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Cecil Porter
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% IgD + MHCII + (Gated on B0 + Events) c d Supplementary Figure 1 MHC mediates IgA response against gut microbiota. (a) Representative F.C. plots and data sets comparing the relative surface expression of MHC on dendritic cells and naïve B cells from MHC congenic animals (H bb -n=15; H dd -n=1; H kk -n=15, CH/HeJ-n=9).

1 Unique IgM CDR AA Sequences IgM Affinity Maturation Index a b cdc MHCII MFI.% naïve B cell MHCII MFI CD11c + Bacterial Abundance (per 1oong fecal DNA) Supplementary Figures MHCII + (Gated on CD0 + CD + Events) 9.% IgD + MHCII + (Gated on B0 + Events) c d Supplementary Figure 1 MHC mediates IgA response against gut microbiota. (a) Representative F.C. plots and data sets comparing the relative surface expression of MHC on dendritic cells and naïve B cells from MHC congenic animals (H bb -n=15; H dd -n=1; H kk -n=15, CH/HeJ-n=9). (b) There is no difference in the relative abundance of fecal bacteria in H congenic animals (H bb -n=5, H dd -n=5, H kk - n=5). (c,d) Comparison of naïve IgM repertoire among MHC genotypes (H bb -n=, H dd -n=5, H kk -n=5). There is no difference between MHC genotypes when (c) sequence diversity and (d) affinity maturation scores of the naïve IgM repertoire are compared among MHC genotypes. (a-c) Bars represent group means. (d) Error bars represent S.E.M. A two-tailed unpaired Student s t-test was used for all pair-wise statistical comparisons (****=p< ; ***=p<0.001; **=p<0.01; *=p<0.05).

(OTU Sequence Abundance) SFB (Candidtatus arthromitus) (OTU Sequence Abundance) Helicobacter spp. (OTU Sequence Abundance) N.D. N.D. Rikenella spp. (OTU Sequence Abundance) Bacteroides spp.

2 OTU Abundance (%) PC (1.%) PC (1.%) Akermansia spp. (OTU Sequence Abundance) Prevotella spp. (OTU Sequence Abundance) Barnesiella spp. (OTU Sequence Abundance) Enterobacteriaceae (OTU Sequence Abundance) N.D. N.D. PC (1.%) Lactobacillus spp. (OTU Sequence Abundance) SFB (Candidtatus arthromitus) (OTU Sequence Abundance) Helicobacter spp. (OTU Sequence Abundance) N.D. N.D. Rikenella spp. (OTU Sequence Abundance) Bacteroides spp. (OTU Sequence Abundance) a Weighted UniFrac b PC1 (.1%) WT B M -/- MHCII -/- (WT vs. B M -/-, p<0.00) (WT vs. MHCII -/-, p<0.00) c Weighted UniFrac d Weighted UniFrac Mucosal Fecal e PC1 (59.%) H bb H dd H kk (Genotype Effect, p=0.0) PC1 (1.%) H bb H dd H kk (Fecal vs. Mucosal, p=0.001) Mucosal (genotype effect), p=0.00) Fecal (genotype effect), p=0.001) Exp#1: Figure a-d Exp#: Figure e-h Exp#: Figure i-l Supplementary Figure MHC sculpts microbiota composition in the gut. (a) PcoA plot based on weighted UniFrac analysis of fecal microbiotas from WT, B M -/-, and MHCII -/- animals. (b) OTU abundance plots of specific bacterial groups among WT, B M -/-, and MHCII -/- animals. N.D =not detected. All pairwise comparisons are results of Student s t-test (****=p<0.0001; ***=p<0.001; **=p<0.01; *=p<0.05). (c) PcoA plot based on weighted UniFrac analysis of fecal microbiotas from female H congenic animals. (d) PcoA plot based on weighted UniFrac analysis of fecal microbiotas from male H congenic animals used for comparison of fecal and microbiota communities. (a,c,d) P-values represent the results of a PERMANOVA based on 999 simulations. Ellipses in PcoA plots are for illustrative purposes only and are non-quantitative. (e) Stacked bar charts represent relative abundance among significantly differentially detected OTUs within each bacterial clade. Bacterial families consistently enriched for significant MHC effects across the independent experiments described in Figure are highlighted by colored boxes (see Supplementary Tables - for full list of OTUs and results of kruskal-wallis statistical tests).

F/0 + CD11b + (%) T H 1 Cells (%) T H 1 Cells (%) CD9 + CD - T H Cells (%) CD11b + LyG + (%) S.

dd H kk d e CX CR1 + LyG + 0.19% CD11c + (gated on lymphocytes).9% CD11b + CDL + CD9 +.9% f (gated on granulocytes) 0.

% (gated on CD5 + lymphocytes) (gated on CD + CDe + lymphocytes) Supplementary Figure MHC mediates susceptibility to

(a) Qualitative analysis of Salmonella loads in the feces of mice (n=-5 per genotype) at defined time-points after

Fecal pellets were collected at each time point, homogenized with pestel, and plated on MacConkey agar.

experiments demonstrating that infection of H bb (n=5), but not H dd (n=5) or H kk (n=5), elicits an immune response

3 F/0 + CD11b + (%) T H 1 Cells (%) T H 1 Cells (%) CD9 + CD - T H Cells (%) CD11b + LyG + (%) S.typhimurium Load (CFU per mg feces) CX CR1 + CD11c + (%) a b Hours Post Infection H bb H dd H kk d e CX CR1 + LyG % CD11c + (gated on lymphocytes).9% CD11b + CDL + CD9 +.9% f (gated on granulocytes) 0.% c (gated on CD + CDe + lymphocytes) 0.1 % CD11b + F/0 + IL1 + IFNγ +.% (gated on CD5 + lymphocytes) (gated on CD + CDe + lymphocytes) Supplementary Figure MHC mediates susceptibility to S.e.typhimurium infection and this is not due to an enhanced immune response in resistant genotypes. (a) Qualitative analysis of Salmonella loads in the feces of mice (n=-5 per genotype) at defined time-points after oral gavage of 10 CFUs. Fecal pellets were collected at each time point, homogenized with pestel, and plated on MacConkey agar. Salmonella loads are standardized per mg feces. A smoothed trendline is shown. (b,c) Results of F.C. experiments demonstrating that infection of H bb (n=5), but not H dd (n=5) or H kk (n=5), elicits an immune response as measured by increases in the abundance of (b) activated CD + T H cells, and (c) inflammatory T H 1 and T H 1 cells. (d-f) Results of F.C. experiments demonstrating that infection does not result from differential recruitment of phagocytes (CX CR1 + CD11c + monocytes, LyG + CD11b + neutrophils, CD11b + F/0 + macrophages) among H congenic genotypes. (b-f) Representative F.C. plots are provided for all F.C. data sets (percentages are provided to identify relevant subgate). Unpaired two-tailed Student s t-test (****=p<0.0001; ***=p<0.001; **=p<0.01; *p<0.05).

