Supplementary Materials

Supplementary Material for:

Identifying Gut Microbe–Host Phenotype Relationships Using Combinatorial Communities in Gnotobiotic Mice

Jeremiah J. Faith, Philip P. Ahern, Vanessa K. Ridaura, Jiye Cheng, Jeffrey I. Gordon*

*Corresponding author. E-mail: jgordon@wustl.edu

Published 22 January 2014, Sci. Transl. Med. 6, 220ra11 (2014)
DOI: 10.1126/scitranslmed.3008051

This PDF file includes:

  • A screening platform based on out-of-the-isolator gnotobiotic mice Fig. S1. Simulating phenotype effect size and saturation as a function of microbial community size.
  • Fig. S2. Simulating phenotype effect size as a function of microbial community size.
  • Fig. S3. Phenotypic responses as a function of community membership size.
  • Fig. S4. Modeling identifies individual bacterial strains that modulate cecal metabolite concentrations in complex communities.
  • Fig. S5. Representative flow cytometry plots of FoxP3 and CD103 expression in the colons of monocolonized and germ-free mice.

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Other Supplementary Material for this manuscript includes the following:

  • Table S1 (Microsoft Excel format). Human subject metadata.
  • Table S2 (Microsoft Excel format). Influence of donor microbiota on the proportion of Tregs and on host adiposity.
  • Table S3 (Microsoft Excel format). Bacterial strains represented in clonally arrayed culture collection from donor F60T2.
  • Table S4 (Microsoft Excel format). Community composition and phenotypic responses in mice harboring subsets of the arrayed culture collection from donor F60T2.
  • Table S5 (Microsoft Excel format). Cecal metabolites with significantly different concentrations or variances between germ-free mice and mice colonized with subsets of bacterial strains from donor F60T2.
  • Table S6 (Microsoft Excel format). Modeling phenotypic variation as a function of community composition.
  • Table S7 (Microsoft Excel format). Differences in adiposity between germ-free mice and mice monocolonized with bacterial strains from the donor F60T2 culture collection.
  • Table S8 (Microsoft Excel format). Differences in microbial biomass [DNA (ng)/wet weight of feces (mg)] between germ-free mice and animals monocolonized with bacterial strains from the culture collection from donor F60T2.
  • Table S9 (Microsoft Excel format). Differences in the percentage of Tregs (% FoxP3+ in CD4+ T cells) of the colonic lamina propria between germ-free mice and animals monocolonized with bacterial strains from the donor F60T2 culture collection.
  • Table S10 (Microsoft Excel format). Differences in the percentage of Tregs (% FoxP3+ in CD4+ T cells) in mesenteric lymph nodes and spleens between germfree mice and animals monocolonized (C57BL/6J) with bacterial strains from the donor F60T2 culture collection.
  • Table S11 (Microsoft Excel format). Differences in the percentage of peripheral Tregs (Nrp1lo/− cells in CD4+FoxP3+ T cells) in mesenteric lymph nodes and spleens between germ-free mice and animals monocolonized (C57BL/6J) with bacterial strains from the donor F60T2 culture collection.
  • Table S12 (Microsoft Excel format). Differences in short-chain fatty acid concentrations in cecal contents between germ-free mice and animals monocolonized (C57BL/6J) with bacterial strains from the donor F60T2 culture collection.
  • Table S13 (Microsoft Excel format). Median relative abundance of reads from strains used in monocolonization experiments in recipient animals’ fecal DNA.

[Tables S1 to S13 ]