Microbial community compositions in the gastrointestinal tract of Chinese Mongolian sheep using Illumina MiSeq sequencing revealed high microbial diversity

Abstract

Chinese Mongolian sheep are an important ruminant raised for wool and meat production. However, little is known about the microbiota of the gastrointestinal tract (GIT) of Chinese Mongolian sheep. To increase our understanding of the microbial community composition in the GIT of Chinese Mongolian sheep, microbiota of five sheep is investigate for the first time using the Illumina MiSeq platform. High microbial diversity was obtained from the GIT, and the microbiota exhibited a higher biodiversity in the stomach and large intestine than in the small intestine. Firmicutes (44.62%), Bacteroidetes (38.49%), and Proteobacteria (4.11%) were the three most abundant phyla present in the GIT of the sheep. The present study also revealed the core genera of Prevotella, Bacteroides, Ruminococcus, Oscillospira, Treponema, and Desulfovibrio in the GIT. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States indicated that the metabolic pathway related to carbohydrate metabolism was the richest in the sheep GIT. In addition, a series of metabolic pathways related to plant secondary metabolism was most abundant in the stomach and large intestine than in the small intestine. Overall, the present study provides insight into the microbial community composition in GIT of the Chinese Mongolian sheep which is highly diverse and needs to be studied further to exploit the complex interactions with the host.

Keywords: Chinese Mongolian sheep; Gastrointestinal tract; Illumina MiSeq; Metabolic pathways; Microbiota.

Fig. 1

The PCoA analysis of the GIT samples (unweighted UniFrac metric). The colored circles represent the gut microbiota from the rumen, reticulum, omasum, abomasum, duodenum, jejunum, ileum, cecum, colon, and rectum, respectively

Fig. 2

The heatmap of beta diversity of samples. The different color intensities represent the relative bacteria abundance in each sample. The number following the sample names stand for the sheep number. For example, reticulum 1, reticulum 2, reticulum 3, reticulum 4, and reticulum 5 stands for the reticulum samples from the 1st, 2nd, 3rd, 4th, and 5th sheep

Fig. 3

GIT microbiota at the phylum and genus level. Relative abundance of OTUs at the phylum level in individuals (a). Relative abundance of OTUs from Firmicutes (b) and Bacteroidetes (c) at the genus level in individuals. Only phyla or genera with greater than 1% representation are shown

Fig. 4

Venn diagrams of shared OTUs and bacterial genera. The shared OTUs between the stomach, small intestine, and large intestine microbiomes (a). The unique and shared bacterial genera (with the percentage of >1% colonized in segment) at the genus level in the sheep GIT (b)

Fig. 5

Predicted function of the gut micorbiota in the sheep of GIT. KEGG pathways were shown in two heatmaps. The bootstrap Mann–Whitney u-test was used to detect the gene distribution with cutoffs of P < 0.05, FDR <0.2, Mean counts >10,000 (a) and P < 0.01, FDR <0.1, Mean counts >10 (b)