Supplementary Materials

The PDF file includes:

  • Materials and Methods
  • Fig. S1. Etiology and cluster analysis of patients with diarrhea.
  • Fig. S2. Microbial community and host phenotypes of healthy-like and dysbiotic mice.
  • Fig. S3. Technical and biological replication of healthy-like and dysbiotic microbial communities.
  • Fig. S4. Metatranscriptomics and metabolomics indicate that SCFAs and secondary bile acids inhibit C. difficile colonization.
  • Fig. S5. Metabolic properties of healthy-like and dysbiotic human stool samples.
  • Fig. S6. Dietary intervention reduces early C. difficile colonization in dysbiotic mice.
  • Fig. S7. FMT decreases susceptibility to CDI and normalizes the metabolic milieu.
  • Fig. S8. Distribution of healthy-like and dysbiotic individuals by risk factors that are predictive of dysbiosis.
  • Table S1. Patient cohort demographics.
  • Table S2. Taxonomic differences between healthy-like and dysbiotic individuals.
  • Table S3. Etiology of diarrhea by community type.
  • Table S4. Efficiency of transfer of human gut microbiota to mice at the family level.
  • Table S5. Colon inflammation scores.
  • Table S6. Custom diet formulations.
  • Table S7. Demographics and risk factors predictive of dysbiosis.
  • References (5562)

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Other Supplementary Material for this manuscript includes the following:

  • Data file S1 (Microsoft Excel format). Untargeted metabolomics with metabolites increased in healthy-like mice.
  • Data file S2 (Microsoft Excel format). Untargeted metabolomics with metabolites increased in dysbiotic mice.
  • Data file S3 (Microsoft Excel format). Source data for main figures and tables.
  • Data file S4 (Microsoft Excel format). Source data for supplementary figures and tables.