 SRP145069 PRJNA392687 Microbiota composition was determined in the colonic luminal content of 8-10 mice per diet group at the age of 6 and 28 months, resulting in a total of 68 samples. Genomic DNA was extracted from the colonic luminal content using the ZR Fecal DNA MicroPrep kit (ZYMO Research, Irvine, CA, USA) according to the instructions of the manufacturer. Subsequently, the V3-V4 region of the 16S rRNA gene was amplified using a 2-step PCR. First, 10-25 ng of DNA was amplified using the 341F (5'-CCTACGGGNGGCWGCAG-3') and 785R (5'-GACTACHVGGGTATCTAATCC-3') primers appended with Illumina adaptor sequences. Amplicons were purified using the ZR-96 DNA Clean and Concentrator-5 Kit (ZYMO Research, Irvine, CA, USA). To quantify DNA content of the resulting amplicon, the Qubit Fluorometric Quantitation device (ThermoFisher Scientific, Waltham, MA, USA) was used. Besides, the amplicons were run on a 2%-agarose gel to confirm amplicon size and amount. Purified PCR products were used for the second PCR in combination with sample-specific barcoded primers (Nextera XT index kit, Illumina, San Diego, CA, USA). Purified PCR products with an amplicon length of 550 base pairs (bp) (including adaptors) were submitted for sequencing in the paired-end (2x) modus (300 bp) on the MiSeq platform (Illumina, San Diego, CA, USA) at the BaseClear service laboratory (BaseClear BV, Leiden, The Netherlands). FASTQ files were generated and de-multiplexed based on sample-specific barcodes using the Casava pipeline (version 1.8.3, Illumina, San Diego, CA, USA). Sequence reads of low quality (only "passing filter" reads were selected) or containing the adapters or PhiX control signals were removed and the FASTQC pipeline (version 0.10.0, (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was applied for the initial quality control. One sample was excluded (old mouse on MF diet) because the coverage was below the threshold (50% of the median number of reads). SRS2529821 C4_3 C4_3_13234_6G_ATGCGCAGCGTCTAAT_L001 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3203459 C1_7_13236_3D_GCGTAGTAGCGTAAGA_L001 SRP145069 PRJNA392687 Microbiota composition was determined in the colonic luminal content of 8-10 mice per diet group at the age of 6 and 28 months, resulting in a total of 68 samples. Genomic DNA was extracted from the colonic luminal content using the ZR Fecal DNA MicroPrep kit (ZYMO Research, Irvine, CA, USA) according to the instructions of the manufacturer. Subsequently, the V3-V4 region of the 16S rRNA gene was amplified using a 2-step PCR. First, 10-25 ng of DNA was amplified using the 341F (5'-CCTACGGGNGGCWGCAG-3') and 785R (5'-GACTACHVGGGTATCTAATCC-3') primers appended with Illumina adaptor sequences. Amplicons were purified using the ZR-96 DNA Clean and Concentrator-5 Kit (ZYMO Research, Irvine, CA, USA). To quantify DNA content of the resulting amplicon, the Qubit Fluorometric Quantitation device (ThermoFisher Scientific, Waltham, MA, USA) was used. Besides, the amplicons were run on a 2%-agarose gel to confirm amplicon size and amount. Purified PCR products were used for the second PCR in combination with sample-specific barcoded primers (Nextera XT index kit, Illumina, San Diego, CA, USA). Purified PCR products with an amplicon length of 550 base pairs (bp) (including adaptors) were submitted for sequencing in the paired-end (2x) modus (300 bp) on the MiSeq platform (Illumina, San Diego, CA, USA) at the BaseClear service laboratory (BaseClear BV, Leiden, The Netherlands). FASTQ files were generated and de-multiplexed based on sample-specific barcodes using the Casava pipeline (version 1.8.3, Illumina, San Diego, CA, USA). Sequence reads of low quality (only "passing filter" reads were selected) or containing the adapters or PhiX control signals were removed and the FASTQC pipeline (version 0.10.0, (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was applied for the initial quality control. One sample was excluded (old mouse on MF diet) because the coverage was below the threshold (50% of the median number of reads). SRS2529822 C1_7 C1_7_13236_3D_GCGTAGTAGCGTAAGA_L001 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3203460 C1_12_13236_4G_CGGAGCCTGAGCCTTA_L001 SRP145069 PRJNA392687 Microbiota composition was determined in the colonic luminal content of 8-10 mice per diet group at the age of 6 and 28 months, resulting in a total of 68 samples. Genomic DNA was extracted from the colonic luminal content using the ZR Fecal DNA MicroPrep kit (ZYMO Research, Irvine, CA, USA) according to the instructions of the manufacturer. Subsequently, the V3-V4 region of the 16S rRNA gene was amplified using a 2-step PCR. First, 10-25 ng of DNA was amplified using the 341F (5'-CCTACGGGNGGCWGCAG-3') and 785R (5'-GACTACHVGGGTATCTAATCC-3') primers appended with Illumina adaptor sequences. Amplicons were purified using the ZR-96 DNA Clean and Concentrator-5 Kit (ZYMO Research, Irvine, CA, USA). To quantify DNA content of the resulting amplicon, the Qubit Fluorometric Quantitation device (ThermoFisher Scientific, Waltham, MA, USA) was used. Besides, the amplicons were run on a 2%-agarose gel to confirm amplicon size and amount. Purified PCR products were used for the second PCR in combination with sample-specific barcoded primers (Nextera XT index kit, Illumina, San Diego, CA, USA). Purified PCR products with an amplicon length of 550 base pairs (bp) (including adaptors) were submitted for sequencing in the paired-end (2x) modus (300 bp) on the MiSeq platform (Illumina, San Diego, CA, USA) at the BaseClear service laboratory (BaseClear BV, Leiden, The Netherlands). FASTQ files were generated and de-multiplexed based on sample-specific barcodes using the Casava pipeline (version 1.8.3, Illumina, San Diego, CA, USA). Sequence reads of low quality (only "passing filter" reads were selected) or containing the adapters or PhiX control signals were removed and the FASTQC pipeline (version 0.10.0, (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was applied for the initial quality control. One sample was excluded (old mouse on MF diet) because the coverage was below the threshold (50% of the median number of reads). SRS2529823 C1_12 C1_12_13236_4G_CGGAGCCTGAGCCTTA_L001 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3203461 BC4_15_13236_9G_CCTAAGACGAGCCTTA_L001 SRP145069 PRJNA392687 Microbiota composition was determined in the colonic luminal content of 8-10 mice per diet group at the age of 6 and 28 months, resulting in a total of 68 samples. Genomic DNA was extracted from the colonic luminal content using the ZR Fecal DNA MicroPrep kit (ZYMO Research, Irvine, CA, USA) according to the instructions of the manufacturer. Subsequently, the V3-V4 region of the 16S rRNA gene was amplified using a 2-step PCR. First, 10-25 ng of DNA was amplified using the 341F (5'-CCTACGGGNGGCWGCAG-3') and 785R (5'-GACTACHVGGGTATCTAATCC-3') primers appended with Illumina adaptor sequences. Amplicons were purified using the ZR-96 DNA Clean and Concentrator-5 Kit (ZYMO Research, Irvine, CA, USA). To quantify DNA content of the resulting amplicon, the Qubit Fluorometric Quantitation device (ThermoFisher Scientific, Waltham, MA, USA) was used. Besides, the amplicons were run on a 2%-agarose gel to confirm amplicon size and amount. Purified PCR products were used for the second PCR in combination with sample-specific barcoded primers (Nextera XT index kit, Illumina, San Diego, CA, USA). Purified PCR products with an amplicon length of 550 base pairs (bp) (including adaptors) were submitted for sequencing in the paired-end (2x) modus (300 bp) on the MiSeq platform (Illumina, San Diego, CA, USA) at the BaseClear service laboratory (BaseClear BV, Leiden, The Netherlands). FASTQ files were generated and de-multiplexed based on sample-specific barcodes using the Casava pipeline (version 1.8.3, Illumina, San Diego, CA, USA). Sequence reads of low quality (only "passing filter" reads were selected) or containing the adapters or PhiX control signals were removed and the FASTQC pipeline (version 0.10.0, (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was applied for the initial quality control. One sample was excluded (old mouse on MF diet) because the coverage was below the threshold (50% of the median number of reads). SRS2529824 BC4_15 BC4_15_13236_9G_CCTAAGACGAGCCTTA_L001 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3203462 C1_1_13235_5B_GGACTCCTTTCTAGCT_L001 SRP145069 PRJNA392687 Microbiota composition was determined in the colonic luminal content of 8-10 mice per diet group at the age of 6 and 28 months, resulting in a total of 68 samples. Genomic DNA was extracted from the colonic luminal content using the ZR Fecal DNA MicroPrep kit (ZYMO Research, Irvine, CA, USA) according to the instructions of the manufacturer. Subsequently, the V3-V4 region of the 16S rRNA gene was amplified using a 2-step PCR. First, 10-25 ng of DNA was amplified using the 341F (5'-CCTACGGGNGGCWGCAG-3') and 785R (5'-GACTACHVGGGTATCTAATCC-3') primers appended with Illumina adaptor sequences. Amplicons were purified using the ZR-96 DNA Clean and Concentrator-5 Kit (ZYMO Research, Irvine, CA, USA). To quantify DNA content of the resulting amplicon, the Qubit Fluorometric Quantitation device (ThermoFisher Scientific, Waltham, MA, USA) was used. Besides, the amplicons were run on a 2%-agarose gel to confirm amplicon size and amount. Purified PCR products were used for the second PCR in combination with sample-specific