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


METHODS
The 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.


RESULTS
Metagenomic sequencing showed that more than 85% of ribosomal RNA (rRNA) gene sequences belonged to the phylumFirmicutesandBacteroidetes, indicating that the familyRuminococcaceae(46.5%),Rikenellaceae(11.3%),Lachnospiraceae(10.0%), andBacteroidaceae(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.


CONCLUSIONS
Yaks' 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 classClostridia,Bacteroidia, andLentisphaeria, as well as the phylumFirmicutes,Bacteroidetes,Lentisphaerae,Tenericutes, andCyanobacteria, varied more greatly during yaks' growth, especially in young animals (0.5 and 1.5 years old). Gut microbes, includingBacteroides,Clostridium, andLentisphaeria, make a contribution to the energy metabolism and synthesis of amino acid, which are essential to the normal growth of yaks.
Key Laboratory of Biological Resources and Ecological Environment, College of Life Sciences, Sichuan University, Chengdu, Sichuan, 610064, China.
Yuanyang
Y
Nie
Key Laboratory of Biological Resources and Ecological Environment, College of Life Sciences, Sichuan University, Chengdu, Sichuan, 610064, China.
Zhiwei
Z
Zhou
Sichuan Grassland Science Academy, Chengdu, Sichuan, 611731, China.
Jiuqiang
J
Guan
Key Laboratory of Biological Resources and Ecological Environment, College of Life Sciences, Sichuan University, Chengdu, Sichuan, 610064, China.
Baixue
B
Xia
Sichuan Grassland Science Academy, Chengdu, Sichuan, 611731, China.
Xiaolin
X
Luo
Key Laboratory of Biological Resources and Ecological Environment, College of Life Sciences, Sichuan University, Chengdu, Sichuan, 610064, China.
Yang
Y
Yang
Key Laboratory of Biological Resources and Ecological Environment, College of Life Sciences, Sichuan University, Chengdu, Sichuan, 610064, China.
Yu
Y
Fu
Key Laboratory of Biological Resources and Ecological Environment, College of Life Sciences, Sichuan University, Chengdu, Sichuan, 610064, China.
Qun
Q
Sun
Gut Microbiota; Metabolic Pathways; Metagenomic Sequencing; Polymerase Chain Reaction-Denaturing Gradient Gel Electrophoresis (PCR-DGGE); Yak