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Antibiotic perturbations to the gut microbiome
Open accessAbstract
Antibiotic-mediated perturbation of the gut microbiome is associated with numerous infectious and autoimmune diseases of the gastrointestinal tract. Yet, as the gut microbiome is a complex ecological network of microorganisms, the effects of antibiotics can be highly variable. With the advent of multi-omic approaches for systems-level profiling of microbial communities, we are beginning to identify microbiome-intrinsic and microbiome-extrinsic factors that affect microbiome dynamics during antibiotic exposure and subsequent recovery. In this Review, we discuss factors that influence restructuring of the gut microbiome on antibiotic exposure. We present an overview of the currently complex picture of treatment-induced changes to the microbial community and highlight essential considerations for future investigations of antibiotic-specific outcomes. Finally, we provide a synopsis of available strategies to minimize antibiotic-induced damage or to restore the pretreatment architectures of the gut microbial community.
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“Median times to pathogen identification with standard techniques have been reported near 96 h, a critical window during which unnecessary antimicrobial exposure can increase adverse events and the risk of colonization by resistant organisms (3–5).”
From Optimized use of the FilmArray Meningitis/Encephalitis panel for early discontinuation of antibiotic therapy (2026) · cites this paper as [4]
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Cites
Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis
Murray, C. J. L., Ikuta, K. S., Sharara, F., Swetschinski, L., Robles Aguilar, G., Gray, A., Han, C., Bisignano, C., Rao, P., Wool, E., et al. (2022) · The Lancet · doi:10.1016/s0140-6736(21)02724-0 · Cited by 16,316
Changes of Intestinal Functions in Liver Cirrhosis
Fukui, H., & Wiest, R. (2016) · Inflammatory Intestinal Diseases · doi:10.1159/000444436 · Cited by 6,820
Antibiotic resistance threats in the United States, 2019
(U.S.), C. F. D. C. A. P. (2019) · doi:10.15620/cdc:82532 · Cited by 5,782
Host-Bacterial Mutualism in the Human Intestine
Bäckhed, F., Ley, R. E., Sonnenburg, J. L., Peterson, D. A., & Gordon, J. I. (2005) · Science · doi:10.1126/science.1104816 · Cited by 5,277 · cited 1×
“From birth, the gut microbiome works in cohesion with the gut epithelium and surrounding organs to digest and transform nutrients, provide colonization resistance against pathogens and regulate the immune system 2–4 .”
BackgroundGlobal increase and geographic convergence in antibiotic consumption between 2000 and 2015
Klein, E. Y., Van Boeckel, T. P., Martinez, E. M., Pant, S., Gandra, S., Levin, S. A., Goossens, H., & Laxminarayan, R. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1717295115 · Cited by 3,232
CARD 2020: Antibiotic Resistome Surveillance with the Comprehensive Antibiotic Resistance Database
Alcock, B. P., Raphenya, A. R., Lau, T. T. Y., Tsang, K. K., Bouchard, M., Edalatmand, A., Huynh, W., Nguyen, A.-L. V., Cheng, A. A., Liu, S., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz935 · Cited by 3,202
Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases
Lloyd-Price, J., Arze, C., Ananthakrishnan, A. N., Schirmer, M., Avila-Pacheco, J., Poon, T. W., Andrews, E., Ajami, N. J., Bonham, K. S., Brislawn, C. J., et al. (2019) · Nature · doi:10.1038/s41586-019-1237-9 · Cited by 3,143
Current understanding of the human microbiome
Gilbert, J. A., Blaser, M. J., Caporaso, J. G., Jansson, J. K., Lynch, S. V., & Knight, R. (2018) · Nature Medicine · doi:10.1038/nm.4517 · Cited by 2,609
Dethlefsen, L., Huse, S., Sogin, M. L., & Relman, D. A. (2008) · PLoS Biology · doi:10.1371/journal.pbio.0060280 · Cited by 2,361 · cited 1×
“Foundational studies in healthy adult humans have commonly demonstrated the acute decline in alpha diversity 31 (in the first couple of days of treatment) and the incomplete recovery of the microbiome up to 6 months after treatment (often measured by beta diversity between baseline and…”
BackgroundShotgun metagenomics, from sampling to analysis
Quince, C., Walker, A. W., Simpson, J. T., Loman, N. J., & Segata, N. (2017) · Nature Biotechnology · doi:10.1038/nbt.3935 · Cited by 2,202
Cited by
Sorted by citations
Items 301–400 of 440
Kim, K., Weiss, A., Ma, H. R., Son, H.-I., Zhou, Z., & You, L. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.08.18.608515 · Cited by 1
“Therefore, many studies have examined the mechanisms underlying such restructuring dynamics in response to antibiotics [12, 20-22] and its functional implications [23].”
