Compositional and functional differences of the mucosal microbiota along the intestine of healthy individuals

Abstract

Gut mucosal microbes evolved closest to the host, developing specialized local communities. There is, however, insufficient knowledge of these communities as most studies have employed sequencing technologies to investigate faecal microbiota only. This work used shotgun metagenomics of mucosal biopsies to explore the microbial communities' compositions of terminal ileum and large intestine in 5 healthy individuals. Functional annotations and genome-scale metabolic modelling of selected species were then employed to identify local functional enrichments. While faecal metagenomics provided a good approximation of the average gut mucosal microbiome composition, mucosal biopsies allowed detecting the subtle variations of local microbial communities. Given their significant enrichment in the mucosal microbiota, we highlight the roles of Bacteroides species and describe the antimicrobial resistance biogeography along the intestine. We also detail which species, at which locations, are involved with the tryptophan/indole pathway, whose malfunctioning has been linked to pathologies including inflammatory bowel disease. Our study thus provides invaluable resources for investigating mechanisms connecting gut microbiota and host pathophysiology.

Figure 1

Sampling locations and general overview of the faecal and biopsy-derived metagenomic datasets. (A) For each of the 5 enrolled subjects, gut mucosa biopsies were collected from terminal ileum (TI), transverse colon (TC), and rectum (RE); in one subject, as it was not possible to reach her TI, one biopsy was taken from the adjacent caecum instead (CA). Faeces (FE) were also sampled. (B, C) PCoA plots of the downsized biopsy-faeces dataset (B), colour-coded by sampling-location, and of biopsies data only (C), colour-coded by subject. The only caecal sample of this study is indicated by an asterisk. (D, E) Percentage of shared metagenomic species (in dark red) between biopsy location pairs (D), and between biopsy locations and FE (E).

Figure 2

Taxonomy of metagenomics species (MGSs) from terminal ileum/caecum (TI*), transverse colon (TC), rectum (RE), and faeces (FE); n = 5 for each group. (A, B) Top 10 most highly abundant phyla (A) and classes (B) in the large intestine; phyla/classes are sorted, in the legends, from the most to the least abundant in all three biopsy-locations. The corresponding faecal values are also plotted for comparison, in the same order. (C, D) Scatter-plots of mean relative abundances of all 41 genera shared by biopsies and FE (C), and of the same genera except Bacteroides (D). E Spearman’s linear correlation coefficients between all biopsies and each sampling location. (F–H) Scatter-plots of the genera relative abundances of three sample-pairs: TI* versus TC (F), TC versus RE (G), and RE versus FE (H); data points are colour-coded by subject.

Figure 3

Analysis of antimicrobial resistance genes (ARGs) across biopsy locations (terminal ileum plus caecum (TI*), transverse colon (TC), and rectum (RE)), and in faeces (FE) samples (n = 5 for each group). (A) Spearman’s correlation coefficients between ARGs relative abundances of all biopsies and each sampling location. (B, C) Differential enrichment of drug classes (B), or resistance mechanisms (C).

Figure 4

Simulation results of the genome-scale metabolic models of all Bacteroides and Bifidobacterium species detected in biopsy samples, plus the most highly enriched species at one biopsy location only in at least two patients (Supplementary Fig. 10; Supplementary Table 1). Results are reported by biopsy location: terminal ileum plus caecum (TI*), transverse colon (TC), and rectum (RE). (A) Jaccard index for each modelled species. (B) Biopsy location-based summation of the secretion of the main bacterial metabolites. (C) Uptake and secretion of the metabolites showing a variation across the modelled species. (D–F) Growth rate plots of the modelled species as a function of environmental oxygen level for TI (D), TC (E), and RE (F). The most enriched Bacteroides of the three biopsy locations are highlighted in red (C–F).