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

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 11800 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.