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. 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 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.

Natural and after colon washing fecal samples: the two sides of the coin for investigating the human gut microbiome

“…Most of the inferred organisms (>95%) in both F and LL sample matrices were members of the Bacteroidetes, Firmicutes , and Proteobacteria phyla, which is concordant with other studies on the human gut microbiome (29,37). The Gram-negative bacteria belonging to the Bacteroidetes phylum are common, abundant, and diverse within the human GI tract.…”

“…We first computed taxonomic analysis in matched samples with the purpose to verify the accuracy of F and LL to represent the complexity of human gut and to check the intra-subject taxonomic variability due the two different sampling approaches. Most of the inferred organisms (>95%) in both F and LL sample matrices were members of the Bacteroidetes, Firmicutes, and Proteobacteria phyla, which is concordant with other studies on the human gut microbiome (29,37). The Gram-negative bacteria belonging to the Bacteroidetes phylum are common, abundant, and diverse within the human GI tract.…”

“…Most of the knowledge about bacterial diversity in the human GI tract has been achieved by metagenomics analysis from fecal samples, as also reported in international projects (27,28). However, recent scientific findings showed that fecal sampling approaches may be non-exhaustive for a complete knowledge of the gut microbiota composition distributed in different sites of the GI tract (29). Just think of the different microbial composition resident in the small and large intestine both at mucosal and luminal level (30).…”

Nutritional strategies for mucosal health: the interplay between microbes and mucin glycans

“…This microbial niche is especially present at the mucosal interface in the colon, where the mucus layer is the thickest and is, in turn, divided into an inner and outer layer. The inner mucus layer is described to be devoid of microbes while the outer mucus layer of the colon harbors a stable community of mucosa-colonizing microbes that form an ecological network based on niche-specific conditions, such as low levels of oxygen and the availability of mucin proteins and glycans [12]. Apart from the mucus that covers the gut epithelial cells, fecal pellets are coated with a layer of mucus that creates an additional barrier for microbes to reach epithelial cells by entrapping them in the fecal pellet [5].…”

Digestion‐Promoting Effects and Mechanisms of Dashanzha Pill Based on Raw and Charred Crataegi Fructus

“…[35] Bacteroidetes are known to be specialized anaerobic bileÀ resistant bacteria, one of the dominant genera in the gut, and they are considered to be flexible foragers, able to adapt to changes in microbial composition and polysaccharide utilization. [36,37] Thus, the nutritional deprivation in a state of dyspepsia enriched them in large quantities. Akkermansia increased in the gut microbiota of undernourished neonatal mice, [38] and its abundance was negatively correlated with the body weight of mice and humans.…”