Comparative genomic analysis of the human gut microbiome reveals a broad distribution of metabolic pathways for the degradation of host-synthetized mucin glycans

TL;DR

This study analyzed 397 human gut microbiome genomes to identify pathways for mucin glycan degradation, revealing widespread genetic potential for mucin breakdown and mutualistic interactions among microbes, which enhances understanding of host-microbe dynamics.

Contribution

It provides a comprehensive genomic analysis of mucin glycan degradation pathways in the human gut microbiome, highlighting diversity and mutualistic interactions.

Findings

Genes for mucin glycan cleavage found in 86% of genomes

Genes for monosaccharide catabolism found in 89% of genomes

Most genomes can participate in monosaccharide exchange pathways

Abstract

The colonic mucus layer is a dynamic and complex structure formed by secreted and transmembrane mucins, which are high-molecular-weight and heavily glycosylated proteins. Colonic mucus consists of a loose outer layer and a dense epithelium-attached layer. The outer layer is inhabited by various representatives of the human gut microbiota (HGM). Glycans of the colonic mucus can be used by the HGM as a source of carbon and energy when dietary fibers are not sufficiently available. Here, we analyzed 397 individual HGM genomes to identify pathways for the cleavage of host-synthetized mucin glycans to monosaccharides as well as for the catabolism of the derived monosaccharides. Our key results are as follows: (i) Genes for the cleavage of mucin glycans were found in 86% of the analyzed genomes, whereas genes for the catabolism of derived monosaccharides were found in 89% of the analyzed genomes. (ii) Comparative genomic analysis identified four alternative forms of the monosaccharide-catabolizing enzymes and four alternative forms of monosaccharide transporters. (iii) Eighty-five percent of the analyzed genomes may be involved in exchange pathways for the monosaccharides derived from cleaved mucin glycans. (iv) The analyzed genomes demonstrated different abilities to degrade known mucin glycans. Generally, the ability to degrade at least one type of mucin glycan was predicted for 81% of the analyzed genomes. (v) Eighty-two percent of the analyzed genomes can form mutualistic pairs that are able to degrade mucin glycans and are not degradable by any of the paired organisms alone. Taken together, these findings provide further insight into the inter-microbial communications of the HGM as well as into host-HGM interactions.