4 Supplementary Figure Susceptbility to S.e.typhimurium infection is microbiotadependent. (a-d) Disease scores from Salmonella-infected (10 CFU via oral gavage) resistant H dd animals, and H dd animals that had been administered antibiotics in their drinking water for days (0.5mg/mL of each of the following: Neomycin Sulfate, Ampicillin, Erythromycin, Gentamycin). Animals were taken off antibiotics hours prior to infecting with 10 S.e.typhimurium CFUs via oral gavage. (e-g) Disease scores of Salmonella-infected (10 CFU via oral gavage) GF animals and animals that were born GF and were subsequently reared from birth in and SPF facility until 9 weeks of age (i.e. exgf). (b-right panel, c, e-right panel, f) Results of unpaired two-tailed Student s t-test (****=p<0.0001; ***=p<0.001; **=p<0.01; *=p<0.05). (b and e (left panels)) Error bars represent S.E.M. Asterisks represent significant differences based on results of t-tests comparing weight loss by day and reflect significant differences between Abx-treated and untreated H dd animals in (b) and GF and exgf animals in (e). (d and g) (c,f) Asterisks represent significance based on results of Mann-Whitney U Test, (***=p<0.001).

(b) Dynamics of microbiota colonization of GF animals as inferred from fecal bacterial loads and increasing fecal DNA concentrations over the course

5 Supplementary Figure 5 Fecal transplants recapitulate patterns of susceptibility in colonized GF animals. (a) Illustration for design of microbiota colonization, and Salmonella infection experiments. (b) Dynamics of microbiota colonization of GF animals as inferred from fecal bacterial loads and increasing fecal DNA concentrations over the course of day colonizations (T 0 -n=; T 1 -n=; T -n=; T 5 -n=1; T -n=19). (c) Results of Q-PCR experiment quantifying fecal bacterial loads in GF animals that had been colonized with microbiota derived from H bb (n=), H dd (n=), and H bd (n=)(day time-point).

The reported p-values represent the results of a PERMANOVA based on 999 simulations testing the effect of host genotype, or homozygosity versus heterozygosity.

6 Supplementary Figure MHC heterozygosity influences microbiota composition. (a) PcoA plot based on weighted UniFrac analysis of fecal microbiotas from H bb, H dd, and H bd animals. The reported p-values represent the results of a PERMANOVA based on 999 simulations testing the effect of host genotype, or homozygosity versus heterozygosity. (b,c) Within-community estimates of (b) phylogenetic diversity and (c) Shannon diversity. (d) Distance boxplots of community similarity between H bd heterozygotes and each respective H bb and H dd homozygote parent strains based on unweighted and weighted UniFrac analysis. (b-d) Unpaired two-tailed Student s t-test (p<0.05=*).

a b X X c X X X d Supplementary Figure Breeding design for female MHC congenic mice used for microbiota sequencing experiment described in Figure e-h.

(a) In the case of the H dd (green dotted mice) and (b) H kk (red dotted mice) animals, the 5 animals from each genotype were both litter- and cage-mates (i.e. for each genotype, 5 female animals from the same litter were housed in the same cage and used for analysis).

7 a b X X c X X X d Supplementary Figure Breeding design for female MHC congenic mice used for microbiota sequencing experiment described in Figure e-h. The experiments described in Figure e-h and a represents the results of a single experiment where 5 animals from each of the three different MHC genotypes had their microbiotas sequenced. (a) In the case of the H dd (green dotted mice) and (b) H kk (red dotted mice) animals, the 5 animals from each genotype were both litter- and cage-mates (i.e. for each genotype, 5 female animals from the same litter were housed in the same cage and used for analysis). (c) The H bb animals (blue dotted mice) represent five female animals derived from three different mothers that were housed in three separate cages. This design provides an internal control for the possibility that drift or maternal effects significantly influences our results by demonstrating that H bb animals still significantly cluster by genotype when compared to the other two H congenic cohorts. (a-c) Re-deriving homozygote congenic breeder pairs from heterozygote crosses, and using their progeny for microbiota sequencing analysis, excludes the confounding effect of the independent husbandry of these strains for several decades (the strain isolation effect). (d) 5 heterozygous H bd animals (purple dotted mice) depicted in Figure a were derived from a single breeder pair (H dd x H bb cross) which exposes animals to both H bb and H dd microbiota.

8 Supplementary Tables Supplementary Table 1. MHC Haplotypes of H congenic BALB/c mice Class Ia Class IIa Class Ia Locus K Aβ Aα Eβ Eα D L H d haplotype d d d d d d d H b haplotype b b b b ^ b b H k haplotype k k k k k k ^ ^: null allele Adapted from 1

