Viewing the human microbiome through three-dimensional glasses: integrating structural and functional studies to better define the properties of myriad carbohydrate-active enzymes

Abstract

Recent studies have provided an unprecedented view of the trillions of microbes associated with the human body. The human microbiome harbors tremendous diversity at multiple levels: the species that colonize each individual and each body habitat; the genes that are found in each organism's genome; the expression of these genes and the interactions and activities of their protein products. The sources of this diversity are wide-ranging and reflect both environmental and host factors. A major challenge moving forward is defining the precise functions of members of various families of proteins represented in our microbiomes, including the highly diverse carbohydrate-active enzymes (CAZymes) involved in numerous biologically important chemical transformations, such as the degradation of complex dietary polysaccharides. Coupling metagenomic analyses to structural genomics initiatives and to biochemical and other functional assays of CAZymes will be essential for determining how these as well as other microbiome-encoded proteins operate to shape the properties of microbial communities and their human hosts.

Metagenome of Mehsani Buffalo Rumen Microbiota: An Assessment of Variation in Feed-Dependent Phylogenetic and Functional Classification

“…According to the study on mice gut, the proportion of Bacteroidetes representatives decreased drastically when animals were switched from low levels of fat and high level of plant polysaccharides to a Western diet (high fat, high sugar). Feeding on the diet rich in plant polysaccharides resulted in an enriched set of pathways including N -glycan, glycosaminoglycan, and starch degradation that are typical for Bacteroidetes [Turnbaugh et al, 2010]. The significant increment of Bacteroidetes and Firmicutes population has also been observed in our study across the regimes.…”

A metagenomic insight into our gut's microbiome

“…CAZymes study was nevertheless restricted to cultivated bacterial species. CAZymes diversity has been described in three metagenomics studies focused on the gut microbiome,41 47 48 revealing the presence of at least 81 families of glycoside hydrolases, making the human gut metagenome one of the richest sources of CAZymes 49. Tasse et al applied high-throughput functional screenings on human gut derived metagenomics clones (156 000 clones representing 5.5 Gb of DNA) and identified new CAZymes 50…”

Xylan utilization in human gut commensal bacteria is orchestrated by unique modular organization of polysaccharide-degrading enzymes

“…The CAZy gene catalog of the human genome pales in comparison with that of the gut microbiota, which exceeds the total number of human CAZymes by at least 600-fold (15). This observation suggests that humans rely heavily on their gut microbes to extract energy from dietary carbohydrates (16), especially in their lower GIT. Despite the importance of these genes in energy capture by the gut microbiota, very little is known of the function of their encoded polypeptides.…”