{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,4]],"date-time":"2026-11-04T23:42:21Z","timestamp":1793835741157,"version":"4.6.1"},"reference-count":208,"publisher":"MDPI AG","issue":"7","license":[{"start":{"date-parts":[[2026,7,15]],"date-time":"2026-07-15T00:00:00Z","timestamp":1784073600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100018987","name":"Ministry of Research, Innovation and Digitization","doi-asserted-by":"crossref","award":["PN-IV-P2-2.1-TE-2023-1449"],"award-info":[{"award-number":["PN-IV-P2-2.1-TE-2023-1449"]}],"id":[{"id":"10.13039\/100018987","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Antibiotics"],"abstract":"<jats:p>The gut microbiome is a dynamic ecosystem that plays essential roles in host metabolism, immune regulation, colonization resistance, and maintenance of intestinal homeostasis. Antibiotic exposure profoundly disrupts this ecosystem by reducing microbial diversity, depleting beneficial commensals, reshaping microbial metabolic functions, and remodeling the gut resistome through the selection and dissemination of antibiotic resistance genes (ARGs). Increasing evidence from longitudinal metagenomic, multi-omics, and experimental studies indicates that these perturbations may persist long after antibiotic withdrawal due to incomplete ecological recovery, sustained mobile genetic element-mediated ARG dissemination, and altered microbiome resilience. Beyond antimicrobial resistance, antibiotic-induced dysbiosis has been associated with reduced short-chain fatty acid production, altered bile acid metabolism, impaired epithelial barrier function, and broader disturbances in host metabolic homeostasis, although many of these relationships remain associative rather than causal. This review provides an integrated overview of antibiotic-driven gut microbiome dysbiosis, emphasizing the ecological, functional, metabolic, and resistome-level consequences of antibiotic exposure together with the mechanisms governing microbiome recovery. Current microbiome-targeted restoration strategies, including probiotics, phage therapy, fecal microbiota transplantation, and next-generation microbiome therapeutics, are critically evaluated with particular attention to their evidence maturity, limitations, and translational potential. Finally, key knowledge gaps and future research priorities are discussed to support the development of more effective microbiome-preserving antimicrobial strategies and to limit the long-term dissemination of antimicrobial resistance.<\/jats:p>","DOI":"10.3390\/antibiotics15070688","type":"journal-article","created":{"date-parts":[[2026,7,16]],"date-time":"2026-07-16T06:49:36Z","timestamp":1784184576000},"page":"688","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["Antibiotic-Driven Gut Microbiome Dysbiosis: Resistome Dynamics, Metabolic Disruption, and Paths to Restoration"],"prefix":"10.3390","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8968-504X","authenticated-orcid":false,"given":"Adelina-Gabriela","family":"Niculescu","sequence":"first","affiliation":[{"name":"Research Institute of the University of Bucharest\u2014ICUB, University of Bucharest, 050657 Bucharest, Romania"},{"name":"Department of Science and Engineering of Oxide Materials and Nanomaterials, National University of Science and Technology Politehnica Bucharest, 011061 Bucharest, Romania"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cristina-Maria","family":"Iacob","sequence":"additional","affiliation":[{"name":"Doctoral School, \u201cCarol Davila\u201d University of Medicine and Pharmacy, 050474 Bucharest, Romania"},{"name":"\u201cProf. Dr. Panait S\u00eerbu\u201d Obstetrics and Gynecology Hospital, 060251 Bucharest, Romania"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2979-3433","authenticated-orcid":false,"given":"Elvira","family":"Br\u0103til\u0103","sequence":"additional","affiliation":[{"name":"\u201cProf. Dr. Panait S\u00eerbu\u201d Obstetrics and Gynecology Hospital, 060251 Bucharest, Romania"},{"name":"Obstetrics and Gynecology Department, Faculty of Medicine, \u201cCarol Davila\u201d University of Medicine and Pharmacy, 050474 Bucharest, Romania"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0008-1796-6326","authenticated-orcid":false,"given":"Raluca","family":"Tocariu","sequence":"additional","affiliation":[{"name":"\u201cProf. Dr. Panait S\u00eerbu\u201d Obstetrics and Gynecology Hospital, 060251 Bucharest, Romania"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2043-9307","authenticated-orcid":false,"given":"Ciprian Andrei","family":"Coroleuc\u0103","sequence":"additional","affiliation":[{"name":"\u201cProf. Dr. Panait S\u00eerbu\u201d Obstetrics and Gynecology Hospital, 060251 Bucharest, Romania"},{"name":"Obstetrics and Gynecology Department, Faculty of Medicine, \u201cCarol Davila\u201d University of Medicine and Pharmacy, 050474 Bucharest, Romania"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3011-3108","authenticated-orcid":false,"given":"Nicolae","family":"Corcionivoschi","sequence":"additional","affiliation":[{"name":"Bacteriology Branch, Veterinary Sciences Division, Agri-Food and Biosciences Institute, Belfast BT4 3SD, UK"},{"name":"Academy of Romanian Scientists, 050044 Bucharest, Romania"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Corneliu Ovidiu","family":"Vrancianu","sequence":"additional","affiliation":[{"name":"Research Institute of the University of Bucharest\u2014ICUB, University of Bucharest, 050657 Bucharest, Romania"},{"name":"Doctoral School, \u201cCarol Davila\u201d University of Medicine and Pharmacy, 050474 Bucharest, Romania"},{"name":"National Institute of Research and Development for Biological Sciences, 060031 Bucharest, Romania"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Delia-Laura","family":"Popescu","sequence":"additional","affiliation":[{"name":"Department of Interdisciplinary Studies, Faculty of Interdisciplinary Studies, University of Bucharest, 010798 Bucharest, Romania"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8285-7176","authenticated-orcid":false,"given":"Gabriela Loredana","family":"Popa","sequence":"additional","affiliation":[{"name":"Department of Parasitology, \u201cCarol Davila\u201d University of Medicine and Pharmacy, 020021 Bucharest, Romania"},{"name":"Parasitic Disease Department, Colentina Clinical Hospital, 020125 Bucharest, Romania"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0794-9329","authenticated-orcid":false,"given":"Mircea Ioan","family":"Popa","sequence":"additional","affiliation":[{"name":"Department of Microbiology II, \u201cCarol Davila\u201d University of Medicine and Pharmacy, 020021 Bucharest, Romania"},{"name":"Department of Microbiology, Cantacuzino National Military Medical Institute for Research and Development, 050096 Bucharest, Romania"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Roxana-Elena","family":"Cristian","sequence":"additional","affiliation":[{"name":"Research Institute of the University of Bucharest\u2014ICUB, University of Bucharest, 050657 Bucharest, Romania"},{"name":"National Institute of Research and Development for Biological Sciences, 060031 Bucharest, Romania"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0004-8539-4885","authenticated-orcid":false,"given":"Georgiana-Alexandra","family":"Grigore","sequence":"additional","affiliation":[{"name":"Research Institute of the University of Bucharest\u2014ICUB, University of Bucharest, 050657 Bucharest, Romania"},{"name":"National Institute of Research and Development for Biological Sciences, 060031 Bucharest, Romania"},{"name":"Department of Botany and Microbiology, Faculty of Biology, University of Bucharest, 050095 Bucharest, Romania"},{"name":"Department of Oncologic Dermatology, \u201cElias\u201d Emergency University Hospital, \u201cCarol Davila\u201d University of Medicine and Pharmacy, 020021 Bucharest, Romania"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,7,15]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Konstantinidis, T., Tsigalou, C., Karvelas, A., Stavropoulou, E., Voidarou, C., and Bezirtzoglou, E. 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