9 Cell Subset Markers CD + T H Cells CD + CDε + CD + T CT Cells CDα + CDε + Activated CD + T H Cells CD + CDε + CDL - CD9 + Activated CD + T CT Cells CDα + CDε + CDL - CD9 + Tolerogenic Dendritic Cells CD11c + CD10 + T reg Cells CD + CDε + FoxP + IL10+ Treg Cells CD + CDε + FoxP + IL10 + T H 1 Cells CD + CDε + IFNγ + T H 1 Cells CD + CDε + IL1 + T FH Cells CD + CDε + CXCR5 + PD1 + Naïve B Cells B0 + IgD hi MHCII + GC B Cells B0 + IgD lo GL + FAS + IgA + B Cells B0 + CD1 - IgA + IgA + Plasma Cells B0 - CD1 + IgA + Conventional Dendritic Cells CD0 + CD + CD11c + MHCII + Supplementary Table. Cell Subset, Markers, and Antibodies used for flow cytometry CD-FITC (1/50 dilution, clone RM-5,eBioscience cat#11-00) CDα-PerCP.Cy5.5 (1/50 dilution, clone 5-.,BioLegend cat#100); CDε-Pacific Blue (1/50 dilution, clone 15-C11,eBioscience cat#-001); CDL-PE (1/50 dilution, clone MEL-1,BioLegend cat#100); CD9-PE/Cy (1/50 dilution, clone H1.F,BioLegend cat#10511); CD11c-APC (1/50 dilution, clone N1,eBioscience cat#1-011); CD10-PE (1/50 dilution, clone E,BioLegend cat#1105); FoxP-APC (1/50 dilution, clone FJK-1s,eBioscience cat#1-5); FoxP-PerCP.Cy5.5 (1/50 dilution, clone FJK-1s,eBioscience cat#5-5); IL10-PE (1/50 dilution, clone JES5-1E,eBioscience cat#1-101); IFNγ-PE (1/50 dilution, clone XMG1.,BioLegend cat#5050); IL1A-eFluor0 (1/50 dilution, clone ebio1b,ebioscience cat#50-1); CXCR5-PE (1/50 dilution, clone SPRCL5,eBioscience cat#1-15); CXCR5 isotype control Rat IgGa-PE (1/50 dilution, clone ebra,ebioscience cat#901-1); PD1-PE/Cy (1/50 dilution, clone RMP1-0,BioLegend cat#109109); PD1 isotype control Rat IgGb- PE/Cy (1/50 dilution, clone RTK50,BioLegend cat#001); B0-PerCP.Cy5.5 (1/500 dilution, clone RA-B,BioLegend cat#105); IgD-AlexaFluor (1/50 dilution, clone 11-c.a,BioLegend cat#050); MHCII(IA/IE)-PE (1/50 dilution, clone M5/11.15.,BioLegend cat#100); MHCII- IA k -PE (1/50 dilution, clone 10-.,BioLegend cat#10990); MHCII isotype control Rat IgGb-PE (1/50 dilution, clone eb19,ebioscience cat#1-01); GL-AlexaFluor (1/50 dilution, clone GL-,eBioscience cat#5-590); FAS-PE/Cy (1/50 dilution, clone Jo,BD Biosciences cat#555); CD1-PE (1/50 dilution, clone 1-,BioLegend cat#150); Rat anti-mouse IgA-PE (1/500 dilution, SouthernBiotech catalog#115-09l); CD0-FITC (1/50 dilution, clone HM0-,BioLegend cat#10905); CD-PerCP.Cy5.5 (1/50 dilution, clone GL-1,BioLegend cat#1050); Goat anti-mouse IgA-FITC (1/50 dilution, SouthernBiotech cat#100-0) Notes on antibody staining: -IgA-PE was used to quantify IgA-bound fecal bacteria -FoxP-PerCP.Cy5.5 was used to stain Tregs in PPs

10 -The IA/IE antibody does not bind IA molecules from mice carrying the H kk haplotype. To overcome this, an IA k -specific antibody was mixed with the IA/IE antibody in all MHCII stains.

11 Supplementary Table. Primers used in study Use Target Sequence (1,) Reference Bacterial qpcr Bacterial qpcr Bacterial qpcr Eubacteria Bacteroides/Prevotella spp. Lactobacillus/Lactococcus spp. Forward: 5-ACTCCTACGGGAGGCAGCAGT- Reverse: 5-ATTACCGCGGCTGCTGGC- Forward: 5-CCTWCGATGGATAGGGGTT- Reverse: 5-CACGCTACTTGGCTGGTTCAG- Forward: 5-AGCAGTAGGGAATCTTCCA- Reverse: 5-CACCGCTACACATGGAG- Ig repertoire cdna synthesis, first PCR IgA C H Region AACTGGCTGCTCATGGTGTACC Ig repertoire cdna synthesis, first PCR IgD C H Region TATGGTGCAAGTGTGGTTGAGG Ig repertoire cdna synthesis, first PCR IgG C H Region CTGGACAGGGMTCCAKAGTTC Ig repertoire cdna synthesis, first PCR IgM C H Region CTCTTGGGAGACAGCAASACC Ig repertoire, first PCR Ig V H Regions ACACTCTTTCCCTACACGACGCTCTTCCGATCT(N 19-1) Ig repertoire, second PCR Ig repertoire, second PCR Ig repertoire, second PCR Ig repertoire, second PCR Ig repertoire, second PCR Ig first PCR product Ig first PCR product IgA C H Ig first PCR product IgD C H Ig first PCR product IgG C H Ig first PCR product IgM C H AATGATACGGCGACCACCGAGATCTACACXXXXXXXX ACACTCTTTCCCTACACGACGC CAAGCAGAAGACGGCATACGAGATXXXXXXXXGTGAC TGGAGTTCAGACGTGTGCTCTTCCGATCTGATGGTGGG ATTTCTCGCAGA CAAGCAGAAGACGGCATACGAGATXXXXXXXXGTG ACTGGAGTTCAGACGTGTGCTCTTCCGATCTGGGCT TTGCACTCTGAGAGG CAAGCAGAAGACGGCATACGAGATXXXXXXX XGTGACTGGAGTTCAGACGTGTGCTCTTCCGA TCTGGRCCARKGGATAGACHGATG CAAGCAGAAGACGGCATACGAGATXXXXXXXXG TGACTGGAGTTCAGACGTGTGCTCTTCCGATCTG GGAAGACATTTGGGAAGGAC 1. N 19-1 represents the 1 external primers identified by Rohatgi et al., 00 to target the 1 different V H region families.. Bold sequences are Illumina adapter sequences. XXXXXXXX represents index sequences. 5

12 Supplementary Table References 1 Flurkey, K., Currer, J. M., Leiter, E. H. & Witham, B. (The Jackson Laboratory, Bar Harbor, ME, 009). Amann, R. I. et al. Combination of 1S rrna-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Applied and environmental microbiology 5, (1990). Furet, J. P. et al. Comparative assessment of human and farm animal faecal microbiota using realtime quantitative PCR. FEMS microbiology ecology, 51-, doi: /j x (009). Rinttila, T., Kassinen, A., Malinen, E., Krogius, L. & Palva, A. Development of an extensive set of 1S rdna-targeted primers for quantification of pathogenic and indigenous bacteria in faecal samples by real-time PCR. Journal of applied microbiology 9, 11-11, doi: /j x (00). 5 Rohatgi, S., Ganju, P. & Sehgal, D. Systematic design and testing of nested (RT-)PCR primers for specific amplification of mouse rearranged/expressed immunoglobulin variable region genes from small number of B cells. Journal of immunological methods 9, 05-19, doi:10.101/j.jim (00).

