Early sexual dimorphism in the developing gut microbiome of northern elephant seals

The gut microbiome is an integral part of a species’ ecology, but we know
little about how host characteristics impact its development in wild
populations. Here, we explored the role of such intrinsic factors in
shaping the gut microbiome of northern elephant seals during a critical
developmental window of six weeks after weaning, when the pups stay ashore
without feeding. We found substantial sex-differences in the early-life
gut microbiome, even though males and females could not yet be
distinguished morphologically. Sex and age both explained around 15% of
the variation in gut microbial beta diversity, while microbial communities
sampled from the same individual showed high levels of similarity across
time, explaining another 40% of the variation. Only a small proportion of
the variation in beta diversity was explained by health status, assessed
by full blood counts, but clinically healthy individuals had a greater
microbial alpha diversity than their clinically abnormal peers. Across the
post-weaning period, the northern elephant seal gut microbiome was highly
dynamic. We found evidence for several colonisation and extinction events
as well as a decline in Bacteroides and an increase in Prevotella, a
pattern that has previously been associated with the transition from
nursing to solid food. Lastly, we show that genetic relatedness was
correlated with gut microbiome similarity in males but not females, again
reflecting early sex-differences. Our study represents a naturally
diet-controlled and longitudinal investigation of how intrinsic factors
shape the early gut microbiome in a species with extreme sex differences
in morphology and life history.