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Figure S1. Bacterial load on the small intestinal mucosa in all patients. Figure S2. Bacterial diversity (Chao1 index) within the mucosa-associated microbiota from duodenal biopsies from patients classified as having a functional dyspepsia (FD), iron deficiency (ID), or Crohn’s disease (CD). Figure S3. Bacterial diversity (Chao1 index) within the mucosa-associated microbiota from duodenal biopsies from patients with Crohn’s disease (CD). Table S1. Additional characteristics for the functional/iron deficiency patients included in the cohort (n = 82). Table S2. Additional characteristics for the 20 CD patients included in the cohort, including CD medications. Table S3. OTU table with raw read counts used for subsequent data analysis. Table S4. Relative abundances of bacterial phyla present in the duodenal mucosal microbiota of all patients. Table S5. Relative abundances of bacterial genera present in the duodenal mucosal microbiota of all patients. Table S6. Bacterial phyla present in the duodenal mucosal microbiota of all patients. Table S7. Bacterial genera present in the duodenal mucosal microbiota of all patients. Table S8. Bacterial OTUs that were observed to have significantly different relative abundances in the duodenal mucosal microbiota of all patients. Table S9. p values comparing relative abundances of bacterial genera present in the duodenal mucosal microbiota of either functional dyspepsia (FD) and iron deficiency (ID) patients (Table A), or Crohn’s disease (CD) patients (Table B). Patients were grouped based on smoking status (current smoker, previous smoker, or having never smoked). (PDF 822 kb)

Supplementary Methods. (PDF 163 kb)

Supplementary Methods. (PDF 163 kb)

Figure S1. Bacterial load on the small intestinal mucosa in all patients. Figure S2. Bacterial diversity (Chao1 index) within the mucosa-associated microbiota from duodenal biopsies from patients classified as having a functional dyspepsia (FD), iron deficiency (ID), or Crohn’s disease (CD). Figure S3. Bacterial diversity (Chao1 index) within the mucosa-associated microbiota from duodenal biopsies from patients with Crohn’s disease (CD). Table S1. Additional characteristics for the functional/iron deficiency patients included in the cohort (n = 82). Table S2. Additional characteristics for the 20 CD patients included in the cohort, including CD medications. Table S3. OTU table with raw read counts used for subsequent data analysis. Table S4. Relative abundances of bacterial phyla present in the duodenal mucosal microbiota of all patients. Table S5. Relative abundances of bacterial genera present in the duodenal mucosal microbiota of all patients. Table S6. Bacterial phyla present in the duodenal mucosal microbiota of all patients. Table S7. Bacterial genera present in the duodenal mucosal microbiota of all patients. Table S8. Bacterial OTUs that were observed to have significantly different relative abundances in the duodenal mucosal microbiota of all patients. Table S9. p values comparing relative abundances of bacterial genera present in the duodenal mucosal microbiota of either functional dyspepsia (FD) and iron deficiency (ID) patients (Table A), or Crohn’s disease (CD) patients (Table B). Patients were grouped based on smoking status (current smoker, previous smoker, or having never smoked). (PDF 822 kb)