Research Article: Microbial community and diversity in the feces of Sichuan takin (Budorcas taxicolor tibetana) as revealed by Illumina Miseq sequencing and quantitative real-time PCR

Date Published: April 27, 2018

Publisher: Springer Berlin Heidelberg

Author(s): Hui Zhu, Dong Zeng, Ning Wang, Li-li Niu, Yi Zhou, Yan Zeng, Xue-qin Ni.


The Sichuan takin (Budorcas taxicolor tibetana) is a rare and endangered ruminant distributed in the eastern Himalayas. However, little information is available regarding the intestinal microbiota of the takin. In this study, Illumina Miseq platform targeting the V4 region of the 16S rRNA was employed to characterize microbial community and diversity in the feces of wild (n = 6) and captive takins (n = 6). The takin exhibited an intestinal microbiota dominated by three phyla: Firmicutes (57.4%), Bacteroidetes (24.2%) and Proteobacteria (12.3%). At family/genus level, Ruminococcaceae, Bacteroidaceae, Acinetobacter, Clostridium, Lachnospiraceae, Rikenellaceae, Bacillus, Comamonas and Spirochaetaceae were dominant. Distinctive microbiotas between wild and captive takins were observed based on microbial community structure, captive takins having significantly higher community diversity. Quantitative real-time PCR were also utilized to monitor predominant bacteria in three Sichuan takin individuals housed in Chengdu Zoo over a half-year period, which showed that microbial communities of the three takins were relatively similar to each other and stable during our study period. Our results suggested that diet was a major driver for shaping microbial community composition.

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The microbial populations that reside in the digestive tract of animals are diverse and numerous. Generally, bacteria comprise 40–45% of fecal material on a dry weight basis with populations often exceeding 1011 colony-forming unit (CFU) per gram feces (Eckburg et al. 2005; Stephe and Cummings 1980). The bacteria of the animal gastrointestinal tract constitutes a complex ecosystem which is involved in host physiology, ranging from the structure and functions of the digestive system and the innate and adaptive immune systems, to host energy metabolism (Macfarlane and Macfarlane 2004). Conversely, the composition of the intestinal microbiota is also influenced by diet, social interactions, antibiotic use, host anatomy and phylogeny (Russell and Rychlik 2001; Ley et al. 2008b). Although there is a profound relationship between intestinal bacteria and animal health, this ecosystem of many herbivores remains incompletely characterized and its diversity poorly defined.

To our knowledge, the current work is the first comprehensive study to evaluate the fecal microbiota of the Sichuan takin. In order to effectively study their complex microbial community, Illumina Miseq sequencing and group-specific qPCR had been employed in this study. Based on the results of Illumina Miseq sequencing, the microbial communities of takins were mostly dominated by bacteria belonging to Firmicutes, Bacteroidetes and Proteobacteria, which comprised more than 90% of the total bacteria. These phyla were also dominant in feces from the cattle, muskoxen and sheep hindgut (De Oliveira et al. 2013; Salgadoflores et al. 2016; Zeng et al. 2017). At family/genus level, Ruminococcaceae, Bacteroidaceae, Acinetobacter, Clostridium, Lachnospiraceae, Rikenellaceae, Bacillus, Comamonas, Oscillospira and Spirochaetaceae constituted the major family/genus. Furet et al. also used qPCR for enumeration of fecal bacteria in human and farm animal (rabbits, goats, horses, pigs, sheep and cows) (Furet et al. 2009). In our study, the same range of populations for the total bacteria and dominant/subdominant bacterial groups like Clostridium, Blautia coccoides and Bacteroides–Prevotella group in sheep and cows were also found in takins. Thus, the fecal microbiota of the takin quite resembled that of cattle, muskoxen and sheep. From the phylogenetic perspective, the takin is in an intermediate position between the cattle and sheep. The takin has similar body size and metabolic requirements to cattle, while their external characteristics are rather similar to sheep. In captivity, the takin even had similar diet and living environment to these animals. All these factors might contribute to captive takin possessing a similar microbial profiles (Demment and Van Soest 1985; Ley et al. 2008b).




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