Metagenomic insights into the diversity of carbohydrate-degrading enzymes in the yak fecal microbial community

Abstract

Background: As a special herbivorous ruminant, yak is supposed to utilize the gastrointestinal microbiota to digest plant materials. Although the cellulolytic bacteria of yak rumen have been reported, there is still limited information about whether carbohydrate metabolizing enzymes in its intestinal flora are abundant for the degradation of complex lignocellulosic biomass. Results: Here, this study aimed to decode the structure and function of yak fecal microbiota using deep metagenome sequencing. A comprehensive gene catalog comprising 4.5 million microbial genes was established and functionally annotated to characterize the primary metabolic potential of the microbiome based on metagenomic assemblies from 92 Gb sequencing data. A full spectrum of genes encoding carbohydrate-active enzymes were identified and about three-quarters of these genes assigned to a wide range of enzyme families were involved in the breakdown of complex dietary carbohydrates, including 120 families of glycoside hydrolases, 25 families of polysaccharide lyases, and 15 families of carbohydrate esterases. Inference of taxonomic assignments to the carbohydrate-degrading enzymes revealed the major microbial contributors were the members of Firmicutes and Bacteroidetes, both of which were also the most dominating bacterial populations in the yak fecal microbiome. Metagenomic binning further reconstructed 86 prokaryotic genomes, and a highly diversified profile of glycoside hydrolases associated with plant-derived polysaccharide degradation was also identified in these uncultured genomes, many of which were novel species with highly fibrolytic capability. Conclusions: Our findings shed light on a great diversity of carbohydrate-degrading enzymes in the yak gut microbial community and uncultured species, providing a useful genetic resource for future studies on the discovery of novel enzymes with industrial potential.

Seasonal variations in the composition and functional profiles of gut microbiota reflect dietary changes in plateau pikas

“…Meanwhile, these microbial taxa play an important role in the utilization rate of assimilated nutrients (Krajmalnik-Brown et al 2012;Tett et al 2021), and could help hosts obtain energy from the relatively harsh environments of winter. In contrast to the gut microbiota of other plateau mammals such as the Tibetan wild ass (Equus kiang) (Gao et al 2020) and yak (Gong et al 2020), the abundance of Verrucomicrobiota in the intestines of the plateau pikas was very high, and had the highest relative abundance in summer. Akkermansia, the dominant resident genus of phylum Verrucomicrobiota, is well characterized to be an obligate host mucin degrader and usually be promoted by plant secondary compounds in food (Zhang et al 2018b;Dong et al 2021;Ren et al 2021)-for example, berberine promoted Akkermansia growth via stimulating mucin secretion in colon of mice (Dong et al 2021).…”

“…2020) and yak (Gong et al . 2020), the abundance of Verrucomicrobiota in the intestines of the plateau pikas was very high, and had the highest relative abundance in summer. Akkermansia , the dominant resident genus of phylum Verrucomicrobiota, is well characterized to be an obligate host mucin degrader and usually be promoted by plant secondary compounds in food (Zhang et al .…”

The gastrointestinal microbiome in dairy cattle is constrained by the deterministic driver of the region and the modified effect of diet

“…In contrast, the hindgut-enriched SGBs belonging to Alistipes spp. lacked dockerin modules, and the Kiritimatiellae-affiliated SGBs that were enriched in the small intestine encoded myriad GH109 enzymes to degrade glycans derived from host mucins [18] (Additional file 1: Table S10). These results indicate that microbes placed in the four-chambered stomach provide efficient hydrolysis for complex glycan breakdown to deal with primary dietary substrates.…”

Rumen microbiota of indigenous and introduced ruminants and their adaptation to the Qinghai–Tibetan plateau

“…Other than these cellulolytic bacteria in the rumen, the diversity of the prevalent rumen microorganisms and putative carbohydrate-active enzymes for utilization of lignocellulosic biomass are also important in host adaptation of high plateau ( Bohra et al, 2019 ). Gong et al (2020) suggested complex gene repertoire composed of diverse carbohydrate-degrading enzymes for yak gut microbiota which provide multiple catalytic abilities of various carbohydrate substrates deconstruction. Zhao et al (2022) also reported a larger gene pool encoding rich in carbohydrate-active enzymes in the yak rumen microbiota by metagenomic analysis.…”