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While the effects on host metabolism and rumen function have been described, the impact on the rectal microbiome remains poorly understood. In this study, we performed whole-genome shotgun metagenomic sequencing on fecal samples collected before and after a 30-day toxic fescue seed supplementation from eight pregnant Angus \u00d7 Simmental cows and heifers. We generated 157 Gbp of sequencing data in 16 metagenomes, and assembled 13.1 Gbp de novo microbial contigs, identifying 22 million non-redundant microbial genes from the cattle rectum microbiome. Fescue toxicosis significantly reduced alpha diversity (p &lt; 0.01) and altered beta diversity (PERMANOVA p &lt; 0.01), indicating microbial dysbiosis. We discovered significant enrichment of 31 bacterial species post-treatment, including multiple core rumen taxa. Ruminococcaceae bacterium P7 showed an average of 16-fold increase in fecal abundance (p &lt; 0.01), making it the top-featured species in linear discriminant analysis. Functional pathway analysis revealed a shift from energy metabolism to antimicrobial resistance and DNA replication following toxic seed consumption. Comparative analysis showed increased representation of core rumen taxa in rectal microbiota post-treatment, suggesting disrupted rumen function. These findings demonstrate that fescue toxicosis alters both the composition and functional landscape of the hindgut microbiota. Ruminococcaceae bacterium P7 emerges as a promising biomarker for monitoring fescue toxicosis through non-invasive fecal sampling, with potential applications in herd-level diagnostics and mitigation strategies.<\/jats:p>","DOI":"10.3390\/biology14091197","type":"journal-article","created":{"date-parts":[[2025,9,5]],"date-time":"2025-09-05T12:18:18Z","timestamp":1757074698000},"page":"1197","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["Metagenomic Analysis Revealed Significant Changes in the Beef Cattle Rectum Microbiome Under Fescue Toxicosis"],"prefix":"10.3390","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4091-3168","authenticated-orcid":false,"given":"Gast\u00f3n F.","family":"Alfaro","sequence":"first","affiliation":[{"name":"Department of Animal Sciences, College of Agriculture, Auburn University, Auburn, AL 36849, USA"},{"name":"Department of Animal Sciences, Faculty of Agricultural Sciences, National University of C\u00f3rdoba, C\u00f3rdoba 5000, Argentina"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yihang","family":"Zhou","sequence":"additional","affiliation":[{"name":"Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL 36849, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wenqi","family":"Cao","sequence":"additional","affiliation":[{"name":"Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL 36849, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yue","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL 36849, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2128-9512","authenticated-orcid":false,"given":"Soren P.","family":"Rodning","sequence":"additional","affiliation":[{"name":"Department of Animal Sciences, College of Agriculture, Auburn University, Auburn, AL 36849, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Russell B.","family":"Muntifering","sequence":"additional","affiliation":[{"name":"Department of Animal Sciences, College of Agriculture, Auburn University, Auburn, AL 36849, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wilmer J.","family":"Pacheco","sequence":"additional","affiliation":[{"name":"Department of Poultry Science, College of Agriculture, Auburn University, Auburn, AL 36849, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1776-8721","authenticated-orcid":false,"given":"Sonia J.","family":"Mois\u00e1","sequence":"additional","affiliation":[{"name":"Department of Animal Science, University of Tennessee, Knoxville, TN 37996, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7594-5004","authenticated-orcid":false,"given":"Xu","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL 36849, USA"},{"name":"Center for Advanced Science, Innovation and Commerce, Alabama Agricultural Experiment Station, Auburn, AL 36849, USA"},{"name":"HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,9,5]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Young, C.A., Charlton, N.D., Takach, J.E., Swoboda, G.A., Trammell, M.A., Huhman, D.V., and Hopkins, A.A. 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