Fig S2 Efficiencies of primers used in the taxon-specific qpcr assay. CT: threshold value (A) Universal: 907F R efficiency: 99.

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2 Fig S2 Efficiencies of primers used in the taxon-specific qpcr assay. CT: threshold value (A) Universal: 907F R efficiency: 99.1% (B) Bacteroidetes: Bac960F+Bac1100R efficiency: 98.5% (C) Firmicutes: Firm934F+Firm1060R efficiency: 94.6% (D) Tenericutes: Ten662F+Ten862R efficiency: 96.5% (E) Deferribacteres: Defer1115F+Defer1265R efficiency: 92.6% (F) : Sac1031F+Sac1218R efficiency: 94.6% (G) -Proteobacteria: Beta979F+Beta1130R efficiency: 94.2% (H) -Proteobacteria: Gamma877F+Gamma1066R efficiency: 96.1% (I) -Proteobacteria:Epslion940F+Epsloin1129R efficiency: 92.1%

3 Fig S3 Specificity of each primer pairs analyzed by QPCR with target and non-target 16S rrna s as templates. a, target 16S rrna (5ng); b, non-target 16S rrna 1 (5ng); c, non-target 16S rrna 2 (5ng) 2; d, non-target 16S rrna 3 (5ng); e, ddh2o as template. (A)Primer pair: Sac1031F/Sac1218R. (B)Primer pair: Ten662F/Ten862R. (C)Primer pair: Epslion940F/Epsloin1129R. (D)Primer pair: Gamma877F/Gamma1066R. (E)Primer pair: Firm934F/Firm1060R. (F)Primer pair: Defer1115F/Defer1265R. (G)Primer pair: Beta979F/Beta1130R. (H)Primer pair: Bac960F/Bac1100R. (I)Primer pair: Act664F/Act941R. (J)Primer pair: Ver1165F/Ver1263R. It must be emphasized that each primer pair with least mismatches to the of the non-targets from Fig S3.

4 Table S1. Taxa dominating the bacterial microbiota of the mouse feces Phylum Class Family Genus Actinobacteria Actinobacteria Bifidobacteriales Bifidobacterium Actinobacteria Actinobacteria Coriobacteriaceae Asaccharobacter Actinobacteria Actinobacteria Coriobacteriaceae Enterorhabdus Actinobacteria Actinobacteria Coriobacteriaceae Olsenella Bacteroidetes Bacteroidia Porphyromonadaceae Barnesiella Bacteroidetes Bacteroidia Porphyromonadaceae Odoribacter Bacteroidetes Bacteroidia Porphyromonadaceae Parabacteroides Bacteroidetes Bacteroidia Prevotellaceae Paraprevotella Bacteroidetes Bacteroidia Prevotellaceae Prevotella Bacteroidetes Bacteroidia Rikenellaceae Alistipes Bacteroidetes Bacteroidia Bacteroidaceae Bacteroides Deferribacteres Deferribacteres Deferribacteraceae Mucispirillum Proteobacteria Betaproteobacteria Sutterellaceae Parasutterella Proteobacteria Betaproteobacteria Neisseriaceae Neisseria Proteobacteria Deltaproteobacteria Bdellovibrionaceae Vampirovibrio Proteobacteria Deltaproteobacteria Desulfovibrionaceae Desulfovibrio Proteobacteria Epsilonproteobacteria Helicobacteraceae Helicobacter Proteobacteria Gammaproteobacteria Enterobacteriaceae Klebsiella Proteobacteria Gammaproteobacteria Pasteurellaceae Haemophilus Tenericutes Mollicutes Anaeroplasmataceae Anaeroplasma Tenericutes Mollicutes Mycoplasmataceae Mycoplasma Tenericutes Mollicutes Mycoplasmataceae Ureaplasma Verrucomicrobia Verrucomicrobiae Verrucomicrobiaceae Akkermansia Firmicutes Bacilli Lactobacillaceae Lactobacillus Firmicutes Clostridia Lachnospiraceae Clostridium_XlVa Firmicutes Clostridia Lachnospiraceae Clostridium_XlVb Firmicutes Clostridia Lachnospiraceae Lachnospiracea Firmicutes Clostridia Ruminococcaceae Butyricicoccus Firmicutes Clostridia Ruminococcaceae Flavonifractor Firmicutes Clostridia Ruminococcaceae Oscillibacter Firmicutes Erysipelotrichia Erysipelotrichaceae Allobaculum Firmicutes Erysipelotrichia Erysipelotrichaceae Turicibacter _class_incertae_sedis _family_incertae_sedis _genera_incertae_sedis

