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

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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13568-018-0599-y) contains supplementary material, which is available to authorized users.