barcoded primers (Nextera XT index kit, Illumina, San Diego, CA, USA). Purified PCR products with an amplicon length of 550 base pairs (bp) (including adaptors) were submitted for sequencing in the paired-end (2x) modus (300 bp) on the MiSeq platform (Illumina, San Diego, CA, USA) at the BaseClear service laboratory (BaseClear BV, Leiden, The Netherlands). FASTQ files were generated and de-multiplexed based on sample-specific barcodes using the Casava pipeline (version 1.8.3, Illumina, San Diego, CA, USA). Sequence reads of low quality (only "passing filter" reads were selected) or containing the adapters or PhiX control signals were removed and the FASTQC pipeline (version 0.10.0, (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was applied for the initial quality control. One sample was excluded (old mouse on MF diet) because the coverage was below the threshold (50% of the median number of reads). SRS2529825 C1_1 C1_1_13235_5B_GGACTCCTTTCTAGCT_L001 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3203463 B1_1_13234_4D_CGGAGCCTACTGCATA_L001 SRP145069 PRJNA392687 Microbiota composition was determined in the colonic luminal content of 8-10 mice per diet group at the age of 6 and 28 months, resulting in a total of 68 samples. Genomic DNA was extracted from the colonic luminal content using the ZR Fecal DNA MicroPrep kit (ZYMO Research, Irvine, CA, USA) according to the instructions of the manufacturer. Subsequently, the V3-V4 region of the 16S rRNA gene was amplified using a 2-step PCR. First, 10-25 ng of DNA was amplified using the 341F (5'-CCTACGGGNGGCWGCAG-3') and 785R (5'-GACTACHVGGGTATCTAATCC-3') primers appended with Illumina adaptor sequences. Amplicons were purified using the ZR-96 DNA Clean and Concentrator-5 Kit (ZYMO Research, Irvine, CA, USA). To quantify DNA content of the resulting amplicon, the Qubit Fluorometric Quantitation device (ThermoFisher Scientific, Waltham, MA, USA) was used. Besides, the amplicons were run on a 2%-agarose gel to confirm amplicon size and amount. Purified PCR products were used for the second PCR in combination with sample-specific barcoded primers (Nextera XT index kit, Illumina, San Diego, CA, USA). Purified PCR products with an amplicon length of 550 base pairs (bp) (including adaptors) were submitted for sequencing in the paired-end (2x) modus (300 bp) on the MiSeq platform (Illumina, San Diego, CA, USA) at the BaseClear service laboratory (BaseClear BV, Leiden, The Netherlands). FASTQ files were generated and de-multiplexed based on sample-specific barcodes using the Casava pipeline (version 1.8.3, Illumina, San Diego, CA, USA). Sequence reads of low quality (only "passing filter" reads were selected) or containing the adapters or PhiX control signals were removed and the FASTQC pipeline (version 0.10.0, (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was applied for the initial quality control. One sample was excluded (old mouse on MF diet) because the coverage was below the threshold (50% of the median number of reads). SRS2529826 B1_1 B1_1_13234_4D_CGGAGCCTACTGCATA_L001 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3203464 B1_2_13234_4E_CGGAGCCTAAGGAGTA_L001 SRP145069 PRJNA392687 Microbiota composition was determined in the colonic luminal content of 8-10 mice per diet group at the age of 6 and 28 months, resulting in a total of 68 samples. Genomic DNA was extracted from the colonic luminal content using the ZR Fecal DNA MicroPrep kit (ZYMO Research, Irvine, CA, USA) according to the instructions of the manufacturer. Subsequently, the V3-V4 region of the 16S rRNA gene was amplified using a 2-step PCR. First, 10-25 ng of DNA was amplified using the 341F (5'-CCTACGGGNGGCWGCAG-3') and 785R (5'-GACTACHVGGGTATCTAATCC-3') primers appended with Illumina adaptor sequences. Amplicons were purified using the ZR-96 DNA Clean and Concentrator-5 Kit (ZYMO Research, Irvine, CA, USA). To quantify DNA content of the resulting amplicon, the Qubit Fluorometric Quantitation device (ThermoFisher Scientific, Waltham, MA, USA) was used. Besides, the amplicons were run on a 2%-agarose gel to confirm amplicon size and amount. Purified PCR products were used for the second PCR in combination with sample-specific barcoded primers (Nextera XT index kit, Illumina, San Diego, CA, USA). Purified PCR products with an amplicon length of 550 base pairs (bp) (including adaptors) were submitted for sequencing in the paired-end (2x) modus (300 bp) on the MiSeq platform (Illumina, San Diego, CA, USA) at the BaseClear service laboratory (BaseClear BV, Leiden, The Netherlands). FASTQ files were generated and de-multiplexed based on sample-specific barcodes using the Casava pipeline (version 1.8.3, Illumina, San Diego, CA, USA). Sequence reads of low quality (only "passing filter" reads were selected) or containing the adapters or PhiX control signals were removed and the FASTQC pipeline (version 0.10.0, (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was applied for the initial quality control. One sample was excluded (old mouse on MF diet) because the coverage was below the threshold (50% of the median number of reads). SRS2529827 B1_2 B1_2_13234_4E_CGGAGCCTAAGGAGTA_L001 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3203465 B1_11_13236_11F_TGCAGCTAAAGGCTAT_L001 SRP145069 PRJNA392687 Microbiota composition was determined in the colonic luminal content of 8-10 mice per diet group at the age of 6 and 28 months, resulting in a total of 68 samples. Genomic DNA was extracted from the colonic luminal content using the ZR Fecal DNA MicroPrep kit (ZYMO Research, Irvine, CA, USA) according to the instructions of the manufacturer. Subsequently, the V3-V4 region of the 16S rRNA gene was amplified using a 2-step PCR. First, 10-25 ng of DNA was amplified using the 341F (5'-CCTACGGGNGGCWGCAG-3') and 785R (5'-GACTACHVGGGTATCTAATCC-3') primers appended with Illumina adaptor sequences. Amplicons were purified using the ZR-96 DNA Clean and Concentrator-5 Kit (ZYMO Research, Irvine, CA, USA). To quantify DNA content of the resulting amplicon, the Qubit Fluorometric Quantitation device (ThermoFisher Scientific, Waltham, MA, USA) was used. Besides, the amplicons were run on a 2%-agarose gel to confirm amplicon size and amount. Purified PCR products were used for the second PCR in combination with sample-specific barcoded primers (Nextera XT index kit, Illumina, San Diego, CA, USA). Purified PCR products with an amplicon length of 550 base pairs (bp) (including adaptors) were submitted for sequencing in the paired-end (2x) modus (300 bp) on the MiSeq platform (Illumina, San Diego, CA, USA) at the BaseClear service laboratory (BaseClear BV, Leiden, The Netherlands). FASTQ files were generated and de-multiplexed based on sample-specific barcodes using the Casava pipeline (version 1.8.3, Illumina, San Diego, CA, USA). Sequence reads of low quality (only "passing filter" reads were selected) or containing the adapters or PhiX control signals were removed and the FASTQC pipeline (version 0.10.0, (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was applied for the initial quality control. One sample was excluded (old mouse on MF diet) because the coverage was below the threshold (50% of the median number of reads). SRS2529828 B1_11 B1_11_13236_11F_TGCAGCTAAAGGCTAT_L001 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3203466 B1_12_13236_11G_TGCAGCTAGAGCCTTA_L001 SRP145069 PRJNA392687 Microbiota composition was determined in the colonic luminal content of 8-10 mice per diet group at the age of 6 and 28 months, resulting in a total of 68 samples. Genomic DNA was extracted from the colonic luminal content using the ZR Fecal DNA MicroPrep kit (ZYMO Research, Irvine, CA, USA) according to the instructions of the manufacturer. Subsequently, the V3-V4 region of the 16S rRNA gene was amplified using a 2-step PCR. First, 10-25 ng of DNA was amplified using the 341F (5'-CCTACGGGNGGCWGCAG-3') and 785R (5'-GACTACHVGGGTATCTAATCC-3') primers appended with Illumina adaptor sequences. Amplicons were purified using the ZR-96 DNA Clean and Concentrator-5 Kit (ZYMO Research, Irvine, CA, USA). To quantify DNA content of the resulting amplicon, the Qubit Fluorometric Quantitation device (ThermoFisher Scientific, Waltham, MA, USA) was used. Besides, the amplicons were run on a 2%-agarose gel to confirm amplicon size and amount. Purified PCR products were used for the second PCR in combination with sample-specific barcoded primers (Nextera XT index kit, Illumina, San Diego, CA, USA). Purified PCR products with an amplicon length of 550 base pairs (bp) (including adaptors) were submitted for sequencing in the paired-end (2x) modus (300 bp) on the MiSeq platform (Illumina, San Diego, CA, USA) at the BaseClear service laboratory (BaseClear BV, Leiden, The Netherlands). FASTQ files were generated and de-multiplexed based on sample-specific barcodes using the Casava pipeline (version 1.8.3, Illumina, San Diego, CA, USA). Sequence reads of low quality (only "passing filter" reads were selected) or containing the adapters or PhiX control signals were removed and the FASTQC pipeline (version 0.10.0, (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was applied for the initial quality control. One sample was excluded (old mouse on MF diet) because the coverage was below the threshold (50% of the median number of reads). SRS2529829 B1_12 B1_12_13236_11G_TGCAGCTAGAGCCTTA_L001 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3203467 B1_6_13235_11D_GCTCATGAGCGTAAGA_L001 