Comparative Metagenomics Revealed Commonly Enriched Gene Sets in Human Gut Microbiomes

Abstract

Numerous microbes inhabit the human intestine, many of which are uncharacterized or uncultivable. They form a complex microbial community that deeply affects human physiology. To identify the genomic features common to all human gut microbiomes as well as those variable among them, we performed a large-scale comparative metagenomic analysis of fecal samples from 13 healthy individuals of various ages, including unweaned infants. We found that, while the gut microbiota from unweaned infants were simple and showed a high inter-individual variation in taxonomic and gene composition, those from adults and weaned children were more complex but showed a high functional uniformity regardless of age or sex. In searching for the genes over-represented in gut microbiomes, we identified 237 gene families commonly enriched in adult-type and 136 families in infant-type microbiomes, with a small overlap. An analysis of their predicted functions revealed various strategies employed by each type of microbiota to adapt to its intestinal environment, suggesting that these gene sets encode the core functions of adult and infant-type gut microbiota. By analysing the orphan genes, 647 new gene families were identified to be exclusively present in human intestinal microbiomes. In addition, we discovered a conjugative transposon family explosively amplified in human gut microbiomes, which strongly suggests that the intestine is a ‘hot spot’ for horizontal gene transfer between microbes.

Les Japonais et nous

“…Décrit pour la première fois en 1959 par des chercheurs japonais, le transfert horizontal de gènes (THG) démontrait le passage de la résistance aux antibiotiques entre différentes espèces de bactéries [5]. Ce n'est que plus tard que les implications redoutables de cette observation sont apparues en infectiologie.…”

Anaerobic 4-hydroxyproline utilization: Discovery of a new glycyl radical enzyme in the human gut microbiome uncovers a widespread microbial metabolic activity

“…6 , 7 Furthermore, GREs represent one of the most abundant protein families in human stool metagenomes and metaproteomes. 8 , 9 A GRE must be posttranslationally modified by a partner radical S -adenosylmethionine (SAM) activating enzyme (AE), which installs a radical on the α-carbon of a conserved glycine residue (Fig. 1A).…”

Probiotics and health: An evidence-based review

“…The intestinal microbiota (a term that has now replaced the old denomination of "microflora" [1,2]) is an ecosystem formed by a variety of ecological niches, made of several bacterial species and a very large amount of strains [3][4][5][6][7][8]. The microbiota is in close contact with the intestinal mucosa or epithelial interface which is, after the respiratory area, the largest surface of the body, occupying approximately 250-400 m 2 .…”