BackgroundThe transfer of antibiotic resistance genes between evolutionary distant bacteriaPreprint
Parras-Moltó, M., Lund, D., Ebmeyer, S., Larsson, D. G. J., Johnning, A., & Kristiansson, E. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.10.22.619579 · Cited by 1
Wang, B., Peng, X., Zhou, X. W., Siddique, A., Yao, J., Zhang, H., Li, W., Li, Y., & Yue, M. (2024) · eLife · doi:10.7554/elife.101198.1 · Cited by 1
Parker, J., Marten, S., Rajkov, J., Theising, F. I., Dubin, A., & Roth, O. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.11.25.625175 · Cited by 1
Chowdhury, N. N., Forry, S. P., Servetas, S. L., Hunter, M. E., Dootz, J. N., Dunkers, J. P., & Jackson, S. A. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.11.26.625464 · Cited by 1
Yeganyan, G. A., Avakyan, M., Trachtenberg, T., Zho, J., & Yeganyan, E. (2024) · Bioactive Compounds in Health and Disease · doi:10.31989/bchd.v7i2.1314
Кryvoruchko, І. А., & Sartelli, M. (2024) · The Ukrainian Journal of Clinical Surgery · doi:10.26779/2786-832x.2023.6.44
“The use of oral antibiotics can affect the dynamics of the intestinal microbiome, leading to stronger antibiotic resistance [206].”
BackgroundLiu, T., Xu, X., Wang, T., & Xu, P. (2024) · Research Square · doi:10.21203/rs.3.rs-4516321/v1
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Shapoval, С. D. (2024) · The Ukrainian Journal of Clinical Surgery · doi:10.26779/2786-832x.2024.3.38
Exploring Antibiotic Resistance: An Analysis from the Current Situation to the Consequences
田, 甜. (2024) · Advances in Microbiology · doi:10.12677/amb.2024.133018
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de Oliveira, G. L. V. (2024) · Springer eBooks · doi:10.1007/978-981-97-3790-1_22
Han, M., Wang, X., Su, L., Pan, S., Liu, N., Duan, L., Liu, L., Cui, J., Zhao, H., & Yang, F. (2024) · eLife · doi:10.7554/elife.99282.2
Pavlenko, A. V., Manolov, A. I., Esin, Y. I., Arkhipova, A. L., Vvedenskiy, A. V., Kudryavtsev, A. V., Krieger, E. A., Шагров, Л. Л., Белова, Н. И., & Ilina, E. N. (2024) · Antibiot Khimioter = Antibiotics and Chemotherapy · doi:10.37489/0235-2990-2024-69-7-8-17-24
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Mazel, F. (2025) · médecine/sciences · doi:10.1051/medsci/2024190
Gao, Q., Bai, M., Qi, T., Zhai, J., Song, Y., Zhang, W., & Liang, G. (2025) · International Journal for Vitamin and Nutrition Research · doi:10.31083/ijvnr26126
“Antibiotics often eradicate Bac-teroidetes, Firmicutes and Actinobacteria taxa, thus opening a niche for colonization or proliferation by opportunistic bacteria from the Proteobacteria phylum [33].”
