Effect of supplemental winter feeding on the ruminal bacterial microbiota of roe deer (Capreolus capreolus).

Temperate zone ungulates such as the roe deer face seasonally varying climatic conditions as well as food availability and quality. In some European countries, it is a common practice to provide wildlife with supplemental feeding in winter. We hypothesized that supplemental feeding would significantly affect the composition of the bacterial rumen community, which provides the ruminant host with energy through fermentation of nutrients and production of metabolites. We analyzed the rumen bacterial microbiota composition of eight adult female roe deer by Illumina MiSeq 16S rRNA amplicon sequencing. Furthermore, we compared those from a study area with supplemental feeding sites (n=4), to those not provided with supplemental winter feeding (n=4). DNA extraction was performed from three different substrates: rumen liquid phase, rumen solid phase and rumen wall. Fluorimeter measurements, PCR and qPCR were performed to evaluate the quantity of DNA extracted. We found a significant qualitative difference between the microbiota composition of the two populations studied: easily fermentable supplemental feeding reduced species richness, possibly promoting the proliferation of certain phylotypes (e.g Prevotella-OTU). Our results furthermore confirm that in roe deer, like in other ruminant species, the most represented phyla are Firmicutes (60%) and Bacteroidetes (19%), and that the ruminal microenvironments influence the microbial community composition.