13 Supplementary Table. WT, BM-/-, MHCII-/- Significant differences by OTU* OTU FJ50 EU55 EF090 FJ959 0 GQ DQ0 DQ090 EU5 EU 9 EU JN019 EU51 EU55 EU505 HQ915 0 AY991 5 EU EF09 EU519 DQ159 EU50 1 EU55 Test- Statistic P FDR_P WT mea n BM_KO mean MHCII KO mean taxonomy 0 0. Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; Bacteroidaceae; Bacteroides Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; Bacteroidaceae; Bacteroides Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; Bacteroidaceae; Bacteroides 0 0. Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; Bacteroidaceae; Bacteroides 0 0. Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; Bacteroidaceae; Bacteroides Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; Bacteroidaceae; Bacteroides Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; Bacteroidaceae; Bacteroides Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; Bacteroidaceae; Bacteroides 0 0 Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; Bacteroidaceae; Bacteroides Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; Bacteroidaceae; Bacteroides Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; Bacteroidaceae; Bacteroides Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; Porphyromonadaceae; Barnesi ella.5. 0 Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; Porphyromonadaceae; Odorib acter Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; Porphyromonadaceae; Paraba cteroides Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; Porphyromonadaceae; Paraba cteroides Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; Prevotellaceae; Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; Prevotellaceae; Prevotella Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; Prevotellaceae; Prevotella Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; Rikenellaceae; Alistipes Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; Rikenellaceae; Alistipes Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; Rikenellaceae; Alistipes Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; Rikenellaceae; RC9_gut_grou p

14 EF Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; Rikenellaceae; Rikenella 1 1 EU Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; Rikenellaceae; Rikenella 5 0 EU Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; S-; 1 5 EU Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; S-; 10 5 EF Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; S-; 9 05 EF Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; S-; EU Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; S-; EU Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; S-; 1 0 EU Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; S-; 1 EU Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; S-; 1 1 EU Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; S-; 5 5 EU Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; S-; 01 5 EU Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; S-; 5 5 JQ Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; S-; 5 EU Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; S-; 5 EU Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; S-; 9 09 EU Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; S-; 5 EU Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; S-; EF Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; S-; 0 5 EF Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; S-; 0 5 EU Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; S-; 5 EF Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; S-; 9 EF Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; S-; EF Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; S-; 9 EF Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; S-;

15 9 EU5 1 EF05 EU51 5 EF09 5 FJ99 0 EU51 0 EF09 EU50 0 EF099 9 EU EU EU50 EU55 EF099 EU51 EU EU505 0 AM9 EU910 EF00 1 EF099 EF05 EU5 EF Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; S-; Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; S-; Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; S-; Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; S-; Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; S-; Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; S-; Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; S-; Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; S-; Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; S-; Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; S-;.5.. Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; S-; 0 1 Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; S-; Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; S-; 0 0 Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; S-; 0. 0 Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; S-; Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; S-; Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; S-; Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; S-; Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; S-; Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; S-; Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; S-; Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; S-; Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; S-; Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; S-;

16 EU Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; S-; EU Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; S-; 90 5 EF Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; S-; EF Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; S-; EF Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; S-; EF Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; S-; EF Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; S-; EF Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; S-; 1 01 EU Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; S-; 9 55 EF Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; S-; 59 5 EF Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; S-; EU Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; S-; EF Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; S-; 1 99 EF Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; S-; 1 99 EF Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; S-; 0 EU Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; S-; 9 0 EU Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; S-; 5 DQ Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; S-; 0 1 EF Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; S-; 91 1 AM Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; S-; 05 1 EF Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; S-; 91 EU Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; S-; 91 EU Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; S-; 5 EF Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; S-; 5 1 JQ Bacteria; Cyanobacteria; C0d-; o; f;

17 1 DQ 0 EU5 0 EU EU EU505 1 DQ15 10 EU5 1 EF099 5 HM5 EU5 EU50 95 EU51 EU50 1 EU5 5 EU51 5 EU509 5 EU55 EF0950 EU505 9 EF09 EU 50 EU DQ01 15 EU Bacteria; Cyanobacteria; C0d-; o; f; Bacteria; Firmicutes; Bacilli; Lactobacillales; Lactobacillaceae; Lactobacillus Bacteria; Firmicutes; Bacilli; Lactobacillales; Lactobacillaceae; Lactobacillus.5. 0 Bacteria; Firmicutes; Bacilli; Lactobacillales; Lactobacillaceae; Lactobacillus Bacteria; Firmicutes; Bacilli; Lactobacillales; Lactobacillaceae; Lactobacillus Bacteria; Firmicutes; Bacilli; Lactobacillales; Lactobacillaceae; Lactobacillus Bacteria; Firmicutes; Bacilli; Lactobacillales; Lactobacillaceae; Lactobacillus Bacteria; Firmicutes; Bacilli; Lactobacillales; Lactobacillaceae; Lactobacillus Bacteria; Firmicutes; Bacilli; Lactobacillales; Lactobacillaceae; Lactobacillus Bacteria; Firmicutes; Bacilli; Lactobacillales; Lactobacillaceae; Lactobacillus.5. 0 Bacteria; Firmicutes; Bacilli; Lactobacillales; Lactobacillaceae; Lactobacillus 0.1 Bacteria; Firmicutes; Bacilli; Lactobacillales; Lactobacillaceae; Lactobacillus Bacteria; Firmicutes; Bacilli; Lactobacillales; Lactobacillaceae; Lactobacillus Bacteria; Firmicutes; Bacilli; Lactobacillales; Lactobacillaceae; Lactobacillus 0..5 Bacteria; Firmicutes; Bacilli; Lactobacillales; Lactobacillaceae; Lactobacillus Bacteria; Firmicutes; Clostridia; Clostridiales; Clostridiaceae; Candidatus_Arthromit us Bacteria; Firmicutes; Clostridia; Clostridiales; Family_XIII_Incertae_Sedis; Incertae _Sedis 0. 0 Bacteria; Firmicutes; Clostridia; Clostridiales; Lachnospiraceae; 5 0. Bacteria; Firmicutes; Clostridia; Clostridiales; Lachnospiraceae;.5. 0 Bacteria; Firmicutes; Clostridia; Clostridiales; Lachnospiraceae; 0 0. Bacteria; Firmicutes; Clostridia; Clostridiales; Lachnospiraceae; 0 Bacteria; Firmicutes; Clostridia; Clostridiales; Lachnospiraceae; 0 0 Bacteria; Firmicutes; Clostridia; Clostridiales; Lachnospiraceae; 0 0 Bacteria; Firmicutes; Clostridia; Clostridiales; Lachnospiraceae;