Jia, D., Cao, Y., & Zang, Y. (2025) · Research Square · doi:10.21203/rs.3.rs-6318560/v1
Wang, B., Peng, X., Zhou, X. W., Jin, X., Siddique, A., Yao, J., Zhang, H., Li, W., Li, Y., & Yue, M. (2025) · eLife · doi:10.7554/elife.101198.2
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Håkanson, C. A. (2025) · doi:10.69622/28623185.v1
Nsele, N. W., & Ndlovu, N. (2025) · Student s Journal of Health Research Africa · doi:10.51168/sjhrafrica.v6i6.1720
Wang, B., Peng, X., Zhou, X. W., Jin, X., Siddique, A., Yao, J., Zhang, H., Li, W., Li, Y., & Yue, M. (2025) · eLife · doi:10.7554/elife.101198.3
Gut microbial communities in chronic rhinosinusitis patients in response to 1,8-Cineol treatment
Graspeuntner, S., Heidemann, M., Jeschke, S., Lupatsii, M., Penxová, Z., Künzel, S., Wollenberg, B., Leichtle, A., Ploch, M., Bruchhage, K., et al. (2025) · Current Research in Microbial Sciences · doi:10.1016/j.crmicr.2025.100442
Bai, J., Gong, Y., Ge, J., Pei, J., He, Y., Zhang, L., Min, Y., Liu, X., Yang, X., Luo, C., et al. (2025) · Food & Function · doi:10.1039/d5fo01980j · Cited by 1
The Correlation Between Carbohydrate Loading Diet and Gut Microbiome: A Systematic Review
Elkholy, O., Nichols, L., Elsayed, A. A. R., & Basson, M. D. (2025) · MicrobiologyOpen · doi:10.1002/mbo3.70045
Ren, Q., Lu, W., Zhang, T., Hao, S., Wang, J., Xu, X., Wang, F., Huang, Z., Lei, X., Cao, S., et al. (2025) · Veterinary Sciences · doi:10.3390/vetsci12111022
“To investigate the potential influence of animal age on microbial communities within water pipe biofilms, the functional annotation was performed using the KEGG and the CAZY database [22].”
Boetto, C., Romero, V. B., Henches, L., Frouin, A., Auvergne, A., Patin, É., Bredon, M., Abel, L., Alcover, A., Aschard, H., et al. (2025) · Communications Biology · doi:10.1038/s42003-025-08895-y
Su, H., Han, P., Yan, H., Wu, C., Zeng, S., Zhang, P., Wang, Z., Dong, J., Liang, M., Jing, H., et al. (2025) · Communications Biology · doi:10.1038/s42003-025-09302-2
“Recently, antimicrobial resistance (AMR) has 37 , pigs 38 , giant pandas 39 , monkeys 40 , gibbons 41 , and honeybees 42,43 , etc. ARGs whose hosts belongs to the bacteria and phages have been 44 .”
Chen, X., Hu, M.-Y., Zheng, E., & Pan, J.-Y. (2025) · Frontiers in Microbiology · doi:10.3389/fmicb.2025.1713477
“Much of the existing literature on antibiotics and the gut microbiota focuses on general courses of antibiotics (Fishbein et al., 2023), leaving a gap regarding the precise impact of this specific and commonly prescribed therapeutic regimen.”
Wang, C., Zhang, M., Zhang, H., Yang, Y., Zhang, L., & Zhang, Y.-X. (2025) · Microorganisms · doi:10.3390/microorganisms13122812
“The elimination of pathogenic bacteria also causes irreversible damage to beneficial bacteria, leading to a decrease in microbial diversity, proliferation of opportunistic pathogens, and impairment of metabolic functions [1–3].”
Zebian, G., Kreitmann, L., Houard, M., Piantoni, A., Piga, G., Ruffier des Aimes, S., Holik, B., Wallet, F., Labreuche, J., & Nseir, S. (2024) · Figshare · doi:10.6084/m9.figshare.26729857
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Blake, K. S., & Dantas, G. A. (2025) · CMI Communications · doi:10.1016/j.cmicom.2025.105142
“Dysbiosis has been associated with numerous human pathologies, including inflammatory bowel disease, obesity, and gastrointestinal cancers [ 13 ].”
Self-citationCorrelation Between Dysbiosis and Atrial Fibrillation: What’s New?
