Gut microbiota of Vancouver Island marmots

Conservation breeding programs include translocations of animals across breeding facilities, both <em>in </em>and <em>ex situ</em>, and to/from their natural habitat. Newly reintroduced Vancouver Island marmots originating from the captive breeding program are known to experience high winter mortality. This health concern may be linked to changes in gut microbiota, which can affect metabolic rate prior to hibernation. Furthermore, captivity is known to impact the overall abundance of host-derived substrate degraders in the mammalian gut needed 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 <em>in situ </em>and <em>ex situ </em>facilities, as well as free-ranging marmots during the summer period. Gut microbial diversity was higher in marmots held in <em>ex situ</em> 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 <em>ex situ </em>facility had increased abundance in sulfate producers and possible cross-feeders, while an increase in amino acid metabolism, associated to fiber-degraders of <em>in situ </em>and free-ranging marmots is potentially linked to diet variation between facilities. KEGG pathways indicated that hibernation and captive location altered metabolic functions of gut microbiota of <em>Marmota vancouverensis</em>. These results confirm the interest to transfer animals held at zoos to an <em>in situ </em>facility before relocation and expand our understanding of microbiota variation around hibernation in the context of conservation biology.