Metagenomic insights into the diversity of carbohydrate-degrading enzymes in the yak fecal microbial community
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RESEARCH ARTICLE
Open Access
Metagenomic insights into the diversity of carbohydrate-degrading enzymes in the yak fecal microbial community Ga Gong1, Saisai Zhou1, Runbo Luo1, Zhuoma Gesang2 and Sizhu Suolang1*
Abstract Background: Yaks are able to utilize the gastrointestinal microbiota to digest plant materials. Although the cellulolytic bacteria in the yak rumen have been reported, there is still limited information on the diversity of the major microorganisms and putative carbohydrate-metabolizing enzymes for the degradation of complex lignocellulosic biomass in its gut ecosystem. Results: Here, this study aimed to decode biomass-degrading genes and genomes in the yak fecal microbiota using deep metagenome sequencing. A comprehensive catalog comprising 4.5 million microbial genes from the yak feces were established based on metagenomic assemblies from 92 Gb sequencing data. We identified a full spectrum of genes encoding carbohydrate-active enzymes, three-quarters of which were assigned to highly diversified enzyme families 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 genes revealed the major microbial contributors were Bacteroidaceae, Ruminococcaceae, Rikenellaceae, Clostridiaceae, and Prevotellaceae. Furthermore, 68 prokaryotic genomes were reconstructed and the genes encoding glycoside hydrolases involved in plant-derived polysaccharide degradation were identified in these uncultured genomes, many of which were novel species with lignocellulolytic capability. Conclusions: Our findings shed light on a great diversity of carbohydrate-degrading enzymes in the yak gut microbial community and uncultured species, which provides a useful genetic resource for future studies on the discovery of novel enzymes for industrial applications. Keywords: Yak, Microbiome, Carbohydrate degradation, Lignocellulolytic enzymes, Plant polysaccharides, Taxonomic diversity, Metagenome-assembled genomes
Background Domestic yaks (Bos grunniens) are important livestock that can provide food and livelihood for millions of people living in the Qinghai-Tibet Plateau [1]. Yaks graze on grasses, straw, and lichens, which are plant materials rich in lignocellulosic biomass, such as cellulose, hemicellulose, and starch particles [2, 3]. Digestion of * Correspondence: [email protected] 1 Department of Animal Science, Tibet Agricultural and Animal Husbandry College, Linzhi, Tibet, China Full list of author information is available at the end of the article
complex dietary fiber composed of plant cell wall polysaccharides and resistant starch is essential for preserving numerous physiological processes and host energy metabolism. Since the mammalian genomes generally encode few enzymes linked to digestion [4], a consortium of gastrointestinal microorganisms that harbor multiple carbohydrate-metabolizing enzymes play a significant role in
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