Bacteria and Methanogens Differ along the Gastrointestinal Tract of Chinese Roe Deer (Capreolus pygargus)

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.

Bacterial community composition and fermentation in the rumen of Xinjiang brown cattle (Bos taurus), Tarim red deer (Cervus elaphus yarkandensis), and Karakul sheep (Ovis aries)

“…This result was consistent with the findings for other ruminant species, including Bovinae, Cervidae, Caprinae, Camelidae and Giraffidae (Henderson et al 2015). Moreover, the predominant bacteria in the rumen of red deer were similar to those in elk, white-tailed deer, roe deer, sika deer, reindeer and moose (Gruninger et al 2014;Ishaq and Wright 2014;Li et al 2013;Li et al 2014;Sundset et al 2007). This result suggest an effect on rumen microbiota by host genetics (Moeller et al 2013).…”

First report of foregut microbial community in proboscis monkeys: are diverse forests a reservoir for diverse microbiomes?

“…The five most abundant phyla in the foregut were Bacteroidetes (8.5%–47% of bacterial reads), Firmicutes (16%–82%) and Proteobacteria (1.5%–68%), followed by Actinobacteria (1.4%–4.7%) and Spirochaetes (1.0%–3.1%) (Fig. B), indicating that the foregut microbial community does not deviate substantially from that previously found in captive colobines (Zhou et al ., ; Amato et al ., ) or other foregut fermenters (Pope et al ., ; Dai et al ., ; Godoy‐Vitorino et al ., ; Gruninger et al ., ; Ishaq and Wright, ; Kohl et al ., ; Li et al ., ; Roggenbuck et al ., ; Cersosimo et al ., ; Henderson et al ., ; Dill‐McFarland et al ., ; Salgado‐Flores et al ., ; Shinohara et al ., ). Cyanobacteria reads, possibly derived from plant chloroplast DNA (Clayton et al ., ), were generally detected in the free‐ranging individuals in this study (1.8%–5.8%, but 0.4% in the captive individual).…”

“…Prevotella was higher in the foregut of free‐ranging proboscis monkeys in the riverine forest, that had a more diverse (and possibly better) diet than those living in mangrove forest, consistent with the fact that Prevotella increases in the foregut of cattle fed more energy‐rich diets (McCann et al ., ). A similar foregut microbial pattern (more Prevotella but less Bacteroides ) has been reported not only in a captive golden snub‐nosed monkey ( Rhinopithecus roxellana ), which is one of the species phylogenetically closest to the proboscis monkey (Zhou et al ., ), but also in other foregut‐fermenting animals such as moose ( Alces alces ) (Ishaq and Wright, ) and roe deer ( Capreolus pygargus ) (Li et al ., ). More metagenomic and functional analyses of these bacterial groups will help in the understanding of the specialized physiology of leaf‐eating foregut fermenters.…”

A Post-Genomic View of the Ecophysiology, Catabolism and Biotechnological Relevance of Sulphate-Reducing Prokaryotes

“…In particular, members of the Desulfovibrionaceae have recently been identified in the intestines of the Chinese roe deer Capreolus pygargus (Li, Zhang, Xu, et al, 2014) and Pekin/Muscovy ducks (Vasaï et al, 2014), the digestive tract of the medicinal leech Hirudo verbena (Maltz et al, 2014) and larvae of the beetle Holotrichia parallela (Huang & Zhang, 2013), faecal samples of Mexican black howler (Alouatta pigra) monkeys (Nakamura et al, 2011) and chickens from Czech poultry farms (Videnska et al, 2014), homogenates of the deep-sea sponge Geodia spp. (Brück et al, 2010) and Asbestopluma hypogea (Dupont, Corre, Li, Vacelet, & BourguetKondracki, 2013).…”