Protocol for the assessment of the impact of mycotoxins and glyphosate residues on the gut microbiome and resistome of European fallow deer

Here, we present a protocol to describe the bacteriome of the intestinal content of toxin-exposed fallow deer. We describe steps for measuring fecal mycotoxin (deoxynivalenol, zearalenone, fumonisin B1, and aflatoxin B1) levels using liquid chromatography-mass spectrometry, as well as serum glyphosate. We then detail a short-read shotgun DNA sequencing-based bioinformatic pipeline for the toxin level-associated analysis of the bacteriome and resistome and the construction of metagenome-assembled bacterial genomes. This protocol has potential applications in further toxin level-associated metagenome studies. For complete details on the use and execution of this protocol, please refer to Tóth et al. 1 • Instructions for fecal mycotoxin and serum glyphosate measurements • Experimental steps for shotgun metagenomic sequencing of complex microbiological samples • Guidance on bioinformatic microbiome analysis Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. Here, we present a protocol to describe the bacteriome of the intestinal content of toxin-exposed fallow deer. We describe steps for measuring fecal mycotoxin (deoxynivalenol, zearalenone, fumonisin B1, and aflatoxin B1) levels using liquid chromatography-mass spectrometry, as well as serum glyphosate. We then detail a short-read shotgun DNA sequencing-based bioinformatic pipeline for the toxin level-associated analysis of the bacteriome and resistome and the construction of metagenome-assembled bacterial genomes. This protocol has potential applications in further toxin level-associated metagenome studies.