The DOI matches its Crossref record; 229 of the 229 references it cites were found in a registry or an index.
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.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The check wasn’t confident either way, so it gives no verdict — never disputed.
In the citing paper
“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]
Experimental — accuracy not yet measured
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
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
Hays, K. E., Pfaffinger, J. M., & Ryznar, R. J. (2024) · Gut Microbes · doi:10.1080/19490976.2024.2393270 · Cited by 541
Mechanism of staphylococcal resistance to clinically relevant antibiotics
Brdová, D., Ruml, T., & Viktorová, J. (2024) · Drug Resistance Updates · doi:10.1016/j.drup.2024.101147 · Cited by 144
Antimicrobial resistance crisis: could artificial intelligence be the solution?
Liu, G., Yu, D., Fan, M.-M., Zhang, X., Jin, Z., Tang, C. M., & Liu, X. (2024) · Military Medical Research · doi:10.1186/s40779-024-00510-1 · Cited by 138
“Compared to antibiotics, which are mostly broad-spectrum, phage therapy offers remarkably higher specificity, minimizing disturbances to the microbiota and preventing antibiotic-induced AMR dissemination [136, 137].”
BackgroundUnraveling the Gut Microbiota: Implications for Precision Nutrition and Personalized Medicine
Abeltino, A., Hatem, D., Serantoni, C., Riente, A., Giulio, M. M. D., Spirito, M. D., Maio, F. D., & Maulucci, G. (2024) · Nutrients · doi:10.3390/nu16223806 · Cited by 121
“[90–92] Environmental and lifestyle Both macroenvironmental (e.g., toxic exposure, socioeconomic status) and microenvironmental factors (e.g., smoking, diet, stress) can disrupt microbiome composition, promoting inflammation and long-term disease development.”
Engelsberger, V., Gerhard, M., & Mejías‐Luque, R. (2024) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2024.1339750 · Cited by 110
“Engelsberger et al. 10.3389/fcimb.2024.1339750 Frontiers in Cellular and Infection Microbiology frontiersin.org because of their detrimental impact on the intestinal microbiota and related disorders, such as IBD (Ianiro et al., 2016) (Fishbein et al., 2023).”
BackgroundInfluentialTen golden rules for optimal antibiotic use in hospital settings: the WARNING call to action
Worldwide Antimicrobial Resistance National/International Network Group (WARNING) Collaborators, Sartelli, M., Barie, P. S., Coccolini, F., Abbas, M., Abbo, L. M., Abdukhalilova, G., Abraham, Y., Abubakar, S., Abu‐Zidan, F. M., et al. (2023) · World Journal of Emergency Surgery · doi:10.1186/s13017-023-00518-3 · Cited by 105
“Actually, it is increasingly evident that prescribing oral antibiotics could influence gut microbiome dynamics, promoting more strongly AMR [206].”
BackgroundLi, Z. H. (2024) · Gut · doi:10.1136/gutjnl-2024-331880 · Cited by 79
Antibiotics damage the colonic mucus barrier in a microbiota-independent manner
Sawaed, J., Zelik, L., Levin, Y., Feeney, R. H., Naama, M., Gordon, A., Zigdon, M., Rubin, E., Telpaz, S., Modilevsky, S., et al. (2024) · Science Advances · doi:10.1126/sciadv.adp4119 · Cited by 76
Rahman, M. N., Barua, N., Tin, M. C. F., Dharmaratne, P., Wong, S. H., & Ip, M. (2024) · Gut Microbes · doi:10.1080/19490976.2024.2356279 · Cited by 77
“…prevalence of multiple drug-resistant pathogens man-dates the need to explore alternatives to antibiotics, particularly as antibiotics have long-term effects on gut microbiota and human health, 66–68 and may contribute to increasing undesirable microbial communities and resistant pathogens.”
