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

Abstract

<jats:title>Abstract</jats:title> <jats:p><jats:bold>Background: </jats:bold>As a special herbivorous ruminant, yak is supposed 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. <jats:bold>Results: </jats:bold>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 was 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 <jats:italic>Bacteroidaceae</jats:italic>, <jats:italic>Ruminococcaceae</jats:italic>, <jats:italic>Rikenellaceae</jats:italic>, <jats:italic>Clostridiaceae</jats:italic>, and <jats:italic>Prevotellaceae</jats:italic>. 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. <jats:bold>Conclusions:</jats:bold> 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.</jats:p>

Analysis of gut microbiota in three species belonging to different genera (Hemitragus, Pseudois, and Ovis) from the subfamily Caprinae in the absence of environmental variance

“…The families of Lachnospiraceae and Ruminococcaceae belonging to order Clostridiales are known to have a wide range of metabolic abilities, including proteolytic, saccharolytic, and cellulolytic activity, which could be related to volatile fatty acids (VFAs) production (Biddle et al., 2013; Blasco et al., 2020; Brulc et al., 2009). The bacteria families (Bacteroidaceae, Rikenellaceae, and Prevotellaceae) belonging to the Bacteroidetes phylum, dominated in the three species fecal microbiome had been characterized as the main source of carbohydrate active enzymes (CAZymes) of the rumen microbiome in cattle, and considered to be primary polysaccharide decomposition bacteria in many microecosystems (Flint et al., 2012; Gong et al., 2020; Jose et al., 2017). Furthermore, the high abundance of these families, were consistent with other animals, should be the core and stable microbial community to herbivores, and played roles in food digestion and short‐chain fatty acids (SCFAs) production (Budden et al., 2017; Louis & Flint, 2009).…”

Salvaging complete and high-quality genomes of novel microbial species from a meromictic lake using a workflow combining long- and short-read sequencing platforms

“…Carbohydrate-active enzymes have a range of applications. For instance, CAZymes are used for food processing and food production [24-27]. Exploring novel CAZymes in the metagenome can benefit food industries [24, 25].…”

“…For instance, CAZymes are used for food processing and food production [24-27]. Exploring novel CAZymes in the metagenome can benefit food industries [24, 25]. On the other hand, identifying novel CAZymes modules enables us to produce novel bioactive oligosaccharides that can be used to develop new drugs and supplements [26, 27].…”