{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,13]],"date-time":"2026-07-13T21:18:06Z","timestamp":1783977486606,"version":"3.55.0"},"reference-count":181,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,6,3]],"date-time":"2026-06-03T00:00:00Z","timestamp":1780444800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:p>Antimicrobial resistance (AMR) is one of the most pressing threats to global health system. The human gut harbors a complex microbial ecosystem coordinated through mechanisms of metabolic interdependence. The gut microbiota plays a vital role in normal growth and physiological processes of the human body. It serves both as a target of antibiotic-mediated disruption and as a reservoir for the propagation of antimicrobial resistance genes. Although antibiotics remain indispensable for the treatment of bacterial infections, their broad ecological impact on the gut microbiota can undermine the microbial balance that protects the host against pathogen invasion and metabolic dysfunction. The gut microbiome also functions as a reservoir of antimicrobial resistance genes collectively termed the \u201cresistome,\u201d which can be mobilised and transferred between commensal and pathogenic bacteria via horizontal gene transfer mechanisms such as conjugation, transformation, and transduction. This review examines the composition and functions of the human gut microbiota, the mechanism of antibiotic-induced gut dysbiosis, and the role of host factors like age, genetics, diet and immune status, on microbiome dynamics and AMR development. We further evaluate emerging methods for resistome characterisation, which include PCR, next-generation sequencing, functional metagenomics and artificial intelligence-driven tools. Finally, we discuss microbiome-targeted therapeutic strategies such as faecal microbiota transplantation (FMT), phage therapy, CRISPR-based therapies, and antimicrobial peptides for combating AMR and restoring gut microbial homeostasis. Overall, this review highlights that maintaining and re-establishing the integrity of the gut microbiome should be considered a fundamental component of antimicrobial stewardship strategies aimed at controlling AMR worldwide.<\/jats:p>","DOI":"10.3389\/fmicb.2026.1856738","type":"journal-article","created":{"date-parts":[[2026,6,3]],"date-time":"2026-06-03T06:06:42Z","timestamp":1780466802000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":2,"title":["The role of the gut microbiome in antibiotic-driven antimicrobial resistance"],"prefix":"10.3389","volume":"17","author":[{"given":"Gargi","family":"Joshi","sequence":"first","affiliation":[{"name":"Department of Bio-Medical Sciences, School of Biosciences and Technology, Vellore Institute of Technology (VIT)","place":["Vellore, Tamil Nadu, India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Smriti","family":"Rani","sequence":"additional","affiliation":[{"name":"Department of Bio-Medical Sciences, School of Biosciences and Technology, Vellore Institute of Technology (VIT)","place":["Vellore, Tamil Nadu, India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dipti","family":"Bharti","sequence":"additional","affiliation":[{"name":"Department of Bio-Medical Sciences, School of Biosciences and Technology, Vellore Institute of Technology (VIT)","place":["Vellore, Tamil Nadu, India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Namrata","family":"Panda","sequence":"additional","affiliation":[{"name":"Department of Bio-Medical Sciences, School of Biosciences and Technology, Vellore Institute of Technology (VIT)","place":["Vellore, Tamil Nadu, India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Prerana","family":"Chavan","sequence":"additional","affiliation":[{"name":"Department of Bio-Medical Sciences, School of Biosciences and Technology, Vellore Institute of Technology (VIT)","place":["Vellore, Tamil Nadu, India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shalini","family":"Mathpal","sequence":"additional","affiliation":[{"name":"Department of Bio-Sciences, School of Biosciences and Technology, Vellore Institute of Technology (VIT)","place":["Vellore, Tamil Nadu, India"]},{"name":"Medical and Biological Computing Laboratory, School of Biosciences and Technology, Vellore Institute of Technology (VIT)","place":["Vellore, Tamil Nadu, India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sudha","family":"Ramaiah","sequence":"additional","affiliation":[{"name":"Department of Bio-Sciences, School of Biosciences and Technology, Vellore Institute of Technology (VIT)","place":["Vellore, Tamil Nadu, India"]},{"name":"Medical and Biological Computing Laboratory, School of Biosciences and Technology, Vellore Institute of Technology (VIT)","place":["Vellore, Tamil Nadu, India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anand","family":"Anbarasu","sequence":"additional","affiliation":[{"name":"Medical and Biological Computing Laboratory, School of Biosciences and Technology, Vellore Institute of Technology (VIT)","place":["Vellore, Tamil Nadu, India"]},{"name":"Department of Biotechnology, School of Biosciences and Technology, Vellore Institute of Technology (VIT)","place":["Vellore, Tamil Nadu, India"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,6,3]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"107","DOI":"10.3934\/microbiol.2024007","article-title":"What we need to know about the germ-free animal models","volume":"10","author":"Aghighi","year":"2024","journal-title":"AIMS Microbiol."},{"key":"ref2","doi-asserted-by":"publisher","first-page":"e61476","DOI":"10.7759\/cureus.61476","article-title":"A comprehensive review of innovative paradigms in microbial detection and antimicrobial resistance: beyond traditional cultural methods","volume":"16","author":"Ahmad","year":"2024","journal-title":"Cureus"},{"key":"ref3","doi-asserted-by":"publisher","first-page":"e46","DOI":"10.4110\/in.2022.22.e46","article-title":"Context-dependent regulation of Type17 immunity by microbiota at the intestinal barrier","volume":"22","author":"Akuzum","year":"2022","journal-title":"Immune Netw."},{"key":"ref4","doi-asserted-by":"publisher","first-page":"414","DOI":"10.1038\/s43856-025-01090-4","article-title":"A One Health framework for global and local stewardship across the antimicrobial lifecycle","volume":"5","author":"Altevogt","year":"2025","journal-title":"Commun. 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Sci."},{"key":"ref39","doi-asserted-by":"publisher","first-page":"1041","DOI":"10.1093\/jac\/dkr547","article-title":"Nosocomial outbreak of carbapenem-resistant Enterobacter cloacae highlighting the interspecies transferability of the blaOXA-48 gene in the gut flora","volume":"67","author":"Cremet","year":"2012","journal-title":"J. Antimicrob. Chemother."},{"key":"ref40","doi-asserted-by":"publisher","first-page":"371","DOI":"10.3390\/antibiotics14040371","article-title":"The impact of antibiotic therapy on intestinal microbiota: dysbiosis, antibiotic resistance, and restoration strategies","volume":"14","author":"Cusumano","year":"2025","journal-title":"Antibiotics"},{"key":"ref41","doi-asserted-by":"publisher","first-page":"20","DOI":"10.1186\/s40168-021-01216-5","article-title":"Long-read metagenomic sequencing reveals shifts in associations of antibiotic resistance genes with mobile genetic elements from sewage to activated sludge","volume":"10","author":"Dai","year":"2022","journal-title":"Microbiome"},{"key":"ref42","doi-asserted-by":"publisher","first-page":"559","DOI":"10.1038\/nature12820","article-title":"Diet rapidly and reproducibly alters the human gut microbiome","volume":"505","author":"David","year":"2014","journal-title":"Nature"},{"key":"ref43","doi-asserted-by":"publisher","first-page":"101012","DOI":"10.1016\/j.drup.2023.101012","article-title":"Antibiotic failure: beyond antimicrobial resistance","volume":"71","author":"de la Fuente-Nunez","year":"2023","journal-title":"Drug Resist. Updat."