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.Electronic supplementary materialThe online version of this article (doi:10.1186/s13568-017-0378-1) contains supplementary material, which is available to authorized users.

Gut microbial diversity in two insectivorous bats: Insights into the effect of different sampling sources

“…The current study revealed significant differences of the microbial community composition (the alpha diversity) in different sampling sources (the large intestine, small intestine, and feces) in two bat species ( R. sinicus and M. altarium ) although no significant variations of beta diversity were observed. These results were in line with the previous studies in mice (Gu et al., ; Pang, Vogensen, Nielsen, & Hansen, ; Weldon et al., ), pigs (Looft et al., ; Mu et al., ), and sheep (Zeng et al., ). Observed differences across the sampling sources may be caused by environmental heterogeneity in different intestinal compartments and niches, such as different oxygen exposure, pH, and substrate availability (Hao & Lee, ).…”

“…Gut microbiota is often called the "forgotten organ" in its symbiotic host (O'Hara & Shanahan, 2006) and plays essential roles in food digestion, energy harvest, metabolism, and immune training of its host (Donaldson, Lee, & Mazmanian, 2016;Hooper, Littman, & Macpherson, 2012;Hooper, Midtvedt, & Gordon, 2002;Qin et al, 2010;Turnbaugh et al, 2006;Velagapudi et al, 2010). In mammals, large-scale studies of gut microbiota have been conducted in humans (Huttenhower et al, 2012;Lozupone, Stombaugh, Gordon, Jansson, & Knight, 2012;Saraswati & Sitaraman, 2015;Yatsunenko et al, 2012), mice (Gu et al, 2013;Tanca et al, 2017), other domestic animals such as pigs (Mu, Yang, Su, Zoetendal, & Zhu, 2017) and sheep (Zeng et al, 2017), and to a lesser extent in wild animals, such as bats (Chiroptera). Bats have been largely overlooked in terms of their gut microbiota although they represent the second largest mammalian order and over 20% of mammal species (Simmons, 2005).…”

Bizon Sindirim Sisteminden İzole Edilen Bacillus spp.’den Selülaz ve Ksilanaz Üretiminin Değerlendirilmesi

“…Results confirmed that the isolates were members of two major phyla namely Firmicutes (95.65%, the most dominant culturable rumen and dung microbiota) and Actinobacteria (4.35%) and three families Streptomycetaceae, Enterococcaceae and Bacillaceae. Our findings were parallel to those in earlier studies on microbiota from the gastrointestinal tract of ruminants [8,26] . Our results were also consistent with previous studies those isolated Bacillus species from the rumen, cow dung and Tibetan pig's intestine [27,28] .…”

Microbiome analysis as a platform R&D tool for parasitic nematode disease management

“…) Conversely, when comparing adult nematodes with ovine abomasal washings, 2494 shared ASVs of a possible 6936 unique ASVs were identified across both groups. Samples clustered definitively based on the host animal of origin.Next, we reviewed several recent studies that have profiled the ovine microbiome at various sites in the digestive tract according to the abundances of endogenous bacteria present(28,29). We then examined our own nematode microbiome data for the presence of bacteriafound in sheep in relatively high abundances.…”