Impact of Mycotoxins and Glyphosate residue on the Gut Microbiome and Resistome of European Fallow Deer

Abstract

Mycotoxins and herbicides residue significant threats to animal health. This study investigated the impact of these toxins on the gut microbiome of the fallow deer, a valuable game species. We analyzed the intestinal contents of deer exposed to varying levels of zearalenone (ZEA) and other mycotoxins and toxic compounds such as aflatoxins, deoxynivalenol, fumonisin B1 and glyphosate residues. Metagenomic analysis revealed significant alterations in the bacterial community composition, particularly in the abundance of specific taxa. Higher ZEA levels were associated with decreased alpha diversity, whereas higher aflatoxin levels had the opposite effect. We also observed changes in the abundance of antibiotic resistance genes (ARGs), suggesting a potential link between mycotoxin exposure and antimicrobial resistance. Furthermore, five complete bacterial genomes were assembled from the metagenomic data. These findings highlight the complex interplay between environmental toxins, the gut microbiota, and animal health. Understanding these interactions is crucial for developing strategies to mitigate the negative effects of toxin exposure on wildlife populations.