SRP145069 PRJNA392687 Microbiota composition was determined in the colonic luminal content of 8-10 mice per diet group at the age of 6 and 28 months, resulting in a total of 68 samples. Genomic DNA was extracted from the colonic luminal content using the ZR Fecal DNA MicroPrep kit (ZYMO Research, Irvine, CA, USA) according to the instructions of the manufacturer. Subsequently, the V3-V4 region of the 16S rRNA gene was amplified using a 2-step PCR. First, 10-25 ng of DNA was amplified using the 341F (5'-CCTACGGGNGGCWGCAG-3') and 785R (5'-GACTACHVGGGTATCTAATCC-3') primers appended with Illumina adaptor sequences. Amplicons were purified using the ZR-96 DNA Clean and Concentrator-5 Kit (ZYMO Research, Irvine, CA, USA). To quantify DNA content of the resulting amplicon, the Qubit Fluorometric Quantitation device (ThermoFisher Scientific, Waltham, MA, USA) was used. Besides, the amplicons were run on a 2%-agarose gel to confirm amplicon size and amount. Purified PCR products were used for the second PCR in combination with sample-specific barcoded primers (Nextera XT index kit, Illumina, San Diego, CA, USA). Purified PCR products with an amplicon length of 550 base pairs (bp) (including adaptors) were submitted for sequencing in the paired-end (2x) modus (300 bp) on the MiSeq platform (Illumina, San Diego, CA, USA) at the BaseClear service laboratory (BaseClear BV, Leiden, The Netherlands). FASTQ files were generated and de-multiplexed based on sample-specific barcodes using the Casava pipeline (version 1.8.3, Illumina, San Diego, CA, USA). Sequence reads of low quality (only "passing filter" reads were selected) or containing the adapters or PhiX control signals were removed and the FASTQC pipeline (version 0.10.0, (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was applied for the initial quality control. One sample was excluded (old mouse on MF diet) because the coverage was below the threshold (50% of the median number of reads). SRS2529830 B1_6 B1_6_13235_11D_GCTCATGAGCGTAAGA_L001 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3203468 B1_7_13235_11E_GCTCATGACTATTAAG_L001 SRP145069 PRJNA392687 Microbiota composition was determined in the colonic luminal content of 8-10 mice per diet group at the age of 6 and 28 months, resulting in a total of 68 samples. Genomic DNA was extracted from the colonic luminal content using the ZR Fecal DNA MicroPrep kit (ZYMO Research, Irvine, CA, USA) according to the instructions of the manufacturer. Subsequently, the V3-V4 region of the 16S rRNA gene was amplified using a 2-step PCR. First, 10-25 ng of DNA was amplified using the 341F (5'-CCTACGGGNGGCWGCAG-3') and 785R (5'-GACTACHVGGGTATCTAATCC-3') primers appended with Illumina adaptor sequences. Amplicons were purified using the ZR-96 DNA Clean and Concentrator-5 Kit (ZYMO Research, Irvine, CA, USA). To quantify DNA content of the resulting amplicon, the Qubit Fluorometric Quantitation device (ThermoFisher Scientific, Waltham, MA, USA) was used. Besides, the amplicons were run on a 2%-agarose gel to confirm amplicon size and amount. Purified PCR products were used for the second PCR in combination with sample-specific barcoded primers (Nextera XT index kit, Illumina, San Diego, CA, USA). Purified PCR products with an amplicon length of 550 base pairs (bp) (including adaptors) were submitted for sequencing in the paired-end (2x) modus (300 bp) on the MiSeq platform (Illumina, San Diego, CA, USA) at the BaseClear service laboratory (BaseClear BV, Leiden, The Netherlands). FASTQ files were generated and de-multiplexed based on sample-specific barcodes using the Casava pipeline (version 1.8.3, Illumina, San Diego, CA, USA). Sequence reads of low quality (only "passing filter" reads were selected) or containing the adapters or PhiX control signals were removed and the FASTQC pipeline (version 0.10.0, (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was applied for the initial quality control. One sample was excluded (old mouse on MF diet) because the coverage was below the threshold (50% of the median number of reads). SRS2529831 B1_7 B1_7_13235_11E_GCTCATGACTATTAAG_L001 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3203469 B1_3_13235_4D_TCCTGAGCGCGTAAGA_L001 SRP145069 PRJNA392687 Microbiota composition was determined in the colonic luminal content of 8-10 mice per diet group at the age of 6 and 28 months, resulting in a total of 68 samples. Genomic DNA was extracted from the colonic luminal content using the ZR Fecal DNA MicroPrep kit (ZYMO Research, Irvine, CA, USA) according to the instructions of the manufacturer. Subsequently, the V3-V4 region of the 16S rRNA gene was amplified using a 2-step PCR. First, 10-25 ng of DNA was amplified using the 341F (5'-CCTACGGGNGGCWGCAG-3') and 785R (5'-GACTACHVGGGTATCTAATCC-3') primers appended with Illumina adaptor sequences. Amplicons were purified using the ZR-96 DNA Clean and Concentrator-5 Kit (ZYMO Research, Irvine, CA, USA). To quantify DNA content of the resulting amplicon, the Qubit Fluorometric Quantitation device (ThermoFisher Scientific, Waltham, MA, USA) was used. Besides, the amplicons were run on a 2%-agarose gel to confirm amplicon size and amount. Purified PCR products were used for the second PCR in combination with sample-specific barcoded primers (Nextera XT index kit, Illumina, San Diego, CA, USA). Purified PCR products with an amplicon length of 550 base pairs (bp) (including adaptors) were submitted for sequencing in the paired-end (2x) modus (300 bp) on the MiSeq platform (Illumina, San Diego, CA, USA) at the BaseClear service laboratory (BaseClear BV, Leiden, The Netherlands). FASTQ files were generated and de-multiplexed based on sample-specific barcodes using the Casava pipeline (version 1.8.3, Illumina, San Diego, CA, USA). Sequence reads of low quality (only "passing filter" reads were selected) or containing the adapters or PhiX control signals were removed and the FASTQC pipeline (version 0.10.0, (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was applied for the initial quality control. One sample was excluded (old mouse on MF diet) because the coverage was below the threshold (50% of the median number of reads). SRS2529833 B1_3 B1_3_13235_4D_TCCTGAGCGCGTAAGA_L001 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3203470 B1_5_13235_4E_TCCTGAGCCTATTAAG_L001 SRP145069 PRJNA392687 Microbiota composition was determined in the colonic luminal content of 8-10 mice per diet group at the age of 6 and 28 months, resulting in a total of 68 samples. Genomic DNA was extracted from the colonic luminal content using the ZR Fecal DNA MicroPrep kit (ZYMO Research, Irvine, CA, USA) according to the instructions of the manufacturer. Subsequently, the V3-V4 region of the 16S rRNA gene was amplified using a 2-step PCR. First, 10-25 ng of DNA was amplified using the 341F (5'-CCTACGGGNGGCWGCAG-3') and 785R (5'-GACTACHVGGGTATCTAATCC-3') primers appended with Illumina adaptor sequences. Amplicons were purified using the ZR-96 DNA Clean and Concentrator-5 Kit (ZYMO Research, Irvine, CA, USA). To quantify DNA content of the resulting amplicon, the Qubit Fluorometric Quantitation device (ThermoFisher Scientific, Waltham, MA, USA) was used. Besides, the amplicons were run on a 2%-agarose gel to confirm amplicon size and amount. Purified PCR products were used for the second PCR in combination with sample-specific barcoded primers (Nextera XT index kit, Illumina, San Diego, CA, USA). Purified PCR products with an amplicon length of 550 base pairs (bp) (including adaptors) were submitted for sequencing in the paired-end (2x) modus (300 bp) on the MiSeq platform (Illumina, San Diego, CA, USA) at the BaseClear service laboratory (BaseClear BV, Leiden, The Netherlands). FASTQ files were generated and de-multiplexed based on sample-specific barcodes using the Casava pipeline (version 1.8.3, Illumina, San Diego, CA, USA). Sequence reads of low quality (only "passing filter" reads were selected) or containing the adapters or PhiX control signals were removed and the FASTQC pipeline (version 0.10.0, (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was applied for the initial quality control. One sample was excluded (old mouse on MF diet) because the coverage was below the threshold (50% of the median number of reads). SRS2529832 B1_5 B1_5_13235_4E_TCCTGAGCCTATTAAG_L001 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3203471 C4_9_13235_9D_AAGAGGCAGCGTAAGA_L001 SRP145069 PRJNA392687 Microbiota composition was determined in the colonic luminal content of 8-10 mice per diet group at the age of 6 and 28 months, resulting in a total of 68 samples. Genomic DNA was extracted from the colonic luminal content using the ZR Fecal DNA MicroPrep kit (ZYMO Research, Irvine, CA, USA) according to the instructions of the manufacturer. Subsequently, the V3-V4 region of the 16S rRNA gene was amplified using a 2-step PCR. First, 10-25 ng of DNA was amplified using the 341F (5'-CCTACGGGNGGCWGCAG-3') and 785R (5'-GACTACHVGGGTATCTAATCC-3') primers appended with Illumina adaptor sequences. Amplicons were purified using the ZR-96 DNA Clean and Concentrator-5 Kit (ZYMO Research, Irvine, CA, USA). To quantify DNA content of the resulting amplicon, the Qubit Fluorometric Quantitation device (ThermoFisher Scientific, Waltham, MA, USA) was used. Besides, the amplicons were run on a 2%-agarose gel to confirm amplicon size and amount. Purified PCR products were used for the second PCR in combination with