Microbiota characterisation in the Tasmanian devil
The Tasmanian devil (Sarcophilus harrisii), the world’s largest remaining carnivorous marsupial, faces extinction due to the spread of a contagious cancer called Devil Facial Tumour Disease (DFTD). The lack of a description of the bacterial community composition in the species represents a major gap in our knowledge of Tasmanian devil biology. In this study we characterised 12 microbiomes from four body sites, including mouth, gut, skin and pouch, in five Tasmanian devils via PCR amplification of 16S rRNA gene V1-V3 regions followed by 454 sequencing. A total of 249,224 reads with an average sequence length of 489 bp were obtained after length and quality filtering. The reads further clustered into 14533 operational taxonomic units (OTUs; sequence identity cutoff of >97%) that were classified to 24 phyla spanning 275 families. Higher levels of bacterial species richness were observed in the pouch and skin than in the mouth and gut. The pouch and skin showed similar microflora compositions, which may vary between animals, possibly due to different environments. Distinct from the previously reported koala gut microbiota , which is dominated by Bacteroidetes and Firmicutes, the devil gut microbiota was found to be dominated by Fusobacteria, Firmicutes and Proteobacteria, comprising up to 73.7-94.3% of the community. This study has greatly improved our understanding of the microbial communities in the Tasmanian devil, which will significantly contribute to the effort to conserve the species.