Abstract
The current study provides the insight into the bacteria in the gastrointestinal tract (GIT) and methanogens presented in the rumen and cecum of the Chinese roe deer (Capreolus pygargus). The ruminal, ileal, cecal, and colonic contents, as well as feces, were obtained from each of the three, free-range, roe deer ingesting natural pasture after euthanasia. For the bacterial community, a total of 697,031 high-quality 16S rRNA gene sequences were generated using high-throughput sequencing, and assigned to 2,223 core operational taxonomic units (OTUs) (12 bacterial phyla and 87 genera). The phyla Firmicutes (51.2%) and Bacteroidetes (39.4%) were the dominant bacteria in the GIT of roe deer. However, the bacterial community in the rumen was significantly (P<0.01) different from the other sampled regions along the GIT. Secondly, Prevotella spp., Anaerovibrio spp., and unidentified bacteria within the families Veillonellaceae and Paraprevotellaceae were more abundant in the rumen than in the other regions. Unidentified bacteria within the family Enterobacteriaceae, Succinivibrio spp., and Desulfovibrio spp. were more predominant in the colon than in other regions. Unidentified bacteria within the family Ruminococcaceae, and Bacteroides spp. were more prevalent in the ileum, cecum and fecal pellets. For methanogens in the rumen and cecum, a total of 375,647 high quality 16S rRNA gene sequences were obtained and assigned to 113 core OTUs. Methanobrevibacter millerae was the dominant species accounting for 77.3±7.4 (S.E) % and 68.9±4.4 (S.E) % of total sequences in the rumen and cecum of roe deer, respectively. However, the abundance of Methanobrevibacter smithii was higher in the rumen than in the cecum (P = 0.004). These results revealed that there was intra variation in the bacterial community composition across the GIT of roe deer, and also showed that the methanogen community in the rumen differed from that in the cecum.
Highlights
The rumen is inhabited by a dense and diverse consortium of microorganisms, including bacteria, archaea, protozoa and fungi that have a symbiotic relationship with the ruminant, with bacteria playing the critical role in biomass degradation [1]
The results showed that 697,031 high-quality bacterial sequences were assigned to 2,223 core operational taxonomic units (OTUs) ranging from 1,331 to 2,705 OTUs for each sample (Table 1)
375,647 high-quality methanogen 16S rRNA gene sequences were assigned to 113 core OTUs, with the range of 102 and 111 OTUs for each sample (Table 1)
Summary
The rumen is inhabited by a dense and diverse consortium of microorganisms, including bacteria, archaea, protozoa and fungi that have a symbiotic relationship with the ruminant, with bacteria playing the critical role in biomass degradation [1]. This has led to a variety of studies investigating rumen bacterial structure in domesticated ruminants, such as cows, sheep, yak, reindeer and sika deer [2,3,4,5,6]. Understanding the structure of the bacterial communities in the GIT of roe deer could improve our understanding of the breadth of microbial diversity in wild ruminants, and may be useful for developing new livestock management technologies, in nutrition and sustain ability systems
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