Marinacci, B., Mencarelli, N., Stornelli, G., Pellegrini, B., Amedei, A., Gallorini, M., & Grande, R. (2025) · International Journal of Molecular Sciences · doi:10.3390/ijms27010073
Eishi, Y. (2026) · Microorganisms · doi:10.3390/microorganisms14010147
“The prevailing view for much of the twentieth century was that health depended on eliminating microbes rather than understanding or maintaining host–microbe coexistence [28,36,46–48].”
Guo, D., Yj, S., Yuan, L., Chu, W., Dong, Y., & Wang, D. (2026) · Postgraduate Medicine · doi:10.1080/00325481.2026.2619422
Are we overlooking a hidden organ in sepsis-associated AKI?
Lydon, E., Liu, K. D., & Calfee, C. S. (2026) · American Journal of Respiratory and Critical Care Medicine · doi:10.1093/ajrccm/aamaf098
Zhao, C., Wei, J., Yao, W., & Wang, Z. (2026) · BMC Microbiology · doi:10.1186/s12866-026-04760-y
“This finding is consistent with earlier reports that early, prolonged, or broad-spectrum antibiotic exposure can promote the emergence of resistant organisms [26, 27].”
Mei, L.-N., Shen, J.-S., Duan, Y., Shi, Z.-Q., Peng, H., & Luo, X. (2026) · Natural Products and Bioprospecting · doi:10.1007/s13659-025-00584-x
“However, the overuse of antibiotics always result in dysbiosis and depletion of the intestinal microbiome, inhibiting sensitive and beneficial bacterial populations [5].”
Yang, Y., Chen, M., Gao, K., Wang, Y., Wu, G., Ning, X., Zeng, B., Guo, Q., & Zhou, Y. (2026) · Journal of Functional Foods · doi:10.1016/j.jff.2026.107225
Chen, X., Fan, Y., Hao, J., Zhang, S., Hao, S., Sun, Y., Li, J., Zhang, L., Yu, S., & Hu, H. (2026) · Acta Pharmaceutica Sinica B · doi:10.1016/j.apsb.2026.03.018
Heng, Y., Wang, M., Zhang, Z., Jian, E., Wu, C., Zhang, C., Chen, Q., Yu, X., Zhu, Y., & Cai, P. (2026) · European Journal of Clinical Microbiology & Infectious Diseases · doi:10.1007/s10096-026-05455-y
Liu, Y., Cai, Q., Hu, X., Liu, X., Guo, P., Zhang, Y., Liu, H., Wang, W., Zheng, D., Pan, C., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.03.14.711758
Yang, P., Zhou, Q., Jia, M., Li, K., Qu, Q., Ren, W., Peng, X., Li, G., Xie, Y., Li, B., et al. (2026) · Probiotics and Antimicrobial Proteins · doi:10.1007/s12602-026-10988-x
Peng, Y., Hu, Q., & Gao, C. (2026) · Frontiers in Medicine · doi:10.3389/fmed.2026.1766362
Matos, S., Moniz, B., Mil-Homens, D., Pereira, I. C., & Pimenta, A. (2026) · bioRxiv · doi:10.64898/2026.03.24.714029
The gut microbiome as a fingerprint of antibiotic use history
(2026) · Nature Medicine · doi:10.1038/s41591-026-04360-3
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Li, M., Chen, Y., Chen, X., Lu, W., Liao, J., Wang, J., Liu, Q., Chang, Y., Xu, Z., Tu, Y., et al. (2026) · iMetaMed · doi:10.1002/imm3.70039
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Lubrano, P., Magnan, M., Steiner, C., Birgy, A., Chassaing, B., Deschasaux, M., Gutierrez, A., Barreto, H. C., Hobson, C. A., Magréault, S., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.04.24.720353
The Role of Inflammation in the Brain: A Gut-Driven Phenomenon
Mahbub, N. U., Islam, M. M., & Hong, S. T. (2026) · Springer eBooks · doi:10.1007/978-981-95-7494-0_9
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Jafari, M., Malekiantaghi, A., Mirzaee, H. S., Talesh, S. A., Shafiei, A., & Eftekhari, K. (2026) · Archives of Pediatric Infectious Diseases · doi:10.5812/apid-165415
Zhang, P., Zhao, M., Cheng, Z., Ding, Y., 夏时海, & Guo, J. (2026) · The ISME Journal · doi:10.1093/ismejo/wrag126
“Disruption of microbial homeostasis often favors the overgrowth of Enter-obacteriaceae and expansion of antibiotic resistance genes (ARGs) in human gut, thereby increasing the dissemination risk of AMR [ 4, 5].”
