Microbiota and nutrient portraits of European roe deer (Capreolus capreolus) rumen contents in characteristic southern German habitats

Abstract Roe deer (Capreolus capreolus) are now found in various habitat types, from pure forest cultures to agricultural areas and mountains. In adapting to the geographically and seasonally differentiating food supply, they depend, above all, on an adapted microbiome. However, knowledge about the microbiome of wild ruminants is still minimal, and there are a few publications for individual species with a low number of samples. This study investigated the rumen content of roe deer from seven different characteristic Bavarian habitat types. The focus was on the composition of nutrients, fermentation products, and the rumen bacterial community. To guarantee a high informative value, a total of 311 roe deer samples were analysed. Significant differences in nutrient concentrations and microbial composition were identified for the factor’s habitat, season and age class. These adaptations in the microbiota can be recognized, on the one hand, by specific concentrations of nutrients, and on the other hand, by strong fluctuations in the ingested forage. In addition, a core bacterial community could be identified, which forms the main component of the microbiota in each habitat. As with all wild ruminants, a large proportion of the microbial genera remain largely unclassified at various taxonomic levels. This study provides a more in-depth insight into the diversity and complexity of the roe deer rumen microbiota. It highlights the key microorganisms responsible for the conversion of naturally available nutrients of different botanical origins.