First insights into the microbial diversity in the omasum and reticulum of bovine using Illumina sequencing

Abstract

The digestive systems of mammals harbor a complex gut microbiome, comprising bacteria and other microorganisms that confer metabolic and immunological benefits to the host. Ruminants that digest plant-based foods have a four-compartment stomach consisting of the rumen, reticulum, omasum, and abomasum. The microorganisms in the stomach are essential for providing the host with critical nutrients. However, the majority of these microorganisms are unknown species. The microbiome of the stomach is diverse, and the majority of these organisms cannot be cultured. Next-generation sequencing (NGS) combined with bioinformatic analysis tools have allowed the dissection of the composition of the microbiome in samples collected from a specific environment. In this study, for the first time, the bacterial composition in two compartments, the reticulum and the omasum, of bovine were analyzed using a metagenomic approach and compared to the bacterial composition of the rumen. These data will assist in understanding the biology of ruminants and benefit the agricultural industry. The diversity and composition of the bacterial community in samples collected from the rumen, reticulum, and omasum of bovines in the Changchun Region of Northeast China were analyzed by sequencing the V3 region of the 16S rRNA gene using a barcoded Illumina paired-end sequencing technique, and the primary composition of the microbiome in the rumen, reticulum, and omasum of the bovines was determined. These microbiomes contained 17 phyla and 107 genera in all three samples. Five phyla, Bacteroidetes, Firmicutes, Proteobacteria, Spirochaetes, and Lentisphaerae, were the most abundant taxonomic groups. Additionally, the different stomach compartments harbored different compositions of the microorganisms.

Fig. 1

The number of tags at the different taxonomy levels obtained from each sample. Each bar represents the number of tags that were assigned to the taxonomic level for the identified bacteria

Fig. 2

The relative distribution of the seven most abundant phyla in the three stomachs. The percentage of the 16S V3 sequences assigned to a given phylum is represented by the color-coded bars. The seven most abundant phyla representing more than 98 % of the bacteria identified in the three samples are presented separately, whereas the remaining phyla are indicated as “others”

Fig. 3

The distribution of the microbiota identified in the three stomachs at the genus level. Each bar represents the number of sequence tags of a bacterial genus from the sample

Fig. 4

The taxonomy of the microbiota identified from phylum to genus in the three stomachs. The bacteria that were only identified in one or two stomachs are indicated underneath each taxonomy in parentheses

Fig. 5

The microbiome shared by the stomachs at the genus level. The number of genera unique to each stomach or shared by two or three stomachs is indicated

Fig. 6

The distribution of top ten most abundant genera in the three stomachs: a rumen, b omasum, and c reticulum