Hu, Y., Zhu, Q., Xu, Q., Zhong, W., Chen, Y., & Jiang, C. (2026) · Industrial Crops and Products · doi:10.1016/j.indcrop.2026.123500
Jing, Y., Bai, X., Yin, Y., Liu, X., Li, J., Chen, Z., Zhai, Z., & Hao, Y. (2026) · Foods · doi:10.3390/foods15101815
“…pathogen infection, their use is often associated with significant limitations, including disturbance of the intestinal microbial community, increased susceptibility to secondary infections and the incidence of hemolytic uremic syndrome, as well as the emergence of antibiotic resistance [5].”
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Yi, J. (2026) · International Reviews of Immunology · doi:10.1080/08830185.2026.2677909
Qiu, X., Qiang, L., Wang, Y., Li, B., Lei, Z., & Wang, J. M. (2026) · Frontiers in Pharmacology · doi:10.3389/fphar.2026.1834558
“Beyond the serious challenge of antimicrobial resistance, conventional antibiotics can also lead to microbiota dysbiosis, thereby compromising host anti-infection immunity (Fishbein et al., 2023).”
Herren, C. M. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.05.27.728224
Antibiotic disruption of the gut microbiome triggers IBD-like proteolytic activity
Werner, L., Nissenbaum, T., Fibelman, M., Leibovitzh, H., Cohen, N. A., Brenner, M., Lobel, L., & Maharshak, N. (2026) · Cell Reports · doi:10.1016/j.celrep.2026.117478
Pierro, F. D., Carugno, A., Baggi, E., Franco, V., Salati, B., Casale, F., SOARDO, S., Palla, F., Palazzi, C. M., Bertuccioli, A., et al. (2026) · International Microbiology · doi:10.1007/s10123-026-00843-y
“Indeed, as extensively described (Ramirez et al. 2020, Fishbein et al. 2023) and observed in our study, biodiversity is reduced within a few days of antibiotic use in both the control and treated groups, with no significant differ - ences.”
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Tabi, A., & Solé, R. V. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.06.02.729649
“This recognition has, in turn, motivated the exploration of microbiome-targeted interventions, including antibiotics [14] dietary modulation and probiotics [25], fecal microbiota transplantation [43] and, more recently, virome-based therapies [54].”
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Lin, S., Peng, S., Wang, Z., Liu, S., Shen, Y., Xu, J., & Yu, J. (2026) · SSRN Electronic Journal · doi:10.2139/ssrn.6914247
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Lewandowski, R. (2026) · Future Integrative Medicine · doi:10.14218/fim.2026.00010
Thibodeau, A. J., Mouchet, F., Nguyen, V. X., Moura, T., Vivant, M., Pinelli, É., & Barret, M. (2026) · Environmental Pollution · doi:10.1016/j.envpol.2026.128470
Zhao, W., Si, T., Fan, X., Zheng, J., Mao, R., Cai, S., & Li, F. (2026) · Trends in Food Science & Technology · doi:10.1016/j.tifs.2026.105888
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Bhadana, D., Thanjaivadivel, M., Kumar, R. L., & Ameena, B. (2026) · IGI Global eBooks · doi:10.4018/979-8-3373-4490-4.ch005
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“…were excluded at enrollment, the lingering ecological effects of earlier courses, including selective depletion of obligate anaerobes and facilitation of resistant Proteobacteria blooms, are difficult to quantify and may partly underlie the Proteobacteria enrichment seen in the frailty group (35).”
