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.