Endangered Deep‐Snow Mountain Caribou Have a Distinct Winter Diet and Gut Microbiome That May Be Altered by Maternal Penning

ABSTRACT Understanding species‐ or population‐specific dietary specialisation is key to informing habitat conservation needs and successful ex situ recovery programs for many endangered species. One of the most endangered populations in Canada, the behaviourally distinct deep‐snow ecotype of the Southern Mountain caribou, is characterised by a winter diet of arboreal rather than terrestrial lichens. We hypothesised that this dietary variation would produce a distinct gut microbiome in deep‐snow mountain caribou relative to their shallow‐snow counterparts. We additionally hypothesised that the temporary alteration of natural diets for ex situ conservation programs, including the provision of commercial pelleted feed and volunteer‐collected lichens during maternity penning of pregnant cows, may alter this specialised microbiome. Here, we use faecal DNA metabarcoding to compare diet and gut microbiome composition among various herds of deep‐ and shallow‐snow caribou, captive deep‐snow caribou from the Revelstoke maternity pen, and semi‐domesticated reindeer. Our results confirm that free‐ranging deep‐snow caribou specialise on the arboreal hair lichens Bryoria and Nodobryoria, and we show that this correlates with a microbiome distinct from that of shallow‐snow caribou specialising on the terrestrial lichens Cladonia and Stereocaulon . We also show that maternity penning of deep‐snow caribou significantly altered forage consumption and microbiome composition: penned caribou consumed more foliose lichens and had a distinct microbiome compared to free‐ranging caribou. Our results suggest that managers should carefully consider the preferred forage of caribou populations when designing interventions that require diet modification. We further suggest that faecal samples of caribou and other dietary specialists be routinely monitored for diet and microbiome composition, especially during periods of captivity or diet modification, as an additional component of conservation assessments.