},{"key":"ref44","doi-asserted-by":"publisher","first-page":"2043","DOI":"10.1056\/NEJMoa1910437","article-title":"Drug-Resistant E. coli Bacteremia transmitted by fecal microbiota transplant","volume":"381","author":"DeFilipp","year":"2019","journal-title":"N. Engl. J. Med."},{"key":"ref45","doi-asserted-by":"publisher","first-page":"1593065","DOI":"10.3389\/fmicb.2025.1593065","article-title":"The gut microbiome: an emerging epicenter of antimicrobial resistance?","volume":"16","author":"Deshpande","year":"2025","journal-title":"Front. Microbiol."},{"key":"ref46","doi-asserted-by":"publisher","first-page":"e280","DOI":"10.1371\/journal.pbio.0060280","article-title":"The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing","volume":"6","author":"Dethlefsen","year":"2008","journal-title":"PLoS Biol."},{"key":"ref47","doi-asserted-by":"publisher","first-page":"4554","DOI":"10.1073\/pnas.1000087107","article-title":"Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation","volume":"108","author":"Dethlefsen","year":"2011","journal-title":"Proc. Natl. Acad. Sci."},{"key":"ref48","doi-asserted-by":"publisher","first-page":"2157200","DOI":"10.1080\/19490976.2022.2157200","article-title":"Differential response to prolonged amoxicillin treatment: long-term resilience of the microbiome versus long-lasting perturbations in the gut resistome","volume":"15","author":"Dhariwal","year":"2023","journal-title":"Gut Microbes"},{"key":"ref49","doi-asserted-by":"publisher","first-page":"616979","DOI":"10.3389\/fmicb.2021.616979","article-title":"Review: lessons learned from clinical trials using antimicrobial peptides (AMPs)","volume":"12","author":"Dijksteel","year":"2021","journal-title":"Front. Microbiol."},{"key":"ref50","doi-asserted-by":"publisher","first-page":"735","DOI":"10.1038\/s41577-023-00874-w","article-title":"Early-life interactions between the microbiota and immune system: impact on immune system development and atopic disease","volume":"23","author":"Donald","year":"2023","journal-title":"Nat. Rev. Immunol."},{"key":"ref51","doi-asserted-by":"publisher","first-page":"e00007","DOI":"10.1128\/MMBR.00007-19","article-title":"Gut microbiota and colonization resistance against bacterial enteric infection","volume":"83","author":"Ducarmon","year":"2019","journal-title":"Microbiol. Mol. Biol. 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Microbiol."},{"key":"ref58","doi-asserted-by":"publisher","first-page":"166","DOI":"10.1186\/s40168-023-01610-1","article-title":"Resistome expansion in disease-associated human gut microbiomes","volume":"11","author":"Fredriksen","year":"2023","journal-title":"Microbiome"},{"key":"ref59","doi-asserted-by":"publisher","first-page":"2211","DOI":"10.3390\/nu15092211","article-title":"Short-chain fatty-acid-producing bacteria: key components of the human gut microbiota","volume":"15","author":"Fusco","year":"2023","journal-title":"Nutrients"},{"key":"ref60","doi-asserted-by":"publisher","first-page":"975","DOI":"10.1016\/j.cmi.2022.01.004","article-title":"Changes in the gut microbiota and risk of colonization by multidrug-resistant bacteria, infection, and death in critical care patients","volume":"28","author":"Garcia","year":"2022","journal-title":"Clin. Microbiol. Infect."