18 JQ Bacteria; Firmicutes; Clostridia; Clostridiales; Lachnospiraceae; AY Bacteria; Firmicutes; Clostridia; Clostridiales; Lachnospiraceae; 5 1 EU Bacteria; Firmicutes; Clostridia; Clostridiales; Lachnospiraceae; 5 EU Bacteria; Firmicutes; Clostridia; Clostridiales; Lachnospiraceae; 5 5 DQ Bacteria; Firmicutes; Clostridia; Clostridiales; Lachnospiraceae; 1 51 EU Bacteria; Firmicutes; Clostridia; Clostridiales; Lachnospiraceae; 5 9 EU Bacteria; Firmicutes; Clostridia; Clostridiales; Lachnospiraceae; EU Bacteria; Firmicutes; Clostridia; Clostridiales; Lachnospiraceae; EU Bacteria; Firmicutes; Clostridia; Clostridiales; Lachnospiraceae; 95 EU Bacteria; Firmicutes; Clostridia; Clostridiales; Lachnospiraceae; 1 HQ Bacteria; Firmicutes; Clostridia; Clostridiales; Lachnospiraceae; 5 9 EU Bacteria; Firmicutes; Clostridia; Clostridiales; Lachnospiraceae; 9 91 EU Bacteria; Firmicutes; Clostridia; Clostridiales; Lachnospiraceae; Incertae_Sedis 0 EU Bacteria; Firmicutes; Clostridia; Clostridiales; Lachnospiraceae; Incertae_Sedis 9 51 AY Bacteria; Firmicutes; Clostridia; Clostridiales; Ruminococcaceae; 5 5 EU Bacteria; Firmicutes; Clostridia; Clostridiales; Ruminococcaceae; 1 0 EF Bacteria; Firmicutes; Clostridia; Clostridiales; Ruminococcaceae; 59 EU Bacteria; Firmicutes; Clostridia; Clostridiales; Ruminococcaceae; 0 0 EU Bacteria; Firmicutes; Clostridia; Clostridiales; Ruminococcaceae; 0 1 EU Bacteria; Firmicutes; Clostridia; Clostridiales; Ruminococcaceae; EU Bacteria; Firmicutes; Clostridia; Clostridiales; Ruminococcaceae; 0 9 FJ Bacteria; Firmicutes; Clostridia; Clostridiales; Ruminococcaceae; AY Bacteria; Firmicutes; Clostridia; Clostridiales; Ruminococcaceae; Incertae_Sedis 90 1 EU Bacteria; Firmicutes; Clostridia; Clostridiales; Ruminococcaceae; Incertae_Sedis 1 EF Bacteria; Firmicutes; Clostridia; Clostridiales; Ruminococcaceae; Incertae_Sedis

19 1 EF EF09 0 EU50 5 DQ15 99 JQ05 9 AB0 0 EU50 51 AM9 9 AM9 EU5 AY9900 AM9 9 EU99 05 DQ05 0 EU50 EU *Graphically represented in Supplementary Figure e Bacteria; Firmicutes; Clostridia; Clostridiales; Ruminococcaceae; Incertae_Sedis Bacteria; Firmicutes; Clostridia; Clostridiales; Ruminococcaceae; Oscillibacter Bacteria; Firmicutes; Clostridia; Clostridiales; uncultured; Bacteria; Firmicutes; Erysipelotrichi; Erysipelotrichales; Erysipelotrichaceae; Bacteria; Firmicutes; Erysipelotrichi; Erysipelotrichales; Erysipelotrichaceae; 0 0. Bacteria; Firmicutes; Erysipelotrichi; Erysipelotrichales; Erysipelotrichaceae; Bacteria; Firmicutes; Erysipelotrichi; Erysipelotrichales; Erysipelotrichaceae; Bacteria; Firmicutes; Erysipelotrichi; Erysipelotrichales; Erysipelotrichaceae; Incerta e_sedis Bacteria; Proteobacteria; Deltaproteobacteria; Desulfovibrionales; Desulfovibrionace ae; Desulfovibrio Bacteria; Proteobacteria; Deltaproteobacteria; Desulfovibrionales; Desulfovibrionace ae; Desulfovibrio Bacteria; Proteobacteria; Epsilonproteobacteria; Campylobacterales; Helicobacterac eae; Helicobacter Bacteria; Tenericutes; Mollicutes; Anaeroplasmatales; Anaeroplasmataceae; Anaer oplasma Bacteria; Verrucomicrobia; Verrucomicrobiae; Verrucomicrobiales; Verrucomicrobiac eae; Akkermansia 0 1. Bacteria; Verrucomicrobia; Verrucomicrobiae; Verrucomicrobiales; Verrucomicrobiac eae; Akkermansia Bacteria; Verrucomicrobia; Verrucomicrobiae; Verrucomicrobiales; Verrucomicrobiac eae; Akkermansia Bacteria; Verrucomicrobia; Verrucomicrobiae; Verrucomicrobiales; Verrucomicrobiac eae; Akkermansia Supplementary Table 5. Pathology H Congenics (Figure e-h) Sifnificant differences by OTU* OTU Test- P FDR_P BB DD KK taxonomy

