Characterization of Metagenome-Assembled Genomes and Carbohydrate-Degrading Genes in the Gut Microbiota of Tibetan Pig

Abstract

Tibetan pig is an important domestic mammal, providing products of high nutritional value for millions of people living in the Qinghai-Tibet Plateau. The genomes of mammalian gut microbiota encode a large number of carbohydrate-active enzymes, which are essential for the digestion of complex polysaccharides through fermentation. However, the current understanding of microbial degradation of dietary carbohydrates in the Tibetan pig gut is limited. In this study, we produced approximately 145 gigabases of metagenomic sequence data for the fecal samples from 11 Tibetan pigs. De novo assembly and binning recovered 322 metagenome-assembled genomes taxonomically assigned to 11 bacterial phyla and two archaeal phyla. Of these genomes, 191 represented the uncultivated microbes derived from novel prokaryotic taxa. Twenty-three genomes were identified as metagenomic biomarkers that were significantly abundant in the gut ecosystem of Tibetan pigs compared to the other low-altitude relatives. Further, over 13,000 carbohydrate-degrading genes were identified, and these genes were more abundant in some of the genomes within the five principal phyla: Firmicutes, Bacteroidetes, Spirochaetota, Verrucomicrobiota, and Fibrobacterota. Particularly, three genomes representing the uncultivated Verrucomicrobiota encode the most abundant degradative enzymes in the fecal microbiota of Tibetan pigs. These findings should substantially increase the phylogenetic diversity of specific taxonomic clades in the microbial tree of life and provide an expanded repertoire of biomass-degrading genes for future application to microbial production of industrial enzymes.

Keywords: Tibetan pig; carbohydrate-degrading genes; complex carbohydrates; gut microbiota; metagenome-assembled genomes; uncultivated microorganisms.

FIGURE 1

The characterizations of 322 metagenome-assembled genomes and their carbohydrate degrading enzymes from the fecal microbial community of Tibetan pigs. The internal tree denotes whole-genome phylogenetic relationships among the recovered genomes. The outer rings range from 1 (the innermost ring) to 8 (the outermost ring). The innermost ring and the enlarged leaf nodes are color-coded by the taxonomic distribution of genomes whose organismal identifiers at the phylum or class level are displayed under the circular map. The next three rings show the distribution of carbohydrate-degrading enzymes. The red gradients are in proportion to the numbers of carbohydrate-degrading enzymes encoded in the individual genomes, and the corresponding statistics are listed in Supplementary Table 7. The 5th to 7th rings show the relative abundances of individual genomes in the gut microbial communities of Tibetan pigs, Large White pigs, and Bama minipigs. In these rings, mean values of percent relative abundances are color-coded. The related abundance data of the genomes across the samples are summarized in Supplementary Table 4. The outermost ring shows differentially abundant genomes detected to be metagenomic biomarkers: black triangles stand for the genomes most abundant in the Tibetan pigs, white triangles for the Large White pigs, and black rectangles for the Bama minipigs. In the internal tree, the star leaf nodes denote differential genomes, and their family identifiers are labeled in the gray sectors.

FIGURE 2

Distribution of the percentage sequence identity between the predicted CAZymes and the best hits from NCBI NR. (A) The frequency distribution of the best BLAST hits fell into percentage identity intervals for all the predicted CAZymes. (B) The distribution for eight classes of CAZymes. GHs, glycoside hydrolases; PL, polysaccharide lyases; CEs, carbohydrate esterases; GTs, glycosyl transferases; CBMs carbohydrate-binding modules; AAs, auxiliary activities enzymes; SLHs, S-layer homology domains; Cohesins, cohesin domains.