Captivity conditions matter for the gut microbiota of an endangered obligate hibernator

Conservation breeding programmes include translocations of animals across breeding facilities, both in and ex situ, and to/from their natural habitat. Newly reintroduced Vancouver Island marmots (VIMs) originating from the captive breeding programme are known to experience high winter mortality once reintroduced. Whilst high winter mortality rates amongst reintroduced VIM populations remain a concern of unknown causes, this health issue could potentially be linked to changes in gut microbiota prior to hibernation. Furthermore, captivity is known to impact the gut microbiota of mammals that could be crucial for hibernation. In this study, we explored the diversity of bacterial communities in the gut of captive marmots during the entire active season, both kept in captivity at in situ and ex situ facilities, as well as free-ranging marmots during the summer period. Gut microbial diversity was higher in marmots held in ex situ facilities, outside of their habitat range, compared to captive marmots held within their habitat range, and in the wild, and differences in composition were also observed. In the entire active season, animals kept in the ex situ facility had increased abundance in taxa known to be mucin degraders, sulphate producers and possible cross-feeders, whilst an increase in fibre degraders of in situ and free-ranging marmots is potentially linked to diet variation between facilities. These results confirm the interest to transfer animals held at zoos to an in situ facility before relocation and expand our understanding of microbiota variation according to hibernation cycles in the context of conservation biology.