20 Statisti c me an me an me an New.CleanUp.ReferenceO k Bacteria TU k Bacteria k Bacteria k Bacteria 0 New.CleanUp.ReferenceO TU k Bacteria;p Actinobacteria;c Actinobacteria;o Bifidobacteriales;f Bifidobacteriaceae;g Bifidobacterium k Bacteria;p Actinobacteria;c Actinobacteria;o Bifidobacteriales;f Bifidobacteriaceae;g Bifidobacterium;s pseudolongum New.CleanUp.ReferenceO k Bacteria;p Bacteroidetes;c Bacteroidia;o Bacteroidales TU10 1 New.ReferenceOTU k Bacteria;p Bacteroidetes;c Bacteroidia;o Bacteroidales New.ReferenceOTU k Bacteria;p Bacteroidetes;c Bacteroidia;o Bacteroidales New.CleanUp.ReferenceO TU k Bacteria;p Bacteroidetes;c Bacteroidia;o Bacteroidales;f Bacteroidaceae;g Bactero ides k Bacteria;p Bacteroidetes;c Bacteroidia;o Bacteroidales;f Bacteroidaceae;g Bactero ides;s k Bacteria;p Bacteroidetes;c Bacteroidia;o Bacteroidales;f Rikenellaceae New.ReferenceOTU k Bacteria;p Bacteroidetes;c Bacteroidia;o Bacteroidales;f Rikenellaceae;g Rikenella ;s k Bacteria;p Bacteroidetes;c Bacteroidia;o Bacteroidales;f S-;g ;s New.CleanUp.ReferenceO k Bacteria;p Bacteroidetes;c Bacteroidia;o Bacteroidales;f S-;g ;s TU 5 New.ReferenceOTU k Bacteria;p Bacteroidetes;c Bacteroidia;o Bacteroidales;f S-;g ;s New.ReferenceOTU k Bacteria;p Bacteroidetes;c Bacteroidia;o Bacteroidales;f S-;g ;s k Bacteria;p Bacteroidetes;c Bacteroidia;o Bacteroidales;f S-;g ;s k Bacteria;p Bacteroidetes;c Bacteroidia;o Bacteroidales;f S-;g ;s k Bacteria;p Bacteroidetes;c Bacteroidia;o Bacteroidales;f S-;g ;s k Bacteria;p Bacteroidetes;c Bacteroidia;o Bacteroidales;f S-;g ;s 5 New.ReferenceOTU k Bacteria;p Bacteroidetes;c Bacteroidia;o Bacteroidales;f S-;g ;s 5 New.ReferenceOTU k Bacteria;p Bacteroidetes;c Bacteroidia;o Bacteroidales;f S-;g ;s 5 New.ReferenceOTU k Bacteria;p Bacteroidetes;c Bacteroidia;o Bacteroidales;f S-;g ;s

21 New.ReferenceOTU New.ReferenceOTU New.CleanUp.ReferenceO 9.5 TU New.ReferenceOTU New.ReferenceOTU New.ReferenceOTU New.CleanUp.ReferenceO.55 TU909 9 New.ReferenceOTU New.ReferenceOTU New.ReferenceOTU New.ReferenceOTU k Bacteria;p Bacteroidetes;c Bacteroidia;o Bacteroidales;f S-;g ;s. 0 0 k Bacteria;p Bacteroidetes;c Bacteroidia;o Bacteroidales;f S-;g ;s. 0 0 k Bacteria;p Bacteroidetes;c Bacteroidia;o Bacteroidales;f S-;g ;s k Bacteria;p Bacteroidetes;c Bacteroidia;o Bacteroidales;f S-;g ;s k Bacteria;p Bacteroidetes;c Bacteroidia;o Bacteroidales;f S-;g ;s k Bacteria;p Bacteroidetes;c Bacteroidia;o Bacteroidales;f S-;g ;s k Bacteria;p Bacteroidetes;c Bacteroidia;o Bacteroidales;f S-;g ;s k Bacteria;p Bacteroidetes;c Bacteroidia;o Bacteroidales;f S-;g ;s k Bacteria;p Bacteroidetes;c Bacteroidia;o Bacteroidales;f S-;g ;s k Bacteria;p Bacteroidetes;c Bacteroidia;o Bacteroidales;f S-;g ;s 0. 1 k Bacteria;p Firmicutes. 0. k Bacteria;p Firmicutes k Bacteria;p Firmicutes k Bacteria;p Firmicutes;c Bacilli;o Lactobacillales;f Lactobacillaceae;g Lactobacillus k Bacteria;p Firmicutes;c Bacilli;o Lactobacillales;f Lactobacillaceae;g Lactobacillus. 1.. k Bacteria;p Firmicutes;c Bacilli;o Lactobacillales;f Lactobacillaceae;g Lactobacillus k Bacteria;p Firmicutes;c Bacilli;o Lactobacillales;f Lactobacillaceae;g Lactobacillus;. s k Bacteria;p Firmicutes;c Bacilli;o Lactobacillales;f Lactobacillaceae;g Lactobacillus; s 0... k Bacteria;p Firmicutes;c Bacilli;o Lactobacillales;f Lactobacillaceae;g Lactobacillus; s vaginalis k Bacteria;p Firmicutes;c Bacilli;o Lactobacillales;f Lactobacillaceae;g Lactobacillus; s vaginalis 1 1. k Bacteria;p Firmicutes;c Bacilli;o Turicibacterales;f Turicibacteraceae;g Turicibacter ;s 0 0. k Bacteria;p Firmicutes;c Clostridia;o Clostridiales k Bacteria;p Firmicutes;c Clostridia;o Clostridiales k Bacteria;p Firmicutes;c Clostridia;o Clostridiales

22 k Bacteria;p Firmicutes;c Clostridia;o Clostridiales k Bacteria;p Firmicutes;c Clostridia;o Clostridiales k Bacteria;p Firmicutes;c Clostridia;o Clostridiales k Bacteria;p Firmicutes;c Clostridia;o Clostridiales New.ReferenceOTU k Bacteria;p Firmicutes;c Clostridia;o Clostridiales 5 5 New.CleanUp.ReferenceO k Bacteria;p Firmicutes;c Clostridia;o Clostridiales TU New.ReferenceOTU k Bacteria;p Firmicutes;c Clostridia;o Clostridiales k Bacteria;p Firmicutes;c Clostridia;o Clostridiales k Bacteria;p Firmicutes;c Clostridia;o Clostridiales New.ReferenceOTU k Bacteria;p Firmicutes;c Clostridia;o Clostridiales k Bacteria;p Firmicutes;c Clostridia;o Clostridiales 59 5 New.ReferenceOTU k Bacteria;p Firmicutes;c Clostridia;o Clostridiales New.ReferenceOTU k Bacteria;p Firmicutes;c Clostridia;o Clostridiales k Bacteria;p Firmicutes;c Clostridia;o Clostridiales k Bacteria;p Firmicutes;c Clostridia;o Clostridiales k Bacteria;p Firmicutes;c Clostridia;o Clostridiales k Bacteria;p Firmicutes;c Clostridia;o Clostridiales k Bacteria;p Firmicutes;c Clostridia;o Clostridiales New.ReferenceOTU k Bacteria;p Firmicutes;c Clostridia;o Clostridiales 09 5 New.ReferenceOTU k Bacteria;p Firmicutes;c Clostridia;o Clostridiales k Bacteria;p Firmicutes;c Clostridia;o Clostridiales k Bacteria;p Firmicutes;c Clostridia;o Clostridiales k Bacteria;p Firmicutes;c Clostridia;o Clostridiales k Bacteria;p Firmicutes;c Clostridia;o Clostridiales 05 5 New.ReferenceOTU k Bacteria;p Firmicutes;c Clostridia;o Clostridiales