sample-specific barcoded primers (Nextera XT index kit, Illumina, San Diego, CA, USA). Purified PCR products with an amplicon length of 550 base pairs (bp) (including adaptors) were submitted for sequencing in the paired-end (2x) modus (300 bp) on the MiSeq platform (Illumina, San Diego, CA, USA) at the BaseClear service laboratory (BaseClear BV, Leiden, The Netherlands). FASTQ files were generated and de-multiplexed based on sample-specific barcodes using the Casava pipeline (version 1.8.3, Illumina, San Diego, CA, USA). Sequence reads of low quality (only "passing filter" reads were selected) or containing the adapters or PhiX control signals were removed and the FASTQC pipeline (version 0.10.0, (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was applied for the initial quality control. One sample was excluded (old mouse on MF diet) because the coverage was below the threshold (50% of the median number of reads). SRS2529834 C4_9 C4_9_13235_9D_AAGAGGCAGCGTAAGA_L001 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3203472 B1_8_13236_4D_CGGAGCCTGCGTAAGA_L001 SRP145069 PRJNA392687 Microbiota composition was determined in the colonic luminal content of 8-10 mice per diet group at the age of 6 and 28 months, resulting in a total of 68 samples. Genomic DNA was extracted from the colonic luminal content using the ZR Fecal DNA MicroPrep kit (ZYMO Research, Irvine, CA, USA) according to the instructions of the manufacturer. Subsequently, the V3-V4 region of the 16S rRNA gene was amplified using a 2-step PCR. First, 10-25 ng of DNA was amplified using the 341F (5'-CCTACGGGNGGCWGCAG-3') and 785R (5'-GACTACHVGGGTATCTAATCC-3') primers appended with Illumina adaptor sequences. Amplicons were purified using the ZR-96 DNA Clean and Concentrator-5 Kit (ZYMO Research, Irvine, CA, USA). To quantify DNA content of the resulting amplicon, the Qubit Fluorometric Quantitation device (ThermoFisher Scientific, Waltham, MA, USA) was used. Besides, the amplicons were run on a 2%-agarose gel to confirm amplicon size and amount. Purified PCR products were used for the second PCR in combination with sample-specific barcoded primers (Nextera XT index kit, Illumina, San Diego, CA, USA). Purified PCR products with an amplicon length of 550 base pairs (bp) (including adaptors) were submitted for sequencing in the paired-end (2x) modus (300 bp) on the MiSeq platform (Illumina, San Diego, CA, USA) at the BaseClear service laboratory (BaseClear BV, Leiden, The Netherlands). FASTQ files were generated and de-multiplexed based on sample-specific barcodes using the Casava pipeline (version 1.8.3, Illumina, San Diego, CA, USA). Sequence reads of low quality (only "passing filter" reads were selected) or containing the adapters or PhiX control signals were removed and the FASTQC pipeline (version 0.10.0, (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was applied for the initial quality control. One sample was excluded (old mouse on MF diet) because the coverage was below the threshold (50% of the median number of reads). SRS2529835 B1_8 B1_8_13236_4D_CGGAGCCTGCGTAAGA_L001 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3203473 B1_9_13236_4E_CGGAGCCTCTATTAAG_L001 SRP145069 PRJNA392687 Microbiota composition was determined in the colonic luminal content of 8-10 mice per diet group at the age of 6 and 28 months, resulting in a total of 68 samples. Genomic DNA was extracted from the colonic luminal content using the ZR Fecal DNA MicroPrep kit (ZYMO Research, Irvine, CA, USA) according to the instructions of the manufacturer. Subsequently, the V3-V4 region of the 16S rRNA gene was amplified using a 2-step PCR. First, 10-25 ng of DNA was amplified using the 341F (5'-CCTACGGGNGGCWGCAG-3') and 785R (5'-GACTACHVGGGTATCTAATCC-3') primers appended with Illumina adaptor sequences. Amplicons were purified using the ZR-96 DNA Clean and Concentrator-5 Kit (ZYMO Research, Irvine, CA, USA). To quantify DNA content of the resulting amplicon, the Qubit Fluorometric Quantitation device (ThermoFisher Scientific, Waltham, MA, USA) was used. Besides, the amplicons were run on a 2%-agarose gel to confirm amplicon size and amount. Purified PCR products were used for the second PCR in combination with sample-specific barcoded primers (Nextera XT index kit, Illumina, San Diego, CA, USA). Purified PCR products with an amplicon length of 550 base pairs (bp) (including adaptors) were submitted for sequencing in the paired-end (2x) modus (300 bp) on the MiSeq platform (Illumina, San Diego, CA, USA) at the BaseClear service laboratory (BaseClear BV, Leiden, The Netherlands). FASTQ files were generated and de-multiplexed based on sample-specific barcodes using the Casava pipeline (version 1.8.3, Illumina, San Diego, CA, USA). Sequence reads of low quality (only "passing filter" reads were selected) or containing the adapters or PhiX control signals were removed and the FASTQC pipeline (version 0.10.0, (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was applied for the initial quality control. One sample was excluded (old mouse on MF diet) because the coverage was below the threshold (50% of the median number of reads). SRS2529837 B1_9 B1_9_13236_4E_CGGAGCCTCTATTAAG_L001 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3203474 BC4_8_13235_10B_GTAGAGGATTCTAGCT_L001 SRP145069 PRJNA392687 Microbiota composition was determined in the colonic luminal content of 8-10 mice per diet group at the age of 6 and 28 months, resulting in a total of 68 samples. Genomic DNA was extracted from the colonic luminal content using the ZR Fecal DNA MicroPrep kit (ZYMO Research, Irvine, CA, USA) according to the instructions of the manufacturer. Subsequently, the V3-V4 region of the 16S rRNA gene was amplified using a 2-step PCR. First, 10-25 ng of DNA was amplified using the 341F (5'-CCTACGGGNGGCWGCAG-3') and 785R (5'-GACTACHVGGGTATCTAATCC-3') primers appended with Illumina adaptor sequences. Amplicons were purified using the ZR-96 DNA Clean and Concentrator-5 Kit (ZYMO Research, Irvine, CA, USA). To quantify DNA content of the resulting amplicon, the Qubit Fluorometric Quantitation device (ThermoFisher Scientific, Waltham, MA, USA) was used. Besides, the amplicons were run on a 2%-agarose gel to confirm amplicon size and amount. Purified PCR products were used for the second PCR in combination with sample-specific barcoded primers (Nextera XT index kit, Illumina, San Diego, CA, USA). Purified PCR products with an amplicon length of 550 base pairs (bp) (including adaptors) were submitted for sequencing in the paired-end (2x) modus (300 bp) on the MiSeq platform (Illumina, San Diego, CA, USA) at the BaseClear service laboratory (BaseClear BV, Leiden, The Netherlands). FASTQ files were generated and de-multiplexed based on sample-specific barcodes using the Casava pipeline (version 1.8.3, Illumina, San Diego, CA, USA). Sequence reads of low quality (only "passing filter" reads were selected) or containing the adapters or PhiX control signals were removed and the FASTQC pipeline (version 0.10.0, (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was applied for the initial quality control. One sample was excluded (old mouse on MF diet) because the coverage was below the threshold (50% of the median number of reads). SRS2529836 BC4_8 BC4_8_13235_10B_GTAGAGGATTCTAGCT_L001 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3203475 BC4_9_13235_10C_GTAGAGGACCTAGAGT_L001 SRP145069 PRJNA392687 Microbiota composition was determined in the colonic luminal content of 8-10 mice per diet group at the age of 6 and 28 months, resulting in a total of 68 samples. Genomic DNA was extracted from the colonic luminal content using the ZR Fecal DNA MicroPrep kit (ZYMO Research, Irvine, CA, USA) according to the instructions of the manufacturer. Subsequently, the V3-V4 region of the 16S rRNA gene was amplified using a 2-step PCR. First, 10-25 ng of DNA was amplified using the 341F (5'-CCTACGGGNGGCWGCAG-3') and 785R (5'-GACTACHVGGGTATCTAATCC-3') primers appended with Illumina adaptor sequences. Amplicons were purified using the ZR-96 DNA Clean and Concentrator-5 Kit (ZYMO Research, Irvine, CA, USA). To quantify DNA content of the resulting amplicon, the Qubit Fluorometric Quantitation device (ThermoFisher Scientific, Waltham, MA, USA) was used. Besides, the amplicons were run on a 2%-agarose gel to confirm amplicon size and amount. Purified PCR products were used for the second PCR in combination with sample-specific barcoded primers (Nextera XT index kit, Illumina, San Diego, CA, USA). Purified PCR products with an amplicon length of 550 base pairs (bp) (including adaptors) were submitted for sequencing in the paired-end (2x) modus (300 bp) on the MiSeq platform (Illumina, San Diego, CA, USA) at the BaseClear service laboratory (BaseClear BV, Leiden, The Netherlands). FASTQ files were generated and de-multiplexed based on sample-specific barcodes using the Casava pipeline (version 1.8.3, Illumina, San Diego, CA, USA). Sequence reads of low quality (only "passing filter" reads were selected) or containing the adapters or PhiX control signals were removed and the FASTQC pipeline (version 0.10.0, (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was applied for the initial quality control. One sample was excluded (old mouse on MF diet) because the coverage was below the threshold (50% of the median number of reads). SRS2529839 BC4_9 BC4_9_13235_10C_GTAGAGGACCTAGAGT_L001 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3203476 