Gut feeling: host and habitat as drivers of the microbiome in blackbuck <i>Antilope cervicapra</i>

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. The intrinsic factors are nucleotide diversity (mitochondrial and nuclear) and blackbuck population density, whereas extrinsic factors are temperature, precipitation, distance to human settlement and anthropogenic land‐use. We determined which of these seven variables explains greater variation in the microbiome within (α‐diversity) and between (β‐diversity) the blackbuck hosts. We analysed the microbiome of n = 60 blackbuck hosts from ten different populations across India. We recorded 11 800 unique OTUs across 30 known phyla and 2.9 million reads. We find an average of 2056 OTUs per individual, with Bacillota and Bacteroidota being the most dominant phyla. Overall, we also show that the genetic diversity (intrinsic) of the host is more important than their environment (extrinsic) for both within‐ and between‐host variation in the microbiome of blackbuck. Our results suggest that an increase in genetic relatedness between blackbuck hosts can lead to a decrease in the variation of their gut microbial composition. 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.