Bacterial community and diversity in the rumen of 11 Mongolian cattle as revealed by 16S rRNA amplicon sequencing

Abstract

Through microorganism in the rumen of ruminant, plant fiber can be converted to edible food such as meat and milk. Ruminants had a rich and complex microbial community within the rumen, and the bacteria comprised the dominant proportion of the ruminal microbes. High-throughput sequencing offered a viable solution for the study of rumen microbes. In this study, rumen fluid samples were taken from 11 cattle from Inner Mongolian, the DNA of 11 rumen fluid samples were extracted and bacterial amplicons of the V4 regions of 16S rRNA were subjected to Illumina sequencing. More than 90,000 raw reads and 60,000 effect Tags per sample were obtained. 28,122 operational taxonomic units (OTUs) were observed from 11 samples, in average 2557 ± 361 OTUs for each sample. Bacteroidetes (44.41 ± 7.31%), Firmicutes (29.07 ± 3.78%), and Proteobacteria (7.18 ± 5.63%) were the dominant phyla among the bacteria of rumen, accounting for 82%. At the genus level, the highest relative abundance was Prevotella. Their functions were predicted using the Kyoto Encyclopedia of Genes and Genomes (KEGG). The results showed that they included metabolism, genetic information processing, environmental information processing and cellular processes. It explored the bacterial community diversity and composition of the rumen of Mongolian cattle. On the whole, our research showed that there was a high diversity as well as rich bacterial flora function of rumen bacteria in Mongolian cattle. Meanwhile, these findings provided information for further studies on the relationship between the community, diversity, functions of rumen bacteria and the nutritional physiological functions of the host.

Figure 1

Rarefaction curves of 11 samples. Note: Rarefaction curves showing the number of species versus the number of sequences in per sample.

Figure 2

Beta diversity analysis of ruminal microbiome in 11 samples. Note: (A) Principal co-ordinates analysis (PCoA) based on weighted UniFrac distance of samples. (B) UPGMA clustering tree based on weighted UniFrac distance.

Figure 3

Distribution of species among the 11 samples. Note: (A) Relative abundance of rumen microbial communities at phylum level. (B) Relative abundance of rumen microbial communities at genus level. (C) Species abundance clustering heat map.

Figure 4

Phylogenetic tree constructed from representative sequences of genus level species. Note: The tree shows phylogenetic relationship of top 100 genus, the color of branches represented their corresponding phyla, and each color represented a phylum.

Figure 5

Functional forecasting through the Tax4Fun. Note: (A) Predicted function annotation relative abundance histogram at KEGG level 1. (B) Heat map of functional relative abundance clustering at KEGG level 2.