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Negi, S. S., Pandey, A., Dhiman, V. K., & Singh, D. (2026) · Advances in computational intelligence and robotics book series · doi:10.4018/979-8-3373-8172-5.ch003
Hernandez, J. B., Abiodun, M., Hayer, S. S., Dickson, T., Ayayee, P. A., & Clayton, J. B. (2026) · Gut Microbes · doi:10.1080/19490976.2026.2687925
Xiao, L., Gong, T., Luo, W., Jiang, Y., Peng, X., Zhou, X., Cheng, L., & Zheng, X. (2026) · Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease · doi:10.1016/j.bbadis.2026.168332
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“Dietary patterns and antibiotic exposure may reshape gut microbial composition and metabolite production; in particular, antibiotic exposure is a well-established perturbator of the gut microbiome, although its speci fi c relevance to psoriasis – Crohn ’ s disease overlap remains indirect (80, 83).”
Huang, S.-Q., Gao, X.-P., Liang, H., Feng, Y.-H., Huang, H.-K., Li, Y., Cheng, P.-L., Xie, J., Lu, C.-J., He, G.-H., et al. (2026) · BMC Microbiology · doi:10.1186/s12866-026-05339-3
Matos, S., Moniz, B., Mil‐Homens, D., Pereira, I. A. C., & Pimenta, A. I. (2026) · Microbial Pathogenesis · doi:10.1016/j.micpath.2026.108792
Perinatal ampicillin exposure alters murine maternal fecal bile acid and acylcarnitine profiles
Zuffa, S., Thomas, S. P., Patan, A., Mohanty, I., Abiead, Y. E., Deleray, V., Kvitne, K. E., Kousha, A., Suzuki, E., Tsai, C. M., et al. (2026) · Gut Microbes · doi:10.1080/19490976.2026.2690698 · Cited by 4
Eley, V. A., Martin, E. K., Amoako, A. A., Härtel, G., McCarthy, K. L., Woods, C., Lu, Y., Tan, J., Nanan, R. K. H., Lipman, J., et al. (2026) · International Journal of Obstetric Anesthesia · doi:10.1016/j.ijoa.2026.105222
Crouch, A. L., Rambeau, M., Li‐Pook‐Than, J., Snyder, M. P., Henderson, J. A., Yracheta, J., & Anderson, M. Z. (2026) · Cell Reports · doi:10.1016/j.celrep.2025.116334
Theocharidou, C.-C., Tsinaris, Z., Peristeri, A.-M., Akritidou, O., & Nikopoulou, A. (2026) · Critical Care Science · doi:10.62675/2965-2774.20260392
“(52,53) Disruption of enteral nutrition may also contribute to unfavorable shifts in microbial community composition.”
Yang, G., 洪兴波, Lai, Z., Zhang, H., Xiong, Z., & Xiong, Z. (2026) · Frontiers in Immunology · doi:10.3389/fimmu.2026.1810227
“Indeed, broad-spectrum antibiotics, while necessary for eradicating the primary infection, act as a double-edged sword by inducing signi fi cant microbial dysbiosis (39, 40).”
Purec, D., Iorgoni, V., Iancu, I., Dégi, J., Pascu, C., Costinar, L., Badea, C., Gligor, A., Nistor, P. N., Udrea, A., et al. (2026) · Biology · doi:10.3390/biology15131087
“Antibiotic therapy, while often necessary because of the risk of bacterial translocation in the context of mucosal injury and leukopenia, can reduce microbial diversity and alter community structure, potentially influencing subsequent reassembly [33–36].”
InfluentialYuan, F., Song, S., Chen, Z., Lu, J., Wang, S., Han, Z., Chen, S., Li, T., & Zhou, J. (2026) · Spectrochimica Acta Part A Molecular and Biomolecular Spectroscopy · doi:10.1016/j.saa.2026.128412
Gut Physiology and the Microbiome
Klingensmith, N. J. (2026) · Springer eBooks · doi:10.1007/978-3-032-22660-0_24
Lipan, L. E., Vihta, K.-D., Marcu, A. D., Avramescu, I., Jardan, D., Palade, A., Coliţă, A., Dima, S., Constantinescu, I., Iordan, I., et al. (2026) · GERMS · doi:10.3390/germs16030017
“Our finding of lower Shannon diversity in patients exposed to carbapenems (median 4.02 vs. 4.97, p adj = 0.02) confirms previous research showing that carbapenems have significant effects on the gut microbiome [14–16].”
