Additional file 2 of Dietary fibers boost gut microbiota-produced B vitamin pool and alter host immune landscape

Supplementary Material 2: Supplementary Table 1. Composition of rodent diets. Composition of all diets used in this study: standard chow 1 (SC1), standard chow 2 (SC2), inulin-supplemented (IN), fiber-supplemented (FS) or fiber-free (FF). Supplementary Table 2. CyTOF antibody panel. Antibody panel used to stain cells isolated from colonic lamina propria, lung, and spleen samples for CyTOF analysis. Supplementary Table 3: Colonic lamina propria CD45+ cell abundances by CyTOF. Colonic lamina propria immune cell populations acquired by CyTOF, expressed as a percentage of all CD45+ cells. Cell populations were identified by clustering in FlowSOM and by manual gating in FlowJo for CD4+ populations. N indicates number of samples included in the analyses; batch number indicates independent experiments for a given diet. Supplementary Table 4: Spleen CD45+ cell abundances by CyTOF. Splenic immune cell populations acquired by CyTOF, expressed as a percentage of all CD45+ cells. Cell populations were identified by manual gating in FlowJo. N indicates number of samples included in the analyses; batch number indicates independent experiments for a given diet. Supplementary Table 5: Lung CD45+ cell abundances by CyTOF. Lung immune cell populations acquired by CyTOF, expressed as a percentage of all CD45+ cells. Cell populations were identified by manual gating in FlowJo. N indicates number of samples included in the analyses; batch number indicates independent experiments for a given diet. Supplementary Table 6. Microbiome composition by 16S rRNA gene sequencing. Composition of fecal microbiota by 16S rRNA gene sequencing of specific-pathogen-free (SPF) mice before (day 0) and after 40 days of feeding (day 40) for all diets: standard chow 1 (SC1), standard chow 2 (SC2), inulin-supplemented (IN), fiber-supplemented (FS) or fiber-free (FF). Supplementary Table 7. Cecum metabolome of germ-free (GF) and gnotobiotic (14SM) mice. Concentrations of metabolites detected by CE-TOFMS in cecal contents of gnotobiotic (14SM), and germ-free (GF) mice fed a standard chow 1 (SC1) or fiber-free (FF) diet. Supplementary Table 8. Cecum metabolome of specific-pathogen-free (SPF) mice. Concentrations of metabolites detected by CE-TOFMS in cecal contents of specific-pathogen-free (SPF) mice fed all diets: standard chow 1 (SC1), standard chow 2 (SC2), inulin-supplemented (IN), fiber-supplemented (FS) or fiber-free (FF). Supplementary Table 9. Serum metabolome of specific-pathogen-free (SPF) mice. Concentrations of metabolites detected by CE-TOFMS in serum of specific-pathogen-free (SPF) mice fed all diets: standard chow 1 (SC1), standard chow 2 (SC2), inulin-supplemented (IN), fiber-supplemented (FS) or fiber-free (FF). Supplementary Table 10. B vitamin metatranscriptome. Relative abundance of transcripts mapping to bacterial genes involved in synthesis (S) or downstream utilization (D) of enzymes involved in B vitamin metabolism in cecal contents of specific-pathogen-free (SPF) mice fed an inulin-supplemented (IN), standard chow 2 (SC2), or fiber-free (FF) diet. Supplementary Table 11. Metatranscriptome mapped by Enzyme Classification (EC) identifiers. Transcripts mapping to bacterial genes with the specified Enzyme Classification (EC) identifier, expressed as counts per million reads, in cecal contents of specific-pathogen-free (SPF) mice fed an inulin-supplemented (IN), standard chow 2 (SC2), or fiber-free (FF) diet.