{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,28]],"date-time":"2026-09-28T18:07:59Z","timestamp":1790618879019,"version":"4.1.0"},"reference-count":129,"publisher":"MDPI AG","issue":"11","license":[{"start":{"date-parts":[[2021,11,16]],"date-time":"2021-11-16T00:00:00Z","timestamp":1637020800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001665","name":"Agence Nationale de la Recherche","doi-asserted-by":"publisher","award":["ANR-11-LABX-0048"],"award-info":[{"award-number":["ANR-11-LABX-0048"]}],"id":[{"id":"10.13039\/501100001665","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Animals"],"abstract":"<jats:p>Antibiotics are major disruptors of the gastrointestinal microbiota, depleting bacterial species beneficial for the host health and favoring the emergence of potential pathogens. Furthermore, the intestine is a reactor of antibiotic resistance emergence, and the presence of antibiotics exacerbates the selection of resistant bacteria that can disseminate in the environment and propagate to further hosts. We reviewed studies analyzing the effect of antibiotics on the intestinal microbiota and antibiotic resistance conducted on animals, focusing on the main food-producing and companion animals. Irrespective of antibiotic classes and animal hosts, therapeutic dosage decreased species diversity and richness favoring the bloom of potential enteropathogens and the selection of antibiotic resistance. These negative effects of antibiotic therapies seem ineluctable but often were mitigated when an antibiotic was administered by parenteral route. Sub-therapeutic dosages caused the augmentation of taxa involved in sugar metabolism, suggesting a link with weight gain. This result should not be interpreted positively, considering that parallel information on antibiotic resistance selection was rarely reported and selection of antibiotic resistance is known to occur also at low antibiotic concentration. However, studies on the effect of antibiotics as growth promoters put the basis for understanding the gut microbiota composition and function in this situation. This knowledge could inspire alternative strategies to antibiotics, such as probiotics, for improving animal performance. This review encompasses the analysis of the main animal hosts and all antibiotic classes, and highlights the future challenges and gaps of knowledge that should be filled. Further studies are necessary for elucidating pharmacodynamics in animals in order to improve therapy duration, antibiotic dosages, and administration routes for mitigating negative effects of antibiotic therapies. Furthermore, this review highlights that studies on aminoglycosides are almost inexistent, and they should be increased, considering that aminoglycosides are the first most commonly used antibiotic family in companion animals. Harmonization of experimental procedures is necessary in this research field. In fact, current studies are based on different experimental set-up varying for antibiotic dosage, regimen, administration, and downstream microbiota analysis. In the future, shotgun metagenomics coupled with long-reads sequencing should become a standard experimental approach enabling to gather comprehensive knowledge on GIM in terms of composition and taxonomic functions, and of ARGs. Decorticating GIM in animals will unveil revolutionary strategies for medication and improvement of animals\u2019 health status, with positive consequences on global health.<\/jats:p>","DOI":"10.3390\/ani11113280","type":"journal-article","created":{"date-parts":[[2021,11,16]],"date-time":"2021-11-16T10:23:17Z","timestamp":1637058197000},"page":"3280","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":32,"title":["Impact of Antibiotic Therapies on Resistance Genes Dynamic and Composition of the Animal Gut Microbiota"],"prefix":"10.3390","volume":"11","author":[{"given":"Tony","family":"Rocheg\u00fce","sequence":"first","affiliation":[{"name":"Unit\u00e9 Antibior\u00e9sistance et Virulence Bact\u00e9riennes (AVB), ANSES\u2014Universit\u00e9 de Lyon 1, 31 Avenue Tony Garnier, 69007 Lyon, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1333-5603","authenticated-orcid":false,"given":"Marisa","family":"Haenni","sequence":"additional","affiliation":[{"name":"Unit\u00e9 Antibior\u00e9sistance et Virulence Bact\u00e9riennes (AVB), ANSES\u2014Universit\u00e9 de Lyon 1, 31 Avenue Tony Garnier, 69007 Lyon, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stanislas","family":"Mondot","sequence":"additional","affiliation":[{"name":"Micalis Institute, AgroParisTech, Universit\u00e9 Paris-Saclay, INRAE, 78350 Jouy-en-Josas, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chlo\u00e9","family":"Astruc","sequence":"additional","affiliation":[{"name":"3C-G Clinical, 69238 Saint-Symphorien-sur-Coise, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"G\u00e9raldine","family":"Cazeau","sequence":"additional","affiliation":[{"name":"Unit\u00e9 Epid\u00e9miologie et Appui \u00e0 la Surveillance (EAS), ANSES\u2014Universit\u00e9 de Lyon 1, 69007 Lyon, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tristan","family":"Ferry","sequence":"additional","affiliation":[{"name":"Service des Maladies Infectieuses et Tropicales, CHU de Lyon, H\u00f4pital de la Croix-Rousse, 69004 Lyon, France"},{"name":"Centre International de Recherche en Infectiologie, CIRI, Inserm U1111, CNRS UMR5308, ENS de Lyon, UCBL1, 69007 Lyon, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jean-Yves","family":"Madec","sequence":"additional","affiliation":[{"name":"Unit\u00e9 Antibior\u00e9sistance et Virulence Bact\u00e9riennes (AVB), ANSES\u2014Universit\u00e9 de Lyon 1, 31 Avenue Tony Garnier, 69007 Lyon, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5860-9511","authenticated-orcid":false,"given":"Agnese","family":"Lupo","sequence":"additional","affiliation":[{"name":"Unit\u00e9 Antibior\u00e9sistance et Virulence Bact\u00e9riennes (AVB), ANSES\u2014Universit\u00e9 de Lyon 1, 31 Avenue Tony Garnier, 69007 Lyon, France"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2021,11,16]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"496","DOI":"10.1016\/j.tibtech.2015.06.011","article-title":"Proteobacteria: Microbial signature of dysbiosis in gut microbiota","volume":"33","author":"Shin","year":"2015","journal-title":"Trends Biotechnol."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"94","DOI":"10.3389\/fphys.2011.00094","article-title":"Brain-gut-microbe communication in health and disease","volume":"2","author":"Grenham","year":"2011","journal-title":"Front. 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