InfluentialLin, S., Peng, S., Wang, Z., Liu, S. F., Shen, Y., Xu, J., & Ouyang, G. (2026) · Microchemical Journal · doi:10.1016/j.microc.2026.119090
Li, F., Hu, Y., Tai, B., Huangfu, B., He, X. S., Zhang, Z., Zhang, R., Jin, J., & Xing, F. (2026) · Environmental Pollution · doi:10.1016/j.envpol.2026.128788
Farz, S., Ashrafi, S. N., Mohebifar, M., & Ansarian, M. A. (2026) · Journal of Stomatology Oral and Maxillofacial Surgery · doi:10.1016/j.jormas.2026.102915
Windows of opportunity for genotoxic E. coli in colorectal cancer initiation
Boath, J. M., Nardella, L. L., & Puschhof, J. (2026) · Journal of Applied Microbiology · doi:10.1093/jambio/lxag192
Winters, A. D., Rudagi, E., Koka, O., & Angoa‐Pérez, M. (2026) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2026.1822390
“…reports of persistent commensal depletion coupled with opportunist enrichment after antibiotic treatment (Ng et al., 2019; Ramirez et al., 2020; Fishbein et al., 2023; Cusumano et al., 2025), underscoring the marked sensitivity of key commensals and the ecological resilience of opportunistic…”
Precision microbiome medicine and therapeutics: the enabling role of in vitro gut models
Huang, Z., Ng, S. C., Sokol, H., & Rolhion, N. (2026) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuag038
“Higher cumulative concentrations and extended durations of exposure correlate with more profound shifts in the host metabolic landscape and a higher probability of transitioning the microbiome into a long-term dysbiotic state (Pennycook and Scanlan 2021 , Fishbein et al. 2023 ).”
Li, X., Xia, Y., Fan, J., Jiang, F., Li, L., Du, X., Wang, X., & Yu, G. (2026) · The Veterinary Journal · doi:10.1016/j.tvjl.2026.106808
Hu, D., Wang, Z., Xue, Y., Li, X., Li, Y., Liu, S., Gao, L., Liu, H., & Yan, H. (2026) · Precision Clinical Medicine · doi:10.1093/pcmedi/pbag021
“However, as a medically induced factor for perioperative patients, prophylactic antibiotics directly cause severe damage to the composition of the intestinal gut microbiota [ 17 , 18 ].”
Inflammatory gut–liver crosstalk: mechanisms and therapeutic targets
Murao, A., Aziz, M., & Wang, P. (2026) · Experimental & Molecular Medicine · doi:10.1038/s12276-026-01810-3
“For example, antibiotics can rapidly reduce microbial diversity, deplete bene fi cial commensals and promote the expansion of pathobionts 23 .”
Sanchis, E. S., Ortí, J. E. D. L. R., Sancho-Cantus, D., Cunha-Pérez, C., & Mohedo, J. C. (2026) · Pathophysiology · doi:10.3390/pathophysiology33030059
“Our results are consistent with those of recent studies that have identified a link between the prevalence of certain bacterial strains, particularly Akkermansia muciniphila, and an increase in the hippocampal GABA/glutamate ratio [47,48,94,95].”
Beyond the Lungs: ICU Oral Care and Gut Resilience—A Hypothesis-Generating Narrative Review
Sun, X., Jin, T., Zhao, X., & Zhang, J. (2026) · Microorganisms · doi:10.3390/microorganisms14081772
“The perturbation of the gut microbiome by antibiotics is profound and multi-faceted [18,19].”
Mehmood, M. S., Faheem, H. M., Javaid, F., Afroz, E., Ramadan, M. E., Ali, S., & Nazari, M. J. (2026) · Discover Bacteria. · doi:10.1007/s44351-026-00057-7
“Understanding this link is crucial for anticipating the appearance of harmful strains in normally commensal microbial communities [116].”
