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

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.

Diet Transition from High-Forage to High-Concentrate Alters Rumen Bacterial Community Composition, Epithelial Transcriptomes and Ruminal Fermentation Parameters in Dairy Cows

“…A better understanding of the rumen microbiome under extensive feeding conditions is essential due to the complexity of the rumen ecosystem, as the manipulation of ruminal microbiota can improve feed efficiency and optimize rumen function [ 52 , 53 ]. Previous studies have demonstrated that changes in rumen microbial communities are affected by several factors, such as ruminant species, age, health, season, geographical location, feed additives, and diet [ 18 , 54 , 55 , 56 ]. Specifically, a diet switch from high forage to high concentrate will definitely cause an enormous change in the rumen bacterial community, which can negatively affect productivity and has the potential to develop metabolic disorders in ruminants [ 57 ].…”

Changes in the ruminal fermentation and bacterial community structure by a sudden change to a high-concentrate diet in Korean domestic ruminants

“…Studies on microbial communities and ruminal characteristics are important for understanding and manipulating the health and performance of ruminant animals. Previous studies have shown that changes in rumen microbial communities are affected by factors such as ruminant species, diet, age, health, feed additives, season, and geographical location [2,6,18,19]. In particular, a diet switch from high forage to high concentrate can cause a large change in the rumen bacterial community, which can affect productivity and the potential for metabolic disease in ruminants [20].…”

A Single Dose of Synbiotics and Vitamins at Birth Affects Piglet Microbiota before Weaning and Modifies Post-Weaning Performance

“…In our study, bacteria from the Victivillaceae family and Victivillales order, belonging to the Lentisphaeria class, were more abundant in the SUP+ piglets. The study results demonstrated that this class of bacteria may be involved in the nutrient metabolism of the host, especially in the metabolism of carbohydrates, peptides, and amino acids, and affecting protein utilization and providing beneficial metabolites [ 43 ]; thus, their presence is considered beneficial for the host [ 43 ].…”