Abstract
Diseases of the gastrointestinal tract due to changes in the bacterial flora have been described with increasing incidence in the European brown hare. Despite extensive demographic and phylogeographic research, little is known about the composition of its gut microbiota and how it might vary based on potential environmental or host factors. We analysed the intestinal and faecal microbiota of 3 hare populations by Illumina MiSeq 16S rRNA gene amplicon sequencing. The phyla and OTU abundance composition differed significantly between intestinal and faecal samples (PERMANOVA: P = 0.002 and P = 0.031, respectively), but in both sample types Firmicutes and Bacteroidetes dominated the microbial community composition (45.51% and 19.30% relative abundance). Intestinal samples contained an enrichment of Proteobacteria compared with faecal samples (15.71-fold change, P < 0.001). At OTU level, a significant enrichment with best BLAST hits to the Escherichia-Shigella group, Eubacterium limosum, Sphingomonas kyeonggiensis, Flintibacter butyricus and Blautia faecis were detected in intestinal samples (P < 0.05). In our statistical model, geographic location and possibly associated environmental factors had a greater impact on the microbiota composition than host factors. Population had a significant effect on the composition of abundant intestinal and faecal OTUs, and on the abundance of potential pathogenic bacteria of the family Enterobacteriaceae, regularly associated with intestinal dysbiosis in hares, in faecal samples. Our study is the first to describe the microbiota in brown hares and provides a foundation to generate hypothesis aiming to test the role of gut health in population fluctuations of the species.
Highlights
The European brown hare (EBH) (Lepus europaeus) is a widely distributed and important game species throughout Europe
Reads generated for intestinal and faecal samples were distributed homogenously, with 53% reads belonging to intestinal and 47% belonging to faecal samples
Intestinal samples contained an enrichment of Proteobacteria compared with faecal samples (15.71fold change, P < 0.001) and more Actinobacteria (2.09-fold change, P = 0.002)
Summary
The European brown hare (EBH) (Lepus europaeus) is a widely distributed and important game species throughout Europe. The role of environmental factors, such as lifestyle, diet, climate and habitat conditions, as well as changes in land use are described to impact the microbial composition in the gastrointestinal tract (GIT)[31,32,33]. This knowledge cannot be transferred to wildlife species. Studies investigating the gut microbiota of free-ranging wildlife are rare and baseline data of potentially influencing factors of microbial community composition, abundance of specific bacterial taxa associated with host health in wildlife species is lacking[30,33,35,36]. By the use of these molecular high-throughput techniques and community analysis we aimed to identify and describe the gut microbiota, a goal that could not be achieved by previous culture- and/or enrichment-dependent methods
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