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

Tóth, Adrienn Gréta and Paholcsek, Melinda and Solymosi, Norbert and Stágel, Anikó and Gömbös, Patrik and Posta, Katalin and Lakatos, István and Nagy, Sára Ágnes and Ferenczi, Szilamér and Szőke, Zsuzsanna (2026) Protocol for the assessment of the impact of mycotoxins and glyphosate residues on the gut microbiome and resistome of European fallow deer. STAR PROTOCOLS, 7 (2). ISSN 2666-1667

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Abstract

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.

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