Taxonomic and functional fingerprints in the gut microbiota of Iberian hare (Lepus granatensis) inhabiting organic and conventional farming fields.

Intensive farming leading to both landscape homogenization and massive use of pesticides is threatening biodiversity associated with agricultural landscapes. Pesticides may alter the composition of the gut microbiota, which contributes critically to a variety of host metabolic and immune functions, and the consequences on wildlife health are still unknown. We studied potential effects of farming practices on the gut microbiota of wild Iberian hare populations (Lepus granatensis) inhabiting conventional (synthetic pesticide-treated, mostly glyphosate) and organic (synthetic pesticide-free) farming areas in Central Spain. We analyzed duodenum, caecum, and rectum sections and fresh feces by massive 16S rRNA gene sequencing. Our study supports the use of fresh feces as a non-invasive proxy for monitoring dynamic changes in the gut community. The gut metacommunity under conventional farming showed higher richness and diversity (both ecological and phylogenetic) but with more homogeneous composition among hares (lower beta-dispersion) than the gut metacommunity detected in organic farming areas. We did not observe dysbiosis or significant enrichment in pathogenic bacteria. Potential negative effects on community-level abilities for vegetable fiber degradation were observed in conventional farming fields. Ruminococcaceae, which play a key role as cellulose degraders, showed significant lower relative abundances in conventional fields and lower potential for the butyrate metabolism. We show a gut index based on the ratio of fecal Ruminococcaceae that may be helpful for predictive environmental diagnostics. Further experimental research and in situ monitoring of gut microbiota are needed to substantiate these findings and to fully understand the potential undesired effects of synthetic pesticides in untargeted wildlife.