Host’s fitness can be affected by its genotype and gut microbiota, defined as the microbes living in the host’s intestinal tract. This study explored how the genetic diversity of the host influences its bacterial communities in the context of captive breeding programs, for the critically endangered European mink (Mustela lutreola). As stated by the ecosystem on a leash model, mechanisms such as inbreeding depression may lead to changes in immunomodulation and will therefore induce modifications of the gut microbiota. We investigated variation in the gut bacteria through 16S rRNA metabarcoding, related to the genetic diversity of European mink held in captivity in two breeding centers representing separate breeding stocks originating from the western and eastern populations. The genetic diversity of the host was assessed through diversity analysis of the adaptive MHC class I and II genes as well as neutral microsatellite markers. Results indicate lower diversity in neutral and MHC class I genes for the western population, and the opposite for MHC class II. A lower MHC class II gene variability led to an increase in microbial phylogenetic diversity and in abundance depending on the presence of specific MHC-II motifs. This shows the importance of integrating both neutral and adaptive markers when investigating genetic variation in the context of ex situ conservation, as well as gut microbial community assessment. We advocate for more natural mating systems in captive breeding program to foster genetic diversity as a whole to mitigate the effects of genetic drift on those small, isolated populations.

Ecological theory postulates that the niche of co-occurring species must differ along some ecological dimensions in order to allow their stable coexistence. Yet, many biological systems challenge this competitive exclusion principle. For instance, insectivorous bats from the Northern Hemisphere typically form local assemblages of multiple species sharing highly similar functional traits and pertaining to identical feeding guilds. Although their trophic niche can be accessed with unprecedented details using genetic identification of prey, the underlying mechanisms of resource partitioning remain vastly unexplored. Here, we studied the differential diet of three phenotypically and phylogenetically closely-related bat species of the genus Plecotus in an area of sympatry and throughout their entire breeding season (April-October) using DNA metabarcoding. Even at such a small geographic scale, we identified strong seasonal and spatial variation of their trophic niche at both intra- and inter-specific levels. Indeed, while the different bats fed on a distinct array of prey during spring, they showed higher niche overlap during summer and fall, when all three bat species switched their hunting behavior to feed on few temporarily abundant moths. Furthermore, by considering the ecological traits of prey species, we inferred from the menu of each bat species that feeding grounds and hunting techniques differed suggesting that niche partitioning was primarily habitat-driven. As predicted by their phylogenetic relationships, the two most-closely related bat species exhibited the most distinct foraging habitat preferences, while the third, more distantly-related species was more generalist. These results highlight the need of extensive samples to fully understand species coexistence.