Yang, X., Wei, S., Su, S., Su, Y., Lan, L.-C., Chen, X., Huang, T., & Shan, Q.-W. (2026) · Frontiers in Microbiology · doi:10.3389/fmicb.2026.1791355
“Collectively, dysbiosis, barrier impairment, and aberrant macrophage polarization may synergistically drive AAC pathology.”
InfluentialJaiswal, R., Mahmood, T., Awasthi, H., Ahsan, F., & Ali, A. (2026) · Prostaglandins & Other Lipid Mediators · doi:10.1016/j.prostaglandins.2026.107103
Maternal microbiome promotes offspring ovarian reserve via bile acid metabolism
Wang, H., Li, Y., Niu, Y., Chen, X., Liu, J., Feng, W., Cao, J., Liu, H., Liu, C., Liang, X., et al. (2026) · EMBO Reports · doi:10.1038/s44319-026-00912-3
“…are commonly used during daily life, however, increasing evidence shows that they are major sources of disturbance to the human gut microbiome (Fishbein et al, 2023; Patangia et al, 2022); for example, humans are prescribed a combination of antibiotics during Helicobacter pylori treatment…”
Xia, P., Wu, H., Chen, W., Wang, D., Xu, S., Yang, Y., Zeng, T., & Xia, L. (2026) · Frontiers in Microbiology · doi:10.3389/fmicb.2026.1913730
Rubinić, I., Palčevski, D., Rosović, T., Antonić, M., Skočibušić, N., Cepanec, I., Knežević, Z., Šantić, M., Hauser, G., & Vlahović–Palčevski, V. (2026) · BMJ Open · doi:10.1136/bmjopen-2026-119249
Association between antibiotic use and Graves’ disease: a cohort study
Son, Y., Park, S. J., Kang, J. H., Chung, J., Kim, H. J., Yu, J., Park, S., 김재우, Lee, H., Han, C., et al. (2026) · European Journal of Endocrinology · doi:10.1093/ejendo/lvag170
The gut microbiota in Graves’ disease: mechanistic insights and clinical implications
Li, L., Pang, B., Wang, Z., Zhao, D., Wei, J.-P., & Wang, Q. (2026) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2026.1859658
“Medication exposure is another factor to consider in microbiome research; antibiotic-mediated intestinal microbial dysbiosis is associated with various gastrointestinal in fl ammatory and autoimmune diseases (Fishbein et al., 2023; Taitz et al., 2025).”
Metadata
- Authors
- Fishbein, S. R. S., Mahmud, B., & Dantas, G.
- Affiliations
- Washington University in St. Louis (US)
- Corresponding author
- Dantas, Gautam
- Venue
- Nature Reviews Microbiology
- Published
- 2023-07-25
- Volume
- 21
- Issue
- 12
- Pages
- 772-788
- ISSN
- 1740-1526 (ISSN-L)
- 1740-1534
- PMC
- PMC12087466
- OpenAlex
- W4385240643
- Cited by
- 440
- References
- 229
- Citations by year
- 2026: 152 · 2025: 165 · 2024: 115 · 2023: 7
- FWCI
- 11.59
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- Locations
- Nature Reviews Microbiology (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- U.S. Department of Health and Human Services
- National Institutes of Health
- Centers for Disease Control and Prevention (R01OH011578)
- Agency for Healthcare Research and Quality (R01 HS027621)
- National Institute of Allergy and Infectious Diseases (U01AI123394, R01AI155893)
- National Institute of Diabetes and Digestive and Kidney Diseases (T32DK077653)
- National Institute for Occupational Safety and Health (R01 OH011578)
- National Center for Complementary and Integrative Health (R01AT009741)
- Eunice Kennedy Shriver National Institute of Child Health and Human Development (R01HD092414)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Health Sciences › Dentistry › Periodontics › Oral microbiology and periodontitis research
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Keywords
- gut microbiota, antibiotics, microbiome perturbation, microbiome recovery, gastrointestinal diseases, autoimmune disease, multi-omics profiling
- MeSH terms
- Gastrointestinal Microbiome, Anti-Bacterial Agents, Gastrointestinal Tract, Microbiota
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