DOI: 10.5061/dryad.2v6wwpzzq
title: Gut feeling: Host and habitat as drivers of the microbiome in blackbuck (Antilope cervicapra)

description: 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.
description: # Gut feeling: Host and habitat as drivers of the microbiome in blackbuck
 (Antilope cervicapra)
 [https://doi.org/10.5061/dryad.2v6wwpzzq](https://doi.org/10.5061/dryad.2v6wwpzzq) ## Description of the data and file structure The dataset contains raw information about the extrinsic and intrinsic factors that influence the Blackbuck gut microbiome. It also has the accession numbers for the 16S rRNA gene sequence of the gut microbiome of the blackbuck and their corresponding haplotypes assessed in this study. ### Files and variables #### File: blackbuck\_population\_gg\_indiv\_dryad.csv **Description:**  ##### Variables * state: Indian State from where the samples were collected * sample_id: Internal sample ID of the Blackbuck * replicate: replicate ID per sampling location * blackbuck Genbank accession number: haplotype data of the blackbuck * microbe SRA number: 16S rRNA gene sequences of the blackbuck gut * location: name of the place from the samples were collected * longitude (degree East): GPS location * latitude (degree North): GPS location * blackbuck population density (per square km): estimated from field observations and personal communications from surveyors and forest department reports * blackbuck nucleotide diversity: average of the nucleotide differences per base position in the D loop region of the mitochondrial genome across all the pairs of sequences in the population * blackbuck heterozygosity: estimated following genotyping, the method to identify the alleles of each microsatellite * precipitation (mm): average precipitation at each sampling location for the sampling month from 2014 to 2019 * temperature (degree Celsius): average temperature  at each sampling location for the sampling month from 2014 to 2019 * distance to human settlement (meter): distance to the nearest human settlement from the sampling location of the blackbuck * Anthropogenic land-use (%): fraction of total land cover by agricultural lands, settlements, orchards and mixed plantations in 75 km2 area around each blackbuck population ## Access information Data was derived from the following sources: * NCBI SRA under BioProject ID: PRJNA1066065 * Genbank with Accession numbers OP794109 - OP794335