23 New.ReferenceOTU New.ReferenceOTU New.ReferenceOTU New.CleanUp.ReferenceO TU5 1 New.CleanUp.ReferenceO TU New.ReferenceOTU k Bacteria;p Firmicutes;c Clostridia;o Clostridiales. 1. k Bacteria;p Firmicutes;c Clostridia;o Clostridiales k Bacteria;p Firmicutes;c Clostridia;o Clostridiales k Bacteria;p Firmicutes;c Clostridia;o Clostridiales k Bacteria;p Firmicutes;c Clostridia;o Clostridiales 1 0. k Bacteria;p Firmicutes;c Clostridia;o Clostridiales k Bacteria;p Firmicutes;c Clostridia;o Clostridiales k Bacteria;p Firmicutes;c Clostridia;o Clostridiales k Bacteria;p Firmicutes;c Clostridia;o Clostridiales 1.. k Bacteria;p Firmicutes;c Clostridia;o Clostridiales k Bacteria;p Firmicutes;c Clostridia;o Clostridiales 1 0. k Bacteria;p Firmicutes;c Clostridia;o Clostridiales k Bacteria;p Firmicutes;c Clostridia;o Clostridiales k Bacteria;p Firmicutes;c Clostridia;o Clostridiales 0.. k Bacteria;p Firmicutes;c Clostridia;o Clostridiales k Bacteria;p Firmicutes;c Clostridia;o Clostridiales k Bacteria;p Firmicutes;c Clostridia;o Clostridiales k Bacteria;p Firmicutes;c Clostridia;o Clostridiales. 1.. k Bacteria;p Firmicutes;c Clostridia;o Clostridiales 0.. k Bacteria;p Firmicutes;c Clostridia;o Clostridiales 0 k Bacteria;p Firmicutes;c Clostridia;o Clostridiales k Bacteria;p Firmicutes;c Clostridia;o Clostridiales k Bacteria;p Firmicutes;c Clostridia;o Clostridiales k Bacteria;p Firmicutes;c Clostridia;o Clostridiales

24 k Bacteria;p Firmicutes;c Clostridia;o Clostridiales k Bacteria;p Firmicutes;c Clostridia;o Clostridiales k Bacteria;p Firmicutes;c Clostridia;o Clostridiales 55 New.ReferenceOTU k Bacteria;p Firmicutes;c Clostridia;o Clostridiales k Bacteria;p Firmicutes;c Clostridia;o Clostridiales New.CleanUp.ReferenceO k Bacteria;p Firmicutes;c Clostridia;o Clostridiales TU k Bacteria;p Firmicutes;c Clostridia;o Clostridiales k Bacteria;p Firmicutes;c Clostridia;o Clostridiales k Bacteria;p Firmicutes;c Clostridia;o Clostridiales k Bacteria;p Firmicutes;c Clostridia;o Clostridiales k Bacteria;p Firmicutes;c Clostridia;o Clostridiales 9 1 New.ReferenceOTU k Bacteria;p Firmicutes;c Clostridia;o Clostridiales k Bacteria;p Firmicutes;c Clostridia;o Clostridiales k Bacteria;p Firmicutes;c Clostridia;o Clostridiales k Bacteria;p Firmicutes;c Clostridia;o Clostridiales New.ReferenceOTU k Bacteria;p Firmicutes;c Clostridia;o Clostridiales k Bacteria;p Firmicutes;c Clostridia;o Clostridiales k Bacteria;p Firmicutes;c Clostridia;o Clostridiales k Bacteria;p Firmicutes;c Clostridia;o Clostridiales k Bacteria;p Firmicutes;c Clostridia;o Clostridiales New.ReferenceOTU k Bacteria;p Firmicutes;c Clostridia;o Clostridiales k Bacteria;p Firmicutes;c Clostridia;o Clostridiales;f ;g ;s k Bacteria;p Firmicutes;c Clostridia;o Clostridiales;f ;g ;s k Bacteria;p Firmicutes;c Clostridia;o Clostridiales;f ;g ;s k Bacteria;p Firmicutes;c Clostridia;o Clostridiales;f ;g ;s

25 New.CleanUp.ReferenceO 11. TU New.ReferenceOTU New.ReferenceOTU New.ReferenceOTU New.ReferenceOTU New.ReferenceOTU k Bacteria;p Firmicutes;c Clostridia;o Clostridiales;f ;g ;s k Bacteria;p Firmicutes;c Clostridia;o Clostridiales;f ;g ;s k Bacteria;p Firmicutes;c Clostridia;o Clostridiales;f ;g ;s 5. 0 k Bacteria;p Firmicutes;c Clostridia;o Clostridiales;f ;g ;s k Bacteria;p Firmicutes;c Clostridia;o Clostridiales;f ;g ;s. 0. k Bacteria;p Firmicutes;c Clostridia;o Clostridiales;f ;g ;s. 0. k Bacteria;p Firmicutes;c Clostridia;o Clostridiales;f ;g ;s k Bacteria;p Firmicutes;c Clostridia;o Clostridiales;f ;g ;s k Bacteria;p Firmicutes;c Clostridia;o Clostridiales;f ;g ;s k Bacteria;p Firmicutes;c Clostridia;o Clostridiales;f ;g ;s. 0.. k Bacteria;p Firmicutes;c Clostridia;o Clostridiales;f ;g ;s k Bacteria;p Firmicutes;c Clostridia;o Clostridiales;f ;g ;s k Bacteria;p Firmicutes;c Clostridia;o Clostridiales;f ;g ;s k Bacteria;p Firmicutes;c Clostridia;o Clostridiales;f ;g ;s. 1.. k Bacteria;p Firmicutes;c Clostridia;o Clostridiales;f ;g ;s k Bacteria;p Firmicutes;c Clostridia;o Clostridiales;f ;g ;s k Bacteria;p Firmicutes;c Clostridia;o Clostridiales;f ;g ;s. 1. k Bacteria;p Firmicutes;c Clostridia;o Clostridiales;f ;g ;s k Bacteria;p Firmicutes;c Clostridia;o Clostridiales;f ;g ;s k Bacteria;p Firmicutes;c Clostridia;o Clostridiales;f ;g ;s 0 0. k Bacteria;p Firmicutes;c Clostridia;o Clostridiales;f ;g ;s k Bacteria;p Firmicutes;c Clostridia;o Clostridiales;f ;g ;s. 0 1 k Bacteria;p Firmicutes;c Clostridia;o Clostridiales;f ;g ;s k Bacteria;p Firmicutes;c Clostridia;o Clostridiales;f ;g ;s

