Metagenomic analysis reveals the composition and function of intestinal microbiota were affected by different sampling methods and digestive tract segments in monogastric and polygastric animals

Abstract

Background: As a domesticated species vital to humans, cow and donkey are raised worldwide as a source of agricultural industry and food production. The digestion and absorption must rely on the division of labor and cooperation of all the digestive tract segments and microbes. The microbiota plays an important role in the health, diseases, athletic performance, weight and digestion of food in animals. The composition and function of microbial community are closely related to the animals’ physiological structure. Moreover, experimental techniques, like the sampling method, could also influence the identification results. Results: Here, using approximately 300 GB of metagenomic sequencing data from digestive tract samples from 91 samples that represent six (donkeys) and nine (cows) digestive tract segment with swab and fecal samples of monogastric (donkeys) and polygastric (cows) animals. We assembled 4,004,115 (cow) and 2,938,653 (donkey) microbial metagenome assembled contigs, and obtained 9,060,744 genes with an average of 553bp (range 102bp ~ 10,912bp) were obtained by clustering at 95% identity and 90% coverage. There were certainly influences on the microbiota with two sampling methods and fecal sample was recommended due to more abundant diversity of species compared with swab sample. Besides, microbiota in the stomach was significantly different from other segments and colon held the most abundant bacteria in the other intestine. In addition, the microbial community structure of donkey was obviously different from cow for both dominant and endemic microbes. There were 1,942 genera that were characterized by high Lactobacillus, Clostridium and Prevotella in the donkey while 1,744 genera were recognized in the cow. Differ from the donkey, different segments of the cow had different dominate genera such Prevotellafor the stomach, Kandleria for the small intestine and Clostridium for the hindgut. Conclusions: Overall, we solved the scientific problem of fecal sample could more objectively reflect the intestinal microbial community. Meanwhile, the microbial composition showed the shared and distinct features of digestive tract segments in different type animals. Our experimental design and dataset provides a valuable resource for discovery of performance-enhancing microbes and systematic studies of cow and donkey microbiome.