Data from: Fur seal microbiota are shaped by the social and physical environment, show mother-offspring similarities and are associated with host genetic quality

Despite an increasing appreciation of the importance of host-microbe
interactions in ecological and evolutionary processes, the factors shaping
microbial communities in wild populations remain poorly understood. We
therefore exploited a natural experiment provided by two adjacent
Antarctic fur seal (Arctocephalus gazella) colonies of high and low social
density and combined 16S rRNA metabarcoding with microsatellite profiling
of mother-offspring pairs to investigate environmental and genetic
influences on skin microbial communities. Seal-associated bacterial
communities differed profoundly between the two colonies, despite the host
populations themselves being genetically undifferentiated. Consistent with
the hypothesis that social stress depresses bacterial diversity, we found
that microbial alpha diversity was significantly lower in the high-density
colony. Seals from one of the colonies that contained a stream also
carried a subset of freshwater-associated bacteria, indicative of an
influence of the physical environment. Furthermore, mothers and their
offspring shared similar microbial communities, in support of the notion
that microbes may facilitate mother-offspring recognition. Finally, a
significant negative association was found between bacterial diversity and
heterozygosity, a measure of host genetic quality. Our study thus uncovers
a complex interplay between environmental and host genetic effects, while
also providing empirical support for the leash model of host control,
which posits that bacterial communities are driven not only by bottom-up
species interactions, but also by top-down host regulation. Taken
together, our findings have broad implications for understanding
host-microbe interactions as well as prokaryotic diversity in general.