26 k Bacteria;p Firmicutes;c Clostridia;o Clostridiales;f ;g ;s 5 5 New.ReferenceOTU k Bacteria;p Firmicutes;c Clostridia;o Clostridiales;f ;g ;s k Bacteria;p Firmicutes;c Clostridia;o Clostridiales;f ;g ;s k Bacteria;p Firmicutes;c Clostridia;o Clostridiales;f ;g ;s k Bacteria;p Firmicutes;c Clostridia;o Clostridiales;f ;g ;s k Bacteria;p Firmicutes;c Clostridia;o Clostridiales;f ;g ;s k Bacteria;p Firmicutes;c Clostridia;o Clostridiales;f ;g ;s k Bacteria;p Firmicutes;c Clostridia;o Clostridiales;f ;g ;s k Bacteria;p Firmicutes;c Clostridia;o Clostridiales;f ;g ;s k Bacteria;p Firmicutes;c Clostridia;o Clostridiales;f ;g ;s k Bacteria;p Firmicutes;c Clostridia;o Clostridiales;f ;g ;s New.ReferenceOTU k Bacteria;p Firmicutes;c Clostridia;o Clostridiales;f ;g ;s k Bacteria;p Firmicutes;c Clostridia;o Clostridiales;f ;g ;s New.ReferenceOTU k Bacteria;p Firmicutes;c Clostridia;o Clostridiales;f ;g ;s New.ReferenceOTU k Bacteria;p Firmicutes;c Clostridia;o Clostridiales;f ;g ;s New.ReferenceOTU k Bacteria;p Firmicutes;c Clostridia;o Clostridiales;f ;g ;s 5 15 New.CleanUp.ReferenceO k Bacteria;p Firmicutes;c Clostridia;o Clostridiales;f ;g ;s TU k Bacteria;p Firmicutes;c Clostridia;o Clostridiales;f ;g ;s 55 New.ReferenceOTU k Bacteria;p Firmicutes;c Clostridia;o Clostridiales;f ;g ;s 11 New.ReferenceOTU k Bacteria;p Firmicutes;c Clostridia;o Clostridiales;f ;g ;s 1 00 New.ReferenceOTU k Bacteria;p Firmicutes;c Clostridia;o Clostridiales;f ;g ;s k Bacteria;p Firmicutes;c Clostridia;o Clostridiales;f ;g ;s k Bacteria;p Firmicutes;c Clostridia;o Clostridiales;f ;g ;s k Bacteria;p Firmicutes;c Clostridia;o Clostridiales;f ;g ;s New.ReferenceOTU k Bacteria;p Firmicutes;c Clostridia;o Clostridiales;f ;g ;s

27 New.ReferenceOTU New.ReferenceOTU New.ReferenceOTU New.ReferenceOTU k Bacteria;p Firmicutes;c Clostridia;o Clostridiales;f ;g ;s k Bacteria;p Firmicutes;c Clostridia;o Clostridiales;f ;g ;s k Bacteria;p Firmicutes;c Clostridia;o Clostridiales;f ;g ;s k Bacteria;p Firmicutes;c Clostridia;o Clostridiales;f ;g ;s 1. 0 k Bacteria;p Firmicutes;c Clostridia;o Clostridiales;f ;g ;s.. 0 k Bacteria;p Firmicutes;c Clostridia;o Clostridiales;f ;g ;s. 0.. k Bacteria;p Firmicutes;c Clostridia;o Clostridiales;f ;g ;s k Bacteria;p Firmicutes;c Clostridia;o Clostridiales;f ;g ;s 1. 0 k Bacteria;p Firmicutes;c Clostridia;o Clostridiales;f ;g ;s k Bacteria;p Firmicutes;c Clostridia;o Clostridiales;f ;g ;s k Bacteria;p Firmicutes;c Clostridia;o Clostridiales;f ;g ;s 0.. k Bacteria;p Firmicutes;c Clostridia;o Clostridiales;f ;g ;s k Bacteria;p Firmicutes;c Clostridia;o Clostridiales;f ;g ;s k Bacteria;p Firmicutes;c Clostridia;o Clostridiales;f ;g ;s k Bacteria;p Firmicutes;c Clostridia;o Clostridiales;f [Mogibacteriaceae];g ;s k Bacteria;p Firmicutes;c Clostridia;o Clostridiales;f [Mogibacteriaceae];g ;s k Bacteria;p Firmicutes;c Clostridia;o Clostridiales;f Clostridiaceae;g Clostridium 0 0. k Bacteria;p Firmicutes;c Clostridia;o Clostridiales;f Clostridiaceae;g SMB5;s 0. 0 k Bacteria;p Firmicutes;c Clostridia;o Clostridiales;f Clostridiaceae;g SMB5;s k Bacteria;p Firmicutes;c Clostridia;o Clostridiales;f Lachnospiraceae k Bacteria;p Firmicutes;c Clostridia;o Clostridiales;f Lachnospiraceae k Bacteria;p Firmicutes;c Clostridia;o Clostridiales;f Lachnospiraceae k Bacteria;p Firmicutes;c Clostridia;o Clostridiales;f Lachnospiraceae 9 k Bacteria;p Firmicutes;c Clostridia;o Clostridiales;f Lachnospiraceae

Specificity (target gene) Primer name Sequence Product length[bp] GGATTAGATACCCTGGTAGTC TACCTTGTTACGACTT

Specificity (target gene) Primer name Sequence Product length[bp] GGATTAGATACCCTGGTAGTC TACCTTGTTACGACTT Supplementary material for Beneficial Microbes DOI: http://dx.doi.org/10.3920/bm2013.0021 Individual responses of mother sows to a probiotic Enterococcus faecium strain lead to different microbiota composition