},{"key":"ref61","doi-asserted-by":"publisher","first-page":"1199","DOI":"10.1016\/S0140-6736(24)01867-1","article-title":"Global burden of bacterial antimicrobial resistance 1990-2021: a systematic analysis with forecasts to 2050","volume":"404","year":"2024","journal-title":"Lancet"},{"key":"ref62","doi-asserted-by":"publisher","first-page":"279","DOI":"10.1007\/s00203-025-04483-0","article-title":"Novel antimicrobial peptide HFIAP-1 mutant as a \u03b2-lactamase inhibitor against extended-spectrum \u03b2-lactamases of Escherichia coli: a comprehensive in-silico approach","volume":"207","author":"George","year":"2025","journal-title":"Arch. Microbiol."},{"key":"ref63","doi-asserted-by":"publisher","first-page":"273","DOI":"10.1093\/femsre\/fuy042","article-title":"Extracellular membrane vesicles in the three domains of life and beyond","volume":"43","author":"Gill","year":"2019","journal-title":"FEMS Microbiol. 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Pharm."},{"key":"ref158","year":"2020"},{"key":"ref159","doi-asserted-by":"publisher","first-page":"965","DOI":"10.1128\/IAI.01197-12","article-title":"Intestinal microbiota containing Barnesiella species cures vancomycin-resistant Enterococcus faecium colonization","volume":"81","author":"Ubeda","year":"2013","journal-title":"Infect. Immun."},{"key":"ref160","doi-asserted-by":"publisher","first-page":"20140087","DOI":"10.1098\/rstb.2014.0087","article-title":"Philosophical Transactions of the Royal Society B: Biological Sciences","volume":"370","author":"van Schaik","year":"2015","journal-title":"Philos. Trans. R. Soc. Lond. B Biol. Sci."},{"key":"ref161","first-page":"277","article-title":"The antibiotic resistance crisis: part 1: causes and threats","volume":"40","author":"Ventola","year":"2015","journal-title":"P. T."},{"key":"ref162","doi-asserted-by":"publisher","first-page":"173","DOI":"10.3389\/fmicb.2016.00173","article-title":"Dissemination of antimicrobial resistance in microbial ecosystems through horizontal gene transfer","volume":"7","author":"von Wintersdorff","year":"2016","journal-title":"Front. Microbiol."},{"key":"ref163","doi-asserted-by":"publisher","first-page":"1672198","DOI":"10.3389\/fmicb.2025.1672198","article-title":"Phage therapy for intestinal infections: efficacy, challenges, and future directions in translational research","volume":"16","author":"Wang","year":"2025","journal-title":"Front. Microbiol."},{"key":"ref164","doi-asserted-by":"publisher","first-page":"1155","DOI":"10.1038\/s41587-019-0217-9","article-title":"Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome","volume":"37","author":"Wenger","year":"2019","journal-title":"Nat. Biotechnol."},{"key":"ref165","doi-asserted-by":"publisher","first-page":"76","DOI":"10.1186\/s12915-019-0692-y","article-title":"Distinct impact of antibiotics on the gut microbiome and resistome: a longitudinal multicenter cohort study","volume":"17","author":"Willmann","year":"2019","journal-title":"BMC Biol."},{"key":"ref166","doi-asserted-by":"publisher","first-page":"2393727","DOI":"10.1080\/29933935.2024.2393727","article-title":"The effects of ceftriaxone on glutamate transporter expression and the gut microbiome: implications for a role of antibiotic-induced dysbiosis in mediating drug seeking and relapse","volume":"1","author":"Winters","year":"2024","journal-title":"Gut Microbes Rep."},{"key":"ref167","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1016\/S0924-8579(00)00301-0","article-title":"Selective pressure by antibiotic use in livestock","volume":"16","author":"Witte","year":"2000","journal-title":"Int. J. Antimicrob. Agents"},{"key":"ref168","doi-asserted-by":"publisher","first-page":"124","DOI":"10.1186\/s12866-023-02839-4","article-title":"Microbial circadian clocks: host-microbe interplay in diel cycles","volume":"23","author":"Wollmuth","year":"2023","journal-title":"BMC Microbiol."