Dynamic changes of yak (Bos grunniens) gut microbiota during growth revealed by polymerase chain reaction-denaturing gradient gel electrophoresis and metagenomics.

Yuanyang Nie,Yu Fu,Qun Sun,Zhiwei Zhou,Yang Yang,Jiuqiang Guan,Baixue Xia,Xiaolin Luo

doi:10.5713/ajas.16.0836

Abstract

ObjectiveTo understand the dynamic structure, function, and influence on nutrient metabolism in hosts, it was crucial to assess the genetic potential of gut microbial community in yaks of different ages.MethodsThe denaturing gradient gel electrophoresis (DGGE) profiles and Illumina-based metagenomic sequencing on colon contents of 15 semi-domestic yaks were investigated. Unweighted pairwise grouping method with mathematical averages (UPGMA) clustering and principal component analysis (PCA) were used to analyze the DGGE fingerprint. The Illumina sequences were assembled, predicted to genes and functionally annotated, and then classified by querying protein sequences of the genes against the Kyoto encyclopedia of genes and genomes (KEGG) database.ResultsMetagenomic sequencing showed that more than 85% of ribosomal RNA (rRNA) gene sequences belonged to the phylum Firmicutes and Bacteroidetes, indicating that the family Ruminococcaceae (46.5%), Rikenellaceae (11.3%), Lachnospiraceae (10.0%), and Bacteroidaceae (6.3%) were dominant gut microbes. Over 50% of non-rRNA gene sequences represented the metabolic pathways of amino acids (14.4%), proteins (12.3%), sugars (11.9%), nucleotides (6.8%), lipids (1.7%), xenobiotics (1.4%), coenzymes, and vitamins (3.6%). Gene functional classification showed that most of enzyme-coding genes were related to cellulose digestion and amino acids metabolic pathways.ConclusionYaks’ age had a substantial effect on gut microbial composition. Comparative metagenomics of gut microbiota in 0.5-, 1.5-, and 2.5-year-old yaks revealed that the abundance of the class Clostridia, Bacteroidia, and Lentisphaeria, as well as the phylum Firmicutes, Bacteroidetes, Lentisphaerae, Tenericutes, and Cyanobacteria, varied more greatly during yaks’ growth, especially in young animals (0.5 and 1.5 years old). Gut microbes, including Bacteroides, Clostridium, and Lentisphaeria, make a contribution to the energy metabolism and synthesis of amino acid, which are essential to the normal growth of yaks.

Highlights

Yak (Bos grunniens) is the only bovine species adapted to the special high-altitude ecological environment of the Qinghai-Tibet Plateau, and semi-domestic yaks provide the basic resources such as meat, milk, transportation, dung for fuel and hides for tented accommodation that are necessary for Tibetans and other nomadic pastoralists living there [1]
Comparative functional analysis of the gut microbiome from yaks To identify the functions encoded by the gut genome in the yaks, we annotated the metagenomic sequences according to the Kyoto encyclopedia of genes and genomes (KEGG) using a 1e-10 e-value, ≥60% identity threshold and a mini mum of 50 bp alignment length, and we identified a total of 6754 KEGG orthologous groups (KOs)
Functional representation of gut microbiota in yaks According to functional categories of the KOs identified, we found two types of functions among the range clusters: one is required in all bacteria and another potentially specific for gut bacteria

Summary

Introduction

Yak (Bos grunniens) is the only bovine species adapted to the special high-altitude ecological environment of the Qinghai-Tibet Plateau, and semi-domestic yaks provide the basic resources such as meat, milk, transportation, dung for fuel and hides for tented accommodation that are necessary for Tibetans and other nomadic pastoralists living there [1]. While there is the potential to resolve these problems by feeding supplementary silage forage with microbial agents to regulate the gastrointestinal microbiota of yaks, which may promote the normal growth of yaks. The microbial diversity and functional redundancy of gut microbial flora may contribute to the stability of this dynamic ecosystem. The metabolic potential of gut microbiota in ruminants produces energy from the extrac tion of indigestible carbohydrates (dietary fiber) and conversion of the host-derived substances, non-nutritive dietary components. The objective of present study was to reveal the dynamic changes of the gut microbial community during yaks’ growth and to understand the benefits of gut microbiota on nutrient meta bolism of hosts by PCR-DGGE and metagenomic sequencing, in order to assist the searching for potential probiotics which could be beneficial to yaks’ growth through supplementary feeding with these probiotics agents

Methods

Results

Conclusion