C4_13_13236_11D_TGCAGCTAGCGTAAGA_L001 SRP145069 PRJNA392687 Microbiota composition was determined in the colonic luminal content of 8-10 mice per diet group at the age of 6 and 28 months, resulting in a total of 68 samples. Genomic DNA was extracted from the colonic luminal content using the ZR Fecal DNA MicroPrep kit (ZYMO Research, Irvine, CA, USA) according to the instructions of the manufacturer. Subsequently, the V3-V4 region of the 16S rRNA gene was amplified using a 2-step PCR. First, 10-25 ng of DNA was amplified using the 341F (5'-CCTACGGGNGGCWGCAG-3') and 785R (5'-GACTACHVGGGTATCTAATCC-3') primers appended with Illumina adaptor sequences. Amplicons were purified using the ZR-96 DNA Clean and Concentrator-5 Kit (ZYMO Research, Irvine, CA, USA). To quantify DNA content of the resulting amplicon, the Qubit Fluorometric Quantitation device (ThermoFisher Scientific, Waltham, MA, USA) was used. Besides, the amplicons were run on a 2%-agarose gel to confirm amplicon size and amount. Purified PCR products were used for the second PCR in combination with sample-specific barcoded primers (Nextera XT index kit, Illumina, San Diego, CA, USA). Purified PCR products with an amplicon length of 550 base pairs (bp) (including adaptors) were submitted for sequencing in the paired-end (2x) modus (300 bp) on the MiSeq platform (Illumina, San Diego, CA, USA) at the BaseClear service laboratory (BaseClear BV, Leiden, The Netherlands). FASTQ files were generated and de-multiplexed based on sample-specific barcodes using the Casava pipeline (version 1.8.3, Illumina, San Diego, CA, USA). Sequence reads of low quality (only "passing filter" reads were selected) or containing the adapters or PhiX control signals were removed and the FASTQC pipeline (version 0.10.0, (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was applied for the initial quality control. One sample was excluded (old mouse on MF diet) because the coverage was below the threshold (50% of the median number of reads). SRS2529838 C4_13 C4_13_13236_11D_TGCAGCTAGCGTAAGA_L001 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3203477 C4_15_13236_11E_TGCAGCTACTATTAAG_L001 SRP145069 PRJNA392687 Microbiota composition was determined in the colonic luminal content of 8-10 mice per diet group at the age of 6 and 28 months, resulting in a total of 68 samples. Genomic DNA was extracted from the colonic luminal content using the ZR Fecal DNA MicroPrep kit (ZYMO Research, Irvine, CA, USA) according to the instructions of the manufacturer. Subsequently, the V3-V4 region of the 16S rRNA gene was amplified using a 2-step PCR. First, 10-25 ng of DNA was amplified using the 341F (5'-CCTACGGGNGGCWGCAG-3') and 785R (5'-GACTACHVGGGTATCTAATCC-3') primers appended with Illumina adaptor sequences. Amplicons were purified using the ZR-96 DNA Clean and Concentrator-5 Kit (ZYMO Research, Irvine, CA, USA). To quantify DNA content of the resulting amplicon, the Qubit Fluorometric Quantitation device (ThermoFisher Scientific, Waltham, MA, USA) was used. Besides, the amplicons were run on a 2%-agarose gel to confirm amplicon size and amount. Purified PCR products were used for the second PCR in combination with sample-specific barcoded primers (Nextera XT index kit, Illumina, San Diego, CA, USA). Purified PCR products with an amplicon length of 550 base pairs (bp) (including adaptors) were submitted for sequencing in the paired-end (2x) modus (300 bp) on the MiSeq platform (Illumina, San Diego, CA, USA) at the BaseClear service laboratory (BaseClear BV, Leiden, The Netherlands). FASTQ files were generated and de-multiplexed based on sample-specific barcodes using the Casava pipeline (version 1.8.3, Illumina, San Diego, CA, USA). Sequence reads of low quality (only "passing filter" reads were selected) or containing the adapters or PhiX control signals were removed and the FASTQC pipeline (version 0.10.0, (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was applied for the initial quality control. One sample was excluded (old mouse on MF diet) because the coverage was below the threshold (50% of the median number of reads). SRS2529841 C4_15 C4_15_13236_11E_TGCAGCTACTATTAAG_L001 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3203478 BC4_1_13234_5D_TACGCTGCACTGCATA_L001 SRP145069 PRJNA392687 Microbiota composition was determined in the colonic luminal content of 8-10 mice per diet group at the age of 6 and 28 months, resulting in a total of 68 samples. Genomic DNA was extracted from the colonic luminal content using the ZR Fecal DNA MicroPrep kit (ZYMO Research, Irvine, CA, USA) according to the instructions of the manufacturer. Subsequently, the V3-V4 region of the 16S rRNA gene was amplified using a 2-step PCR. First, 10-25 ng of DNA was amplified using the 341F (5'-CCTACGGGNGGCWGCAG-3') and 785R (5'-GACTACHVGGGTATCTAATCC-3') primers appended with Illumina adaptor sequences. Amplicons were purified using the ZR-96 DNA Clean and Concentrator-5 Kit (ZYMO Research, Irvine, CA, USA). To quantify DNA content of the resulting amplicon, the Qubit Fluorometric Quantitation device (ThermoFisher Scientific, Waltham, MA, USA) was used. Besides, the amplicons were run on a 2%-agarose gel to confirm amplicon size and amount. Purified PCR products were used for the second PCR in combination with sample-specific barcoded primers (Nextera XT index kit, Illumina, San Diego, CA, USA). Purified PCR products with an amplicon length of 550 base pairs (bp) (including adaptors) were submitted for sequencing in the paired-end (2x) modus (300 bp) on the MiSeq platform (Illumina, San Diego, CA, USA) at the BaseClear service laboratory (BaseClear BV, Leiden, The Netherlands). FASTQ files were generated and de-multiplexed based on sample-specific barcodes using the Casava pipeline (version 1.8.3, Illumina, San Diego, CA, USA). Sequence reads of low quality (only "passing filter" reads were selected) or containing the adapters or PhiX control signals were removed and the FASTQC pipeline (version 0.10.0, (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was applied for the initial quality control. One sample was excluded (old mouse on MF diet) because the coverage was below the threshold (50% of the median number of reads). SRS2529840 BC4_1 BC4_1_13234_5D_TACGCTGCACTGCATA_L001 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3203479 A1_9_13235_6B_TAGGCATGTTCTAGCT_L001 SRP145069 PRJNA392687 Microbiota composition was determined in the colonic luminal content of 8-10 mice per diet group at the age of 6 and 28 months, resulting in a total of 68 samples. Genomic DNA was extracted from the colonic luminal content using the ZR Fecal DNA MicroPrep kit (ZYMO Research, Irvine, CA, USA) according to the instructions of the manufacturer. Subsequently, the V3-V4 region of the 16S rRNA gene was amplified using a 2-step PCR. First, 10-25 ng of DNA was amplified using the 341F (5'-CCTACGGGNGGCWGCAG-3') and 785R (5'-GACTACHVGGGTATCTAATCC-3') primers appended with Illumina adaptor sequences. Amplicons were purified using the ZR-96 DNA Clean and Concentrator-5 Kit (ZYMO Research, Irvine, CA, USA). To quantify DNA content of the resulting amplicon, the Qubit Fluorometric Quantitation device (ThermoFisher Scientific, Waltham, MA, USA) was used. Besides, the amplicons were run on a 2%-agarose gel to confirm amplicon size and amount. Purified PCR products were used for the second PCR in combination with sample-specific barcoded primers (Nextera XT index kit, Illumina, San Diego, CA, USA). Purified PCR products with an amplicon length of 550 base pairs (bp) (including adaptors) were submitted for sequencing in the paired-end (2x) modus (300 bp) on the MiSeq platform (Illumina, San Diego, CA, USA) at the BaseClear service laboratory (BaseClear BV, Leiden, The Netherlands). FASTQ files were generated and de-multiplexed based on sample-specific barcodes using the Casava pipeline (version 1.8.3, Illumina, San Diego, CA, USA). Sequence reads of low quality (only "passing filter" reads were selected) or containing the adapters or PhiX control signals were removed and the FASTQC pipeline (version 0.10.0, (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was applied for the initial quality control. One sample was excluded (old mouse on MF diet) because the coverage was below the threshold (50% of the median number of reads). SRS2529842 A1_9 A1_9_13235_6B_TAGGCATGTTCTAGCT_L001 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3203480 A1_8_13235_2C_CGTACTAGCCTAGAGT_L001 SRP145069 PRJNA392687 Microbiota composition was determined in the colonic luminal content of 8-10 mice per diet group at the age of 6 and 28 months, resulting in a total of 68 samples. Genomic DNA was extracted from the colonic luminal content using the ZR Fecal DNA MicroPrep kit (ZYMO Research, Irvine, CA, USA) according to the instructions of the manufacturer. Subsequently, the V3-V4 region of the 16S rRNA gene was amplified using a 2-step PCR. First, 10-25 ng of DNA was amplified using the 341F (5'-CCTACGGGNGGCWGCAG-3') and 785R (5'-GACTACHVGGGTATCTAATCC-3') primers appended with Illumina adaptor sequences. Amplicons were purified using the ZR-96 DNA Clean and Concentrator-5 Kit (ZYMO Research, Irvine, CA, USA). To quantify DNA content of the resulting amplicon, the Qubit Fluorometric Quantitation device (ThermoFisher Scientific, Waltham, MA, USA) was used. Besides, the amplicons were run on a 2%-agarose gel to confirm amplicon size and amount. Purified PCR products were used for the second PCR in