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

Saisai Zhou,Zhuoma Gesang,Ga Gong,Zhuofei Xu,Kai Wang,Runbo Luo,Sizhu Suolang,Yifei Wang

doi:10.3389/fmicb.2020.595066

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.

Highlights

Tibetan pig is a local pig breed mainly distributed in the Qinghai-Tibet Plateau (Yang et al, 2011)
We presented 322 metagenomeassembled genomes (MAGs) with completeness greater than 80% and contamination less than 10%. These reconstructed prokaryotic genomes were described as a gut mini-microbiome in Tibetan pigs
The gut microorganisms enable providing a large panel of enzymes involved in the degradation of complex carbohydrates, including plant cell wall polysaccharides, storage carbohydrates, and host glycans (El Kaoutari et al, 2013; Ilmberger et al, 2014; Milani et al, 2017; Wang et al, 2019)

Summary

Introduction

Tibetan pig is a local pig breed mainly distributed in the Qinghai-Tibet Plateau (Yang et al, 2011). It is characterized by stronger adaptability for high-altitude, hypoxia, and cold environments than the lowland pig breeds (Ai et al, 2014; Gan et al, 2019). Tibetan pigs utilize gut microbiota and microbial fermentation in the large intestine to digest plant materials. Uncultivated Microorganisms in Tibetan Pig with high fiber content (Wenk, 2001; Yang et al, 2018). The main products of fermentation by anaerobic microbiota in the large intestine are short-chain fatty acids (SCFAs) that play crucial roles in mammalian energy metabolism, gastrointestinal physiology, and immune function (Den Besten et al, 2013; Silva et al, 2020)

Methods

Results

Conclusion