},{"key":"ref169","doi-asserted-by":"publisher","first-page":"1006","DOI":"10.3390\/antibiotics10081006","article-title":"Metagenomics-based analysis of the age-related cumulative effect of antibiotic resistance genes in gut microbiota","volume":"10","author":"Wu","year":"2021","journal-title":"Antibiotics"},{"key":"ref170","doi-asserted-by":"publisher","first-page":"e169","DOI":"10.1002\/imt2.169","article-title":"Infant age inversely correlates with gut carriage of resistance genes, reflecting modifications in microbial carbohydrate metabolism during early life","volume":"3","author":"Xu","year":"2024","journal-title":"iMeta"},{"key":"ref171","doi-asserted-by":"publisher","first-page":"e0006022","DOI":"10.1128\/cmr.00060-22","article-title":"Fecal microbiota transplantation: current challenges and future landscapes","volume":"37","author":"Yadegar","year":"2024","journal-title":"Clin. Microbiol. Rev."},{"key":"ref172","doi-asserted-by":"publisher","first-page":"1454","DOI":"10.3390\/microorganisms13071454","article-title":"Nutrient-driven metabolic activation and microbial restructuring induced by endophytic bacillus in blight-affected forest soils","volume":"13","author":"Yang","year":"2025","journal-title":"Microorganisms"},{"key":"ref173","doi-asserted-by":"publisher","first-page":"4414","DOI":"10.1128\/AEM.66.10.4414-4420.2000","article-title":"Vesicle-mediated transfer of virulence genes from Escherichia coli O157:H7 to other enteric bacteria","volume":"66","author":"Yaron","year":"2000","journal-title":"Appl. Environ. Microbiol."},{"key":"ref174","doi-asserted-by":"publisher","first-page":"222","DOI":"10.1038\/nature11053","article-title":"Human gut microbiome viewed across age and geography","volume":"486","author":"Yatsunenko","year":"2012","journal-title":"Nature"},{"key":"ref175","doi-asserted-by":"publisher","first-page":"4","DOI":"10.3349\/ymj.2018.59.1.4","article-title":"Disruption of the gut ecosystem by antibiotics","volume":"59","author":"Yoon","year":"2018","journal-title":"Yonsei Med. J."},{"key":"ref176","doi-asserted-by":"publisher","first-page":"2188","DOI":"10.1002\/eji.202049033","article-title":"Innate lymphoid cells and cancer: role in tumor progression and inhibition","volume":"51","author":"Yuan","year":"2021","journal-title":"Eur. J. Immunol."},{"key":"ref177","doi-asserted-by":"publisher","first-page":"djv424","DOI":"10.1093\/jnci\/djv424","article-title":"Genomic testing for gemcitabine-based treatment of pancreatic Cancer","volume":"108","author":"Zhang","year":"2016","journal-title":"J. Natl. Cancer Inst."},{"key":"ref178","doi-asserted-by":"publisher","first-page":"228","DOI":"10.1186\/s12974-023-02915-6","article-title":"Nisin a probiotic bacteriocin mitigates brain microbiome dysbiosis and Alzheimer\u2019s disease-like neuroinflammation triggered by periodontal disease","volume":"20","author":"Zhao","year":"","journal-title":"J. Neuroinflammation"},{"key":"ref179","doi-asserted-by":"publisher","first-page":"1179966","DOI":"10.3389\/fmicb.2023.1179966","article-title":"Oxford nanopore long-read sequencing enables the generation of complete bacterial and plasmid genomes without short-read sequencing","volume":"14","author":"Zhao","year":"","journal-title":"Front. Microbiol."},{"key":"ref180","doi-asserted-by":"publisher","first-page":"492","DOI":"10.1038\/s41422-020-0332-7","article-title":"Interaction between microbiota and immunity in health and disease","volume":"30","author":"Zheng","year":"2020","journal-title":"Cell Res."}],"container-title":["Frontiers in Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2026.1856738\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,6,3]],"date-time":"2026-06-03T06:06:45Z","timestamp":1780466805000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2026.1856738\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,6,3]]},"references-count":181,"alternative-id":["10.3389\/fmicb.2026.1856738"],"URL":"https:\/\/doi.org\/10.3389\/fmicb.2026.1856738","relation":{},"ISSN":["1664-302X"],"issn-type":[{"value":"1664-302X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,6,3]]},"article-number":"1856738"}}