combination with sample-specific barcoded primers (Nextera XT index kit, Illumina, San Diego, CA, USA). Purified PCR products with an amplicon length of 550 base pairs (bp) (including adaptors) were submitted for sequencing in the paired-end (2x) modus (300 bp) on the MiSeq platform (Illumina, San Diego, CA, USA) at the BaseClear service laboratory (BaseClear BV, Leiden, The Netherlands). FASTQ files were generated and de-multiplexed based on sample-specific barcodes using the Casava pipeline (version 1.8.3, Illumina, San Diego, CA, USA). Sequence reads of low quality (only "passing filter" reads were selected) or containing the adapters or PhiX control signals were removed and the FASTQC pipeline (version 0.10.0, (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was applied for the initial quality control. One sample was excluded (old mouse on MF diet) because the coverage was below the threshold (50% of the median number of reads). SRS2529843 A1_8 A1_8_13235_2C_CGTACTAGCCTAGAGT_L001 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3203481 BC4_3_13234_5E_TACGCTGCAAGGAGTA_L001 SRP145069 PRJNA392687 Microbiota composition was determined in the colonic luminal content of 8-10 mice per diet group at the age of 6 and 28 months, resulting in a total of 68 samples. Genomic DNA was extracted from the colonic luminal content using the ZR Fecal DNA MicroPrep kit (ZYMO Research, Irvine, CA, USA) according to the instructions of the manufacturer. Subsequently, the V3-V4 region of the 16S rRNA gene was amplified using a 2-step PCR. First, 10-25 ng of DNA was amplified using the 341F (5'-CCTACGGGNGGCWGCAG-3') and 785R (5'-GACTACHVGGGTATCTAATCC-3') primers appended with Illumina adaptor sequences. Amplicons were purified using the ZR-96 DNA Clean and Concentrator-5 Kit (ZYMO Research, Irvine, CA, USA). To quantify DNA content of the resulting amplicon, the Qubit Fluorometric Quantitation device (ThermoFisher Scientific, Waltham, MA, USA) was used. Besides, the amplicons were run on a 2%-agarose gel to confirm amplicon size and amount. Purified PCR products were used for the second PCR in combination with sample-specific barcoded primers (Nextera XT index kit, Illumina, San Diego, CA, USA). Purified PCR products with an amplicon length of 550 base pairs (bp) (including adaptors) were submitted for sequencing in the paired-end (2x) modus (300 bp) on the MiSeq platform (Illumina, San Diego, CA, USA) at the BaseClear service laboratory (BaseClear BV, Leiden, The Netherlands). FASTQ files were generated and de-multiplexed based on sample-specific barcodes using the Casava pipeline (version 1.8.3, Illumina, San Diego, CA, USA). Sequence reads of low quality (only "passing filter" reads were selected) or containing the adapters or PhiX control signals were removed and the FASTQC pipeline (version 0.10.0, (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was applied for the initial quality control. One sample was excluded (old mouse on MF diet) because the coverage was below the threshold (50% of the median number of reads). SRS2529844 BC4_3 BC4_3_13234_5E_TACGCTGCAAGGAGTA_L001 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3203482 A1_1_13234_2B_GGAGCTACTATCCTCT_L001 SRP145069 PRJNA392687 Microbiota composition was determined in the colonic luminal content of 8-10 mice per diet group at the age of 6 and 28 months, resulting in a total of 68 samples. Genomic DNA was extracted from the colonic luminal content using the ZR Fecal DNA MicroPrep kit (ZYMO Research, Irvine, CA, USA) according to the instructions of the manufacturer. Subsequently, the V3-V4 region of the 16S rRNA gene was amplified using a 2-step PCR. First, 10-25 ng of DNA was amplified using the 341F (5'-CCTACGGGNGGCWGCAG-3') and 785R (5'-GACTACHVGGGTATCTAATCC-3') primers appended with Illumina adaptor sequences. Amplicons were purified using the ZR-96 DNA Clean and Concentrator-5 Kit (ZYMO Research, Irvine, CA, USA). To quantify DNA content of the resulting amplicon, the Qubit Fluorometric Quantitation device (ThermoFisher Scientific, Waltham, MA, USA) was used. Besides, the amplicons were run on a 2%-agarose gel to confirm amplicon size and amount. Purified PCR products were used for the second PCR in combination with sample-specific barcoded primers (Nextera XT index kit, Illumina, San Diego, CA, USA). Purified PCR products with an amplicon length of 550 base pairs (bp) (including adaptors) were submitted for sequencing in the paired-end (2x) modus (300 bp) on the MiSeq platform (Illumina, San Diego, CA, USA) at the BaseClear service laboratory (BaseClear BV, Leiden, The Netherlands). FASTQ files were generated and de-multiplexed based on sample-specific barcodes using the Casava pipeline (version 1.8.3, Illumina, San Diego, CA, USA). Sequence reads of low quality (only "passing filter" reads were selected) or containing the adapters or PhiX control signals were removed and the FASTQC pipeline (version 0.10.0, (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was applied for the initial quality control. One sample was excluded (old mouse on MF diet) because the coverage was below the threshold (50% of the median number of reads). SRS2529845 A1_1 A1_1_13234_2B_GGAGCTACTATCCTCT_L001 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3203483 A1_12_13236_4C_CGGAGCCTCCTAGAGT_L001 SRP145069 PRJNA392687 Microbiota composition was determined in the colonic luminal content of 8-10 mice per diet group at the age of 6 and 28 months, resulting in a total of 68 samples. Genomic DNA was extracted from the colonic luminal content using the ZR Fecal DNA MicroPrep kit (ZYMO Research, Irvine, CA, USA) according to the instructions of the manufacturer. Subsequently, the V3-V4 region of the 16S rRNA gene was amplified using a 2-step PCR. First, 10-25 ng of DNA was amplified using the 341F (5'-CCTACGGGNGGCWGCAG-3') and 785R (5'-GACTACHVGGGTATCTAATCC-3') primers appended with Illumina adaptor sequences. Amplicons were purified using the ZR-96 DNA Clean and Concentrator-5 Kit (ZYMO Research, Irvine, CA, USA). To quantify DNA content of the resulting amplicon, the Qubit Fluorometric Quantitation device (ThermoFisher Scientific, Waltham, MA, USA) was used. Besides, the amplicons were run on a 2%-agarose gel to confirm amplicon size and amount. Purified PCR products were used for the second PCR in combination with sample-specific barcoded primers (Nextera XT index kit, Illumina, San Diego, CA, USA). Purified PCR products with an amplicon length of 550 base pairs (bp) (including adaptors) were submitted for sequencing in the paired-end (2x) modus (300 bp) on the MiSeq platform (Illumina, San Diego, CA, USA) at the BaseClear service laboratory (BaseClear BV, Leiden, The Netherlands). FASTQ files were generated and de-multiplexed based on sample-specific barcodes using the Casava pipeline (version 1.8.3, Illumina, San Diego, CA, USA). Sequence reads of low quality (only "passing filter" reads were selected) or containing the adapters or PhiX control signals were removed and the FASTQC pipeline (version 0.10.0, (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was applied for the initial quality control. One sample was excluded (old mouse on MF diet) because the coverage was below the threshold (50% of the median number of reads). SRS2529847 A1_12 A1_12_13236_4C_CGGAGCCTCCTAGAGT_L001 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3203484 A1_11_13236_4B_CGGAGCCTTTCTAGCT_L001 SRP145069 PRJNA392687 Microbiota composition was determined in the colonic luminal content of 8-10 mice per diet group at the age of 6 and 28 months, resulting in a total of 68 samples. Genomic DNA was extracted from the colonic luminal content using the ZR Fecal DNA MicroPrep kit (ZYMO Research, Irvine, CA, USA) according to the instructions of the manufacturer. Subsequently, the V3-V4 region of the 16S rRNA gene was amplified using a 2-step PCR. First, 10-25 ng of DNA was amplified using the 341F (5'-CCTACGGGNGGCWGCAG-3') and 785R (5'-GACTACHVGGGTATCTAATCC-3') primers appended with Illumina adaptor sequences. Amplicons were purified using the ZR-96 DNA Clean and Concentrator-5 Kit (ZYMO Research, Irvine, CA, USA). To quantify DNA content of the resulting amplicon, the Qubit Fluorometric Quantitation device (ThermoFisher Scientific, Waltham, MA, USA) was used. Besides, the amplicons were run on a 2%-agarose gel to confirm amplicon size and amount. Purified PCR products were used for the second PCR in combination with sample-specific barcoded primers (Nextera XT index kit, Illumina, San Diego, CA, USA). Purified PCR products with an amplicon length of 550 base pairs (bp) (including adaptors) were submitted for sequencing in the paired-end (2x) modus (300 bp) on the MiSeq platform (Illumina, San Diego, CA, USA) at the BaseClear service laboratory (BaseClear BV, Leiden, The Netherlands). FASTQ files were generated and de-multiplexed based on sample-specific barcodes using the Casava pipeline (version 1.8.3, Illumina, San Diego, CA, USA). Sequence reads of low quality (only "passing filter" reads were selected) or containing the adapters or PhiX control signals were removed and the FASTQC pipeline (version 0.10.0, (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was applied for the initial quality control. One sample was excluded (old mouse on MF diet) because the coverage was below the threshold (50% of the median number of reads). SRS2529846 A1_11 A1_11_13236_4B_CGGAGCCTTTCTAGCT_L001 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3203485 