Composition of the gut microbiota of the yellow-necked mouse, Apodemus flavicollis

The gut microbiota plays a key role in the development of vital host functions, such as the immune system. Emerging evidence indicates that pathogens and parasitic helminths also interact with the microbiota to affect host development. However, to date, the interaction between host, microbiota and helminths is not well studied. Wild rodents, such as the yellownecked mouse, are naturally parasitized, and thus represent a promising model to start to address this question. As such, we have investigated the variability of the gut microbiota in five distinct locations of the gut, where parasites are commonly found. We analysed the variability of the gut microbial community in the small intestine, caecum, proximal and distal colon within fifteen yellow-necked mouse Apodemus flavicollis. A higher proportion of reads were assigned to the order Bacteroidales and Clostridiales in faecal samples and the caecum, whereas the small intestine and intestinal membrane were dominated by Lactobacilliales. These results at the class and order level are consistent with previous analyses of other mammal’s gastrointestinal microbiota. Most interestingly, our results at a lower taxonomic level suggest considerable variation in the composition of the microbiota colonizing the digestive tract, and further analyses will allow us to establish to what extent this result is related to the presence of parasites colonizing those locations. To our knowledge this study is the first providing insight into compartment-dependent variation of gastrointestinal microbiota composition in a wild rodent non-captive population