Composition of the gut Microbiota in the naturally parasitised yellow-necked mouse Apodemus flavicollis

The gut microbiota plays a crucial role in vital host functions, such as brain and immune system development. Emerging evidence indicates that parasitic helminths also interact with the gut microbiota to affect host functions. However, to date, the interaction between host, microbiota and helminths is not well studied. Wild rodents, such as the yellow-necked 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 mice (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 mammals' gastrointestinal microbiota. Most interestingly, our results at a lower taxonomic level suggest considerable variation in the composition of the microbiota colonizing the different parts of the gut. Further analyses will determine to what extent this result is related to the presence of parasitic helminths at these 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