A1_10_13235_6C_TAGGCATGCCTAGAGT_L001 SRP145069 PRJNA392687 Microbiota composition was determined in the colonic luminal content of 8-10 mice per diet group at the age of 6 and 28 months, resulting in a total of 68 samples. Genomic DNA was extracted from the colonic luminal content using the ZR Fecal DNA MicroPrep kit (ZYMO Research, Irvine, CA, USA) according to the instructions of the manufacturer. Subsequently, the V3-V4 region of the 16S rRNA gene was amplified using a 2-step PCR. First, 10-25 ng of DNA was amplified using the 341F (5'-CCTACGGGNGGCWGCAG-3') and 785R (5'-GACTACHVGGGTATCTAATCC-3') primers appended with Illumina adaptor sequences. Amplicons were purified using the ZR-96 DNA Clean and Concentrator-5 Kit (ZYMO Research, Irvine, CA, USA). To quantify DNA content of the resulting amplicon, the Qubit Fluorometric Quantitation device (ThermoFisher Scientific, Waltham, MA, USA) was used. Besides, the amplicons were run on a 2%-agarose gel to confirm amplicon size and amount. Purified PCR products were used for the second PCR in combination with sample-specific barcoded primers (Nextera XT index kit, Illumina, San Diego, CA, USA). Purified PCR products with an amplicon length of 550 base pairs (bp) (including adaptors) were submitted for sequencing in the paired-end (2x) modus (300 bp) on the MiSeq platform (Illumina, San Diego, CA, USA) at the BaseClear service laboratory (BaseClear BV, Leiden, The Netherlands). FASTQ files were generated and de-multiplexed based on sample-specific barcodes using the Casava pipeline (version 1.8.3, Illumina, San Diego, CA, USA). Sequence reads of low quality (only "passing filter" reads were selected) or containing the adapters or PhiX control signals were removed and the FASTQC pipeline (version 0.10.0, (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was applied for the initial quality control. One sample was excluded (old mouse on MF diet) because the coverage was below the threshold (50% of the median number of reads). SRS2529848 A1_10 A1_10_13235_6C_TAGGCATGCCTAGAGT_L001 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3203486 A1_7_13235_2B_CGTACTAGTTCTAGCT_L001 SRP145069 PRJNA392687 Microbiota composition was determined in the colonic luminal content of 8-10 mice per diet group at the age of 6 and 28 months, resulting in a total of 68 samples. Genomic DNA was extracted from the colonic luminal content using the ZR Fecal DNA MicroPrep kit (ZYMO Research, Irvine, CA, USA) according to the instructions of the manufacturer. Subsequently, the V3-V4 region of the 16S rRNA gene was amplified using a 2-step PCR. First, 10-25 ng of DNA was amplified using the 341F (5'-CCTACGGGNGGCWGCAG-3') and 785R (5'-GACTACHVGGGTATCTAATCC-3') primers appended with Illumina adaptor sequences. Amplicons were purified using the ZR-96 DNA Clean and Concentrator-5 Kit (ZYMO Research, Irvine, CA, USA). To quantify DNA content of the resulting amplicon, the Qubit Fluorometric Quantitation device (ThermoFisher Scientific, Waltham, MA, USA) was used. Besides, the amplicons were run on a 2%-agarose gel to confirm amplicon size and amount. Purified PCR products were used for the second PCR in combination with sample-specific barcoded primers (Nextera XT index kit, Illumina, San Diego, CA, USA). Purified PCR products with an amplicon length of 550 base pairs (bp) (including adaptors) were submitted for sequencing in the paired-end (2x) modus (300 bp) on the MiSeq platform (Illumina, San Diego, CA, USA) at the BaseClear service laboratory (BaseClear BV, Leiden, The Netherlands). FASTQ files were generated and de-multiplexed based on sample-specific barcodes using the Casava pipeline (version 1.8.3, Illumina, San Diego, CA, USA). Sequence reads of low quality (only "passing filter" reads were selected) or containing the adapters or PhiX control signals were removed and the FASTQC pipeline (version 0.10.0, (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was applied for the initial quality control. One sample was excluded (old mouse on MF diet) because the coverage was below the threshold (50% of the median number of reads). SRS2529849 A1_7 A1_7_13235_2B_CGTACTAGTTCTAGCT_L001 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3203487 BC4_5_13234_12B_TCGACGTCTATCCTCT_L001 SRP145069 PRJNA392687 Microbiota composition was determined in the colonic luminal content of 8-10 mice per diet group at the age of 6 and 28 months, resulting in a total of 68 samples. Genomic DNA was extracted from the colonic luminal content using the ZR Fecal DNA MicroPrep kit (ZYMO Research, Irvine, CA, USA) according to the instructions of the manufacturer. Subsequently, the V3-V4 region of the 16S rRNA gene was amplified using a 2-step PCR. First, 10-25 ng of DNA was amplified using the 341F (5'-CCTACGGGNGGCWGCAG-3') and 785R (5'-GACTACHVGGGTATCTAATCC-3') primers appended with Illumina adaptor sequences. Amplicons were purified using the ZR-96 DNA Clean and Concentrator-5 Kit (ZYMO Research, Irvine, CA, USA). To quantify DNA content of the resulting amplicon, the Qubit Fluorometric Quantitation device (ThermoFisher Scientific, Waltham, MA, USA) was used. Besides, the amplicons were run on a 2%-agarose gel to confirm amplicon size and amount. Purified PCR products were used for the second PCR in combination with sample-specific barcoded primers (Nextera XT index kit, Illumina, San Diego, CA, USA). Purified PCR products with an amplicon length of 550 base pairs (bp) (including adaptors) were submitted for sequencing in the paired-end (2x) modus (300 bp) on the MiSeq platform (Illumina, San Diego, CA, USA) at the BaseClear service laboratory (BaseClear BV, Leiden, The Netherlands). FASTQ files were generated and de-multiplexed based on sample-specific barcodes using the Casava pipeline (version 1.8.3, Illumina, San Diego, CA, USA). Sequence reads of low quality (only "passing filter" reads were selected) or containing the adapters or PhiX control signals were removed and the FASTQC pipeline (version 0.10.0, (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was applied for the initial quality control. One sample was excluded (old mouse on MF diet) because the coverage was below the threshold (50% of the median number of reads). SRS2529851 BC4_5 BC4_5_13234_12B_TCGACGTCTATCCTCT_L001 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3203488 A1_3_13234_6B_ATGCGCAGTATCCTCT_L001 SRP145069 PRJNA392687 Microbiota composition was determined in the colonic luminal content of 8-10 mice per diet group at the age of 6 and 28 months, resulting in a total of 68 samples. Genomic DNA was extracted from the colonic luminal content using the ZR Fecal DNA MicroPrep kit (ZYMO Research, Irvine, CA, USA) according to the instructions of the manufacturer. Subsequently, the V3-V4 region of the 16S rRNA gene was amplified using a 2-step PCR. First, 10-25 ng of DNA was amplified using the 341F (5'-CCTACGGGNGGCWGCAG-3') and 785R (5'-GACTACHVGGGTATCTAATCC-3') primers appended with Illumina adaptor sequences. Amplicons were purified using the ZR-96 DNA Clean and Concentrator-5 Kit (ZYMO Research, Irvine, CA, USA). To quantify DNA content of the resulting amplicon, the Qubit Fluorometric Quantitation device (ThermoFisher Scientific, Waltham, MA, USA) was used. Besides, the amplicons were run on a 2%-agarose gel to confirm amplicon size and amount. Purified PCR products were used for the second PCR in combination with sample-specific barcoded primers (Nextera XT index kit, Illumina, San Diego, CA, USA). Purified PCR products with an amplicon length of 550 base pairs (bp) (including adaptors) were submitted for sequencing in the paired-end (2x) modus (300 bp) on the MiSeq platform (Illumina, San Diego, CA, USA) at the BaseClear service laboratory (BaseClear BV, Leiden, The Netherlands). FASTQ files were generated and de-multiplexed based on sample-specific barcodes using the Casava pipeline (version 1.8.3, Illumina, San Diego, CA, USA). Sequence reads of low quality (only "passing filter" reads were selected) or containing the adapters or PhiX control signals were removed and the FASTQC pipeline (version 0.10.0, (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was applied for the initial quality control. One sample was excluded (old mouse on MF diet) because the coverage was below the threshold (50% of the median number of reads). SRS2529850 A1_3 A1_3_13234_6B_ATGCGCAGTATCCTCT_L001 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3203489 A1_2_13234_2C_GGAGCTACGTAAGGAG_L001 SRP145069 PRJNA392687 Microbiota composition was determined in the colonic luminal content of 8-10 mice per diet group at the age of 6 and 28 months, resulting in a total of 68 samples. Genomic DNA was extracted from the colonic luminal content using the ZR Fecal DNA MicroPrep kit (ZYMO Research, Irvine, CA, USA) according to the instructions of the manufacturer. Subsequently, the V3-V4 region of the 16S rRNA gene was amplified using a 2-step PCR. First, 10-25 ng of DNA was amplified using the 341F (5'-CCTACGGGNGGCWGCAG-3') and 785R (5'-GACTACHVGGGTATCTAATCC-3') primers appended with Illumina adaptor sequences. Amplicons were purified using the ZR-96 DNA Clean and Concentrator-5 Kit (ZYMO Research, Irvine, CA, USA). To quantify DNA content of the resulting amplicon, the Qubit Fluorometric Quantitation device (ThermoFisher Scientific, Waltham, MA, USA) was used. Besides, the amplicons were run on a 2%-agarose gel to confirm amplicon size and amount. Purified PCR products were used for the second