Supplementary Materials

The PDF file includes:

  • Materials and Methods
  • Fig. S1. Comparison of microbial richness between cohorts.
  • Fig. S2. Venn diagram of overlapping taxa between IBD and clinical IBS.
  • Fig. S3. Cohorts, sample collection, and sample processing algorithm.
  • Fig. S4. Principal coordinate analysis plot on Bray-Curtis dissimilarities of controls.
  • Fig. S5. Phenotype data processing algorithm.
  • Fig. S6. Metagenomic sequencing data pipeline.
  • Fig. S7. Overview of statistical analyses.
  • Fig. S8. Prediction model to distinguish cohort of origin in disease.
  • Fig. S9. Prediction model to distinguish cohort of origin in controls.
  • References (3751)

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Other Supplementary Material for this manuscript includes the following:

  • Table S1 (Microsoft Excel format). Summary statistics of phenotypes.
  • Table S2 (Microsoft Excel format). Summary statistics of gut microbiome taxonomy.
  • Table S3 (Microsoft Excel format). Variables included in linear models case-control analyses.
  • Table S4 (Microsoft Excel format). Taxonomy results of CD versus controls.
  • Table S5 (Microsoft Excel format). Taxonomy results of UC versus controls.
  • Table S6 (Microsoft Excel format). Taxonomy results of IBS-GE versus controls.
  • Table S7 (Microsoft Excel format). Taxonomy results in the overlap of IBD and IBS-GE.
  • Table S8 (Microsoft Excel format). Taxonomy results of IBS-POP versus controls.
  • Table S9 (Microsoft Excel format). Taxonomy results of all diseases versus controls.
  • Table S10 (Microsoft Excel format). Strain diversity results of all diseases versus controls.
  • Table S11 (Microsoft Excel format). Bacterial growth rate results of all diseases versus controls.
  • Table S12 (Microsoft Excel format). Prediction accuracy of all prediction models.
  • Table S13 (Microsoft Excel format). Top 20 gut microbiome features in the prediction model.
  • Table S14 (Microsoft Excel format). Summary statistics of gut microbiome MetaCyc function.
  • Table S15 (Microsoft Excel format). Pathway results of all diseases versus controls.
  • Table S16 (Microsoft Excel format). Virulence factor results of all diseases versus controls.
  • Table S17 (Microsoft Excel format). Antibiotic resistance gene results of all diseases versus controls.
  • Table S18 (Microsoft Excel format). Associated phenotypes on gene richness, gut microbiome composition, and Shannon index in CD.
  • Table S19 (Microsoft Excel format). Associated phenotypes on gene richness, gut microbiome composition, and Shannon index in UC.
  • Table S20 (Microsoft Excel format). Associated phenotypes on gene richness, gut microbiome composition, and Shannon index in IBS-GE.
  • Table S21 (Microsoft Excel format). Associated phenotypes on gene richness, gut microbiome composition, and Shannon index in IBS-POP.
  • Table S22 (Microsoft Excel format). Correlation phenotypic factors with an FDR <0.1 from the Adonis analysis in CD.
  • Table S23 (Microsoft Excel format). Correlation phenotypic factors with an FDR <0.1 from the Adonis analysis in UC.
  • Table S24 (Microsoft Excel format). Correlation phenotypic factors with an FDR <0.1 from the Adonis analysis in IBS-GE.
  • Table S25 (Microsoft Excel format). Correlation phenotypic factors with an FDR <0.1 from the Adonis analysis in IBS-POP.
  • Table S26 (Microsoft Excel format). Variables included in multivariate linear models within disease cohorts.
  • Table S27 (Microsoft Excel format). Taxonomy results within the CD univariate model.
  • Table S28 (Microsoft Excel format). Taxonomy results within the CD multivariate model.
  • Table S29 (Microsoft Excel format). Taxonomy results within the UC univariate model.
  • Table S30 (Microsoft Excel format). Taxonomy results within the UC multivariate model.
  • Table S31 (Microsoft Excel format). Taxonomy results within the IBS-GE univariate model.
  • Table S32 (Microsoft Excel format). Taxonomy results within the IBS-GE multivariate model.
  • Table S33 (Microsoft Excel format). Taxonomy results within the IBS-POP univariate model.
  • Table S34 (Microsoft Excel format). Taxonomy results within the IBS-POP multivariate model.
  • Table S35 (Microsoft Excel format). Pathway results within the CD univariate model.
  • Table S36 (Microsoft Excel format). Pathway results within the CD multivariate model.
  • Table S37 (Microsoft Excel format). Pathway results within the UC univariate model.
  • Table S38 (Microsoft Excel format). Pathway results within the UC multivariate model.
  • Table S39 (Microsoft Excel format). Pathway results within the IBS-GE univariate model.
  • Table S40 (Microsoft Excel format). Pathway results within the IBS-GE multivariate model.
  • Table S41 (Microsoft Excel format). Pathway results within the IBS-POP univariate model.
  • Table S42 (Microsoft Excel format). Pathway results within the IBS-POP multivariate model.
  • Table S43 (Microsoft Excel format). Cohort-associated taxa and IBD versus IBS taxonomical associations.