5 Table S2. NCBI BLAST search results and Ribosomal Database Project-II (RDP-II) database classification of 38 clones Clone NCBI Sequence Name Match Description Clone 1 Papyrosolvens strain DSM S ribosomal RNA gene, partial Clone 2 Straminisolvens strain CSK1 16S ribosomal RNA gene, partial Clone 3 Cavendishii strain BL-28 16S ribosomal RNA gene, partial Clone 4 Parasutterella excrementihominis strain YIT S ribosomal RNA gene, Clone 5 Sutterella parvirubra strain YIT S ribosomal RNA gene, Clone 6 Parasutterella secunda strain JCM S ribosomal RNA gene, Clone 7 Mucispirillum schaedleri strain HRI I17 16S ribosomal RNA gene, Clone 8 Calditerrivibrio nitroreducens strain Yu S ribosomal RNA gene, Clone 9 Calditerrivibrio nitroreducens strain DSM S ribosomal RNA gene, complete Clone 10 Desulfovibrio desulfuricans strain Essex 6 16S ribosomal RNA gene, complete Clone 11 Desulfovibrio desulfuricans 16S ribosomal RNA, complete Clone 12 Desulfovibrio vulgaris strain DSM S ribosomal RNA gene, Clone 13 Helicobacter aurati strain MIT c 16S ribosomal RNA gene, GenBank Max Identity Bacterial group Accession Numbers 88% Firmicutes KP % Firmicutes KP % Firmicutes KP % Betaproteobacteria KP % Betaproteobacteria KP % Betaproteobacteria KP % Deferribacteres KP % Deferribacteres KP % Deferribacteres KP % Deltaproteobacteria KP % Deltaproteobacteria KP % Deltaproteobacteria KP % Epsilonproteobacteria KP713730

6 Clone 14 Clone 15 Clone 16 Clone 17 Clone 18 Clone 19 Clone 20 Clone 21 Clone 22 Clone 23 Clone 24 Clone 25 Clone 26 Clone 27 Clone 28 Helicobacter cinaedi PAGU611 strain PAGU611 16S ribosomal RNA, complete Helicobacter muridarum strain ST1 16S ribosomal RNA gene, Anaeroplasma abactoclasticum strain S ribosomal RNA gene, Anaeroplasma varium strain A2-T 16S ribosomal RNA gene, Glaciimonas immobilis strain Cr S ribosomal RNA gene, Parasutterella secunda strain JCM S ribosomal RNA gene, Glaciimonas immobilis strain Cr S ribosomal RNA gene, Akkermansia muciniphila strain ATCC BAA S ribosomal RNA gene, complete Akkermansia muciniphila strain Muc 16S ribosomal RNA gene, complete Cavendishii strain BL-28 16S ribosomal RNA gene, partial Sporosalibacterium faouarense strain SOL3F37 16S ribosomal RNA gene, Mogibacterium neglectum strain P9a-h 16S ribosomal RNA gene, Bifidobacterium pseudolongum strain PNC-2-9G 16S ribosomal RNA gene, Olsenella profusa strain DSM S ribosomal RNA gene, Saccharolyticum strain WM1 16S ribosomal RNA gene, complete 97% Epsilonproteobacteria KP % Epsilonproteobacteria KP % Tenericutes KP % Tenericutes KP % Betaproteobacteria KP % Betaproteobacteria KP % Betaproteobacteria KP % Verrucomicrobia KP % Verrucomicrobia KP % Firmicutes KP % 79% KP KP % Actinobacteria KP % Actinobacteria KP % Firmicutes KP713745

7 Clone 29 Clone 30 Clone 31 Clone 32 Clone 33 Clone 34 Clone 35 Clone 36 Clone 37 Clone 38 Barnesiella viscericola 16S ribosomal RNA, complete Helicobacter aurati strain MIT c 16S ribosomal RNA gene, Clostridium formicaceticum strain DSM 92 16S ribosomal RNA gene, Christensenella minuta strain YIT S ribosomal RNA gene, Coprobacter fastidiosus strain NSB1 16S ribosomal RNA gene, Alistipes senegalensis strain JC50 16S ribosomal RNA gene, partial Paraprevotella xylaniphila strain JCM S ribosomal RNA gene, Anaeroplasma abactoclasticum strain S ribosomal RNA gene, Helicobacter equorum strain EqF1 16S ribosomal RNA gene, complete Helicobacter hepaticus strain Hh-2 16S ribosomal RNA gene, 85% Bacteroidetes KP % Epsilonproteobacteria KP % Firmicutes KP % Firmicutes KP % Bacteroidetes KP % Bacteroidetes KP % Bacteroidetes KP % Tenericutes KP % Epsilonproteobacteria KP % Epsilonproteobacteria KP713755