PCR in combination with sample-specific barcoded primers (Nextera XT index kit, Illumina, San Diego, CA, USA). Purified PCR products with an amplicon length of 550 base pairs (bp) (including adaptors) were submitted for sequencing in the paired-end (2x) modus (300 bp) on the MiSeq platform (Illumina, San Diego, CA, USA) at the BaseClear service laboratory (BaseClear BV, Leiden, The Netherlands). FASTQ files were generated and de-multiplexed based on sample-specific barcodes using the Casava pipeline (version 1.8.3, Illumina, San Diego, CA, USA). Sequence reads of low quality (only "passing filter" reads were selected) or containing the adapters or PhiX control signals were removed and the FASTQC pipeline (version 0.10.0, (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was applied for the initial quality control. One sample was excluded (old mouse on MF diet) because the coverage was below the threshold (50% of the median number of reads). SRS2529852 A1_2 A1_2_13234_2C_GGAGCTACGTAAGGAG_L001 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3203490 BC4_7_13234_12C_TCGACGTCGTAAGGAG_L001 SRP145069 PRJNA392687 Microbiota composition was determined in the colonic luminal content of 8-10 mice per diet group at the age of 6 and 28 months, resulting in a total of 68 samples. Genomic DNA was extracted from the colonic luminal content using the ZR Fecal DNA MicroPrep kit (ZYMO Research, Irvine, CA, USA) according to the instructions of the manufacturer. Subsequently, the V3-V4 region of the 16S rRNA gene was amplified using a 2-step PCR. First, 10-25 ng of DNA was amplified using the 341F (5'-CCTACGGGNGGCWGCAG-3') and 785R (5'-GACTACHVGGGTATCTAATCC-3') primers appended with Illumina adaptor sequences. Amplicons were purified using the ZR-96 DNA Clean and Concentrator-5 Kit (ZYMO Research, Irvine, CA, USA). To quantify DNA content of the resulting amplicon, the Qubit Fluorometric Quantitation device (ThermoFisher Scientific, Waltham, MA, USA) was used. Besides, the amplicons were run on a 2%-agarose gel to confirm amplicon size and amount. Purified PCR products were used for the second PCR in combination with sample-specific barcoded primers (Nextera XT index kit, Illumina, San Diego, CA, USA). Purified PCR products with an amplicon length of 550 base pairs (bp) (including adaptors) were submitted for sequencing in the paired-end (2x) modus (300 bp) on the MiSeq platform (Illumina, San Diego, CA, USA) at the BaseClear service laboratory (BaseClear BV, Leiden, The Netherlands). FASTQ files were generated and de-multiplexed based on sample-specific barcodes using the Casava pipeline (version 1.8.3, Illumina, San Diego, CA, USA). Sequence reads of low quality (only "passing filter" reads were selected) or containing the adapters or PhiX control signals were removed and the FASTQC pipeline (version 0.10.0, (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was applied for the initial quality control. One sample was excluded (old mouse on MF diet) because the coverage was below the threshold (50% of the median number of reads). SRS2529853 BC4_7 BC4_7_13234_12C_TCGACGTCGTAAGGAG_L001 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3203491 C4_5_13235_7D_CTCTCTACGCGTAAGA_L001 SRP145069 PRJNA392687 Microbiota composition was determined in the colonic luminal content of 8-10 mice per diet group at the age of 6 and 28 months, resulting in a total of 68 samples. Genomic DNA was extracted from the colonic luminal content using the ZR Fecal DNA MicroPrep kit (ZYMO Research, Irvine, CA, USA) according to the instructions of the manufacturer. Subsequently, the V3-V4 region of the 16S rRNA gene was amplified using a 2-step PCR. First, 10-25 ng of DNA was amplified using the 341F (5'-CCTACGGGNGGCWGCAG-3') and 785R (5'-GACTACHVGGGTATCTAATCC-3') primers appended with Illumina adaptor sequences. Amplicons were purified using the ZR-96 DNA Clean and Concentrator-5 Kit (ZYMO Research, Irvine, CA, USA). To quantify DNA content of the resulting amplicon, the Qubit Fluorometric Quantitation device (ThermoFisher Scientific, Waltham, MA, USA) was used. Besides, the amplicons were run on a 2%-agarose gel to confirm amplicon size and amount. Purified PCR products were used for the second PCR in combination with sample-specific barcoded primers (Nextera XT index kit, Illumina, San Diego, CA, USA). Purified PCR products with an amplicon length of 550 base pairs (bp) (including adaptors) were submitted for sequencing in the paired-end (2x) modus (300 bp) on the MiSeq platform (Illumina, San Diego, CA, USA) at the BaseClear service laboratory (BaseClear BV, Leiden, The Netherlands). FASTQ files were generated and de-multiplexed based on sample-specific barcodes using the Casava pipeline (version 1.8.3, Illumina, San Diego, CA, USA). Sequence reads of low quality (only "passing filter" reads were selected) or containing the adapters or PhiX control signals were removed and the FASTQC pipeline (version 0.10.0, (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was applied for the initial quality control. One sample was excluded (old mouse on MF diet) because the coverage was below the threshold (50% of the median number of reads). SRS2529854 C4_5 C4_5_13235_7D_CTCTCTACGCGTAAGA_L001 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3203492 BC4_11_13235_12F_ATCTCAGGAAGGCTAT_L001 SRP145069 PRJNA392687 Microbiota composition was determined in the colonic luminal content of 8-10 mice per diet group at the age of 6 and 28 months, resulting in a total of 68 samples. Genomic DNA was extracted from the colonic luminal content using the ZR Fecal DNA MicroPrep kit (ZYMO Research, Irvine, CA, USA) according to the instructions of the manufacturer. Subsequently, the V3-V4 region of the 16S rRNA gene was amplified using a 2-step PCR. First, 10-25 ng of DNA was amplified using the 341F (5'-CCTACGGGNGGCWGCAG-3') and 785R (5'-GACTACHVGGGTATCTAATCC-3') primers appended with Illumina adaptor sequences. Amplicons were purified using the ZR-96 DNA Clean and Concentrator-5 Kit (ZYMO Research, Irvine, CA, USA). To quantify DNA content of the resulting amplicon, the Qubit Fluorometric Quantitation device (ThermoFisher Scientific, Waltham, MA, USA) was used. Besides, the amplicons were run on a 2%-agarose gel to confirm amplicon size and amount. Purified PCR products were used for the second PCR in combination with sample-specific barcoded primers (Nextera XT index kit, Illumina, San Diego, CA, USA). Purified PCR products with an amplicon length of 550 base pairs (bp) (including adaptors) were submitted for sequencing in the paired-end (2x) modus (300 bp) on the MiSeq platform (Illumina, San Diego, CA, USA) at the BaseClear service laboratory (BaseClear BV, Leiden, The Netherlands). FASTQ files were generated and de-multiplexed based on sample-specific barcodes using the Casava pipeline (version 1.8.3, Illumina, San Diego, CA, USA). Sequence reads of low quality (only "passing filter" reads were selected) or containing the adapters or PhiX control signals were removed and the FASTQC pipeline (version 0.10.0, (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was applied for the initial quality control. One sample was excluded (old mouse on MF diet) because the coverage was below the threshold (50% of the median number of reads). SRS2529855 BC4_11 BC4_11_13235_12F_ATCTCAGGAAGGCTAT_L001 AMPLICON METAGENOMIC PCR Illumina MiSeq SRX3203493 BC4_12_13235_12G_ATCTCAGGGAGCCTTA_L001 SRP145069 PRJNA392687 Microbiota composition was determined in the colonic luminal content of 8-10 mice per diet group at the age of 6 and 28 months, resulting in a total of 68 samples. Genomic DNA was extracted from the colonic luminal content using the ZR Fecal DNA MicroPrep kit (ZYMO Research, Irvine, CA, USA) according to the instructions of the manufacturer. Subsequently, the V3-V4 region of the 16S rRNA gene was amplified using a 2-step PCR. First, 10-25 ng of DNA was amplified using the 341F (5'-CCTACGGGNGGCWGCAG-3') and 785R (5'-GACTACHVGGGTATCTAATCC-3') primers appended with Illumina adaptor sequences. Amplicons were purified using the ZR-96 DNA Clean and Concentrator-5 Kit (ZYMO Research, Irvine, CA, USA). To quantify DNA content of the resulting amplicon, the Qubit Fluorometric Quantitation device (ThermoFisher Scientific, Waltham, MA, USA) was used. Besides, the amplicons were run on a 2%-agarose gel to confirm amplicon size and amount. Purified PCR products were used for the second PCR in combination with sample-specific barcoded primers (Nextera XT index kit, Illumina, San Diego, CA, USA). Purified PCR products with an amplicon length of 550 base pairs (bp) (including adaptors) were submitted for sequencing in the paired-end (2x) modus (300 bp) on the MiSeq platform (Illumina, San Diego, CA, USA) at the BaseClear service laboratory (BaseClear BV, Leiden, The Netherlands). FASTQ files were generated and de-multiplexed based on sample-specific barcodes using the Casava pipeline (version 1.8.3, Illumina, San Diego, CA, USA). Sequence reads of low quality (only "passing filter" reads were selected) or containing the adapters or PhiX control signals were removed and the FASTQC pipeline (version 0.10.0, (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was applied for the initial quality control. One sample was excluded (old mouse on MF diet) because the coverage was below the threshold (50% of the median number of reads). SRS2529856 BC4_12 BC4_12_13235_12G_ATCTCAGGGAGCCTTA_L001 AMPLICON METAGENOMIC PCR Illumina MiSeq