Gut feeling: host and habitat as drivers of the microbiome in blackbuck (Antilope cervicapra)

Abstract

The gut microbiome can be shaped by both intrinsic host factors and extrinsic environmental factors. However, the relative importance of intrinsic and extrinsic factors in gut microbial composition has rarely been investigated, particularly for a single host across its natural range. Here, we characterise the gut microbiome of an endemic, endangered antelope, the blackbuck or Antilope cervicapra. We evaluated the influence of seven predictor variables, which were classified into intrinsic and extrinsic factors, on the gut microbiome. We determined which of these seven variables explains greater variation in the microbiome within (-diversity) and between ({beta}-diversity) the blackbuck host. We analysed the microbiome of 60 blackbuck hosts from ten different populations across India. We recorded 11800 unique OTUs across 30 known phyla and 2.9 million reads. We find an average of 2056 OTUs per individual, with firmicutes and bacteroidetes being the most dominant phyla. We find that nucleotide diversity (intrinsic), blackbuck population density (intrinsic), distance to human settlement (extrinsic), and anthropogenic land-use (extrinsic) explain within-host variation. In contrast, precipitation (extrinsic), nucleotide diversity, distance to human settlement, and anthropogenic land-use explain between-host variation. Overall, we also show that the genetic diversity of the host is more important than their environment for both within- and between-host variation in the microbiome, in blackbuck. Therefore, conservation efforts should be directed to not only preserve natural habitats but also increase the genetic pool of the blackbuck populations, which will positively impact their survival through diverse gut microbiomes.