8 Table S3. Representative of qpcr products amplified by group target primers with mouse total fecal DNA as template Classified by Primer pair Sequence(5'to3')* RDP-II Bac960F Bac1100R GTTTAATTCGATGATACGCGAGGAACCTT ACCCGGGCTTGAAATGTGCAGGACTCAA GCAGAGACGCCTGTTTCTTCGGACCTGCA TGTAGGTGCTGCATGGTTGTCGTCAGCTC GTGCCGTGAGGTGTCGGCTTAA Bacteroidetes Firm934F Firm1060R Act664F Act941R Sac1031F Sac1218R Defer1115F Defer1265R Ver1165F Ver1263R Ten662F Ten862R GGAGTATGTGGTTTAATTCGAAGCAACGC GAAGAACCTTACCAAGACTTGACATCGTA TGACCGCCATAGAGATATGGAATTCCCTTT TGGGACATATAGACAGGTGGTGCATGGTT GTCGTCAGCT TGTAGCGGTGGAATGCGCAGATATTGGGA AGAACACCGGCGGCGAAGGCGGCCTTCT GGGCCACGACTGACGCTGAGGCGCGAAA GCTAGGGGAGCGAACAGGATTAGATACCC TGGTAGTCCTAGCCGTAAACGATGGATGC TAGGTGTGGGAGCCAAATGGCTTCCGTGC CGCAGCTAACGCATTAAGCATCCCGCCTG GGGAGTACGGCCGCAAGGCTAAAACTCA AAGGAATTGACGGGGACCCGCACAAGCA GCGGAGCATGTGGCTTAATT AAGAGAACTGTGCCTTCGGGAACCTCGA GACAGGTGATGCATGGCCGTCGTCAGCTC GTGTCGTGAGATGTTTGGTTAAGTCCATC AACGAGCGCAACCCTTGCAACCAGTTGTA TTTTTCTGGTAGGACTGCCCCGGTAACGG GGAGGAAGGAGGGGATGATGTCAGGTCA GTATTTCCCTTACGC CTATTTCCAGTTGCTAACGGGTTAAGCTG AGCACTCTGGAGGGACTGCCAGCGATAA GCTGGAGGAAGGTGGGGACGACGTCAAG TCATCATGGCCCTTATGTCCAGGGCTACAC ACGTGCTACAATGGCATAATCAGAGGGAA GCAGCTC TCAGGTCAGTATGGCCCTTATGCCCAGGG CTGCACACGTACTACAATGCCCAGTACAG AGGGGGCCGAAGCCGCGAGGCGGAGGA AATCCTAAAAACTGGGCGGAGGAAATCCT GAAAACTG ATGTGTAGCGGTAAAATGCGTAAATATATG TAAGAACACCGGTGGCGAAGGCGGCTTG Firmicutes Actinobacteria Deferribacteres Verrucomicrobia Tenericutes

9 Beta979F Beta1130R Epslion940F Epsloin1129R Gamma877F Gamma1066R CTGGGCCTGTACTGACATTGAGGCACGAA AGCGTGGGGAGCAAACAGGATTAGATAC CCTGGTAGTCCACGCCCTAAACGACGAGT ACTAAGTGTTGCCGATAGGCAGTGCTGAA GTTAACGCATTAAGTACTCCGCCTGAGTA GTACGTACGCAAGTAGG AACGCGAAAAACCTTACCTACCCTTGACA TGTCAGAGAAGCTTTTGTAATGAGAGTGT GCCCGCAAGGGCGTCTGAACACAGGTGC TGCATGGCTGTCGTCAGCTCGTGTCGTGA GATGTTGGGTTAAGTCCCGCAACGAGCGC AACCCTTGTCACTAGTTGCTACGAAAGGG CA TAGGCTTGACATTGATAGAATCCTATAGAG ATATGGGAGTGCCCTTTTAGGGAGCTTGA AAACAGGTGCTGCACGGCTGTCGTCAGC TCGTGCCGTGAGATGTTGGGTTAAGTCCC GCAACGAGCGCAACCCTCGTCCTTAGTTG CTAGCAGTTCGGCTGAGCACTCTAAGGAG ACTGCCTTCGTAAG GCTAACGCATTAAGTGTCCCGCCTGGGGA GTACGGTCGCAAGGCTGAAACTCAAAGA AATTGACGGGGGCCCGCACAAGCGGTGG AGTATGTGGTTTAATTCGATGCAACGCGA AGAACCTTACCCAGGCTTGACATCTAGGG AACCTAACAGAGATGTTGGGGTGCTCTTC GGAGAACCCTAAGACAGGTGCTGCATGG C * Base pairs in red are s of primer pairs -proteobacteria -proteobacteria -proteobacteria