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

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: Carbohydrate degradation; Lignocellulolytic enzymes; Metagenome-assembled genomes; Microbiome; Plant polysaccharides; Taxonomic diversity; Yak.

Fig. 1

Community composition of the yak fecal microbiome. Taxonomic distribution of the microbiota based on relative abundances of metagenomic reads assigned to the phylum-level (a) and family-level (b) taxa using Kaiju [15]. Labels denote the most prevalent taxa with relative abundance ≥1%

Fig. 2

Sequence conservation of carbohydrate-active enzymes encoded in the yak fecal metagenome. The distribution of the percentage sequence identity between the annotated CAZymes and the best hits in the NCBI NR protein database is displayed by the box-plot (a) and pie-chart (b), respectively. The proteins allocated to six functional classes (i.e. GHs, GTs, PLs, CEs, CMBs, AAs) of CAZymes are separately shown. The percentage identity intervals are illustrated by the gradient of color

Fig. 3

Comparison of taxonomic assignment to the genes encoding CAZymes with a role in polysaccharide degradation. Phylum- (a) and family-level (B) taxonomic assignments are shown for the genes coding for three CAZyme classes GHs, CEs, and PLs, respectively. The abscissa denotes the percentage of genes affiliated to the individual taxa. The ordinate denotes the detected taxa with relative abundance ≥0.5% in at least one class

Fig. 4

Taxonomic and phylogenetic structure of the uncultured gut prokaryotic species. a The stacked bar plot showing the five most prevalent taxa at the phylum, order, class, family, respectively. b Circular Phylogram of 68 metagenome-assembled genomes and the species representative genomes retrieved from the NCBI RefSeq database. The outermost color strips denote the phylum-level taxa of the draft genomes corresponding to the tips of the phylogenetic tree. The colored tip nodes denote the genome bins and the white nodes for the public reference genomes

Fig. 5

Distribution of the GH families associated with the major lignocellulolytic enzymes across the recovered genomes. The heatmap shows the frequency of the genes affiliated to individual GH families. Only the MAGs carrying at least five genes belonging to any GH are displayed herein