BackgroundElkrief, A., Méndez-Salazar, E. O., Maillou, J., Vanderbilt, C. M., Gogia, P., Desilets, A., Messaoudene, M., Kelly, D., Ladanyi, M., Hellmann, M. D., et al. (2024) · npj Precision Oncology · doi:10.1038/s41698-024-00630-w · Cited by 68
Wang, S., Ju, D., & Zeng, X. L. (2024) · Biomedicines · doi:10.3390/biomedicines12010194 · Cited by 63
Empirical antibiotic therapy for sepsis: save the anaerobic microbiota
Kullberg, R. F. J., Haak, B. W., Chanderraj, R., Prescott, H. C., Dickson, R. P., & Wiersinga, W. J. (2024) · The Lancet Respiratory Medicine · doi:10.1016/s2213-2600(24)00257-1 · Cited by 64
Xu, J., & Lu, Y. (2025) · Frontiers in Microbiology · doi:10.3389/fmicb.2025.1583562 · Cited by 68
Guevara‐Cruz, M., Hernández-Gómez, K. G., Condado-Huerta, C., González-Salazar, L. E., Peña-Flores, A. K., Pichardo‐Ontiveros, E., Serralde-Zúñiga, A. E., Sánchez‐Tapia, M., Maya, O., Vera, I., et al. (2024) · Clinical Nutrition · doi:10.1016/j.clnu.2024.06.036 · Cited by 44
Mechanisms of microbiota-gut-brain axis communication in anxiety disorders
Jiang, M., Li, K., Wang, Y., Zhou, B., Li, H.-Y., Yan, Q., & Liu, Z.-G. (2024) · Frontiers in Neuroscience · doi:10.3389/fnins.2024.1501134 · Cited by 55
The food-associated resistome is shaped by processing and production environments
Quijada, N. M., Cobo-Díaz, J. F., Valentino, V., Barcenilla, C., Filippis, F. D., Cabrera‐Rubio, R., Carlino, N., Pinto, F., Dzieciol, M., Calvete‐Torre, I., et al. (2025) · Nature Microbiology · doi:10.1038/s41564-025-02059-8 · Cited by 41
“Interestingly, even though β-lactam AMRGs were generally not associated with MGE in the study, in K. pneumoniae 75% of them were associated with MGEs, mainly ComTns carrying blaSHV-27 .”
InfluentialLiu, W.-W., Yu, L., Chen, Q., Zhang, C., Wang, L., Yu, N., Peng, D., Ou, J., Chen, W., Zhang, Y., et al. (2025) · Food Research International · doi:10.1016/j.foodres.2025.116671 · Cited by 38
Dissecting microbial communities with single-cell transcriptome analysis
Pountain, A. W., & Yanai, I. (2025) · Science · doi:10.1126/science.adp6252 · Cited by 37
Plasmid-encoded insertion sequences promote rapid adaptation in clinical enterobacteria
Sastre-Domínguez, J., DelaFuente, J., Toribio-Celestino, L., Herencias, C., Herrador-Gómez, P. M., Costas, C., Hernández-García, M., Cantón, R., Rodríguez-Beltrán, J., Santos-López, A., et al. (2024) · Nature Ecology & Evolution · doi:10.1038/s41559-024-02523-4 · Cited by 36
“This effect could help explain how successful associations between pOXA-48 and high-risk bacterial clones emerge in clinical settings, where bacteria face strong selective pressures and changing environments 65,66 .”
Commensal antimicrobial resistance mediates microbiome resilience to antibiotic disruption
Bhattarai, S. K., Du, M., Zeamer, A. L., Mortzfeld, B. M., Kellogg, T. D., Kaya, F., Benjamin, A., Bean, J. M., Zimmerman, M., Mardi, G., et al. (2024) · Science Translational Medicine · doi:10.1126/scitranslmed.adi9711 · Cited by 41
Caffrey, E. B., Perelman, D., Ward, C., Sonnenburg, E. D., Gardner, C. D., & Sonnenburg, J. L. (2025) · Advances in Nutrition · doi:10.1016/j.advnut.2025.100412 · Cited by 37
“A diverse microbiome is associated with better health in a variety of studies, and a more diverse microbiome has been shown to be more resistant to invasion and resilient to perturbations [81,83 – 85].”
Liu, Y., Li, X., Chen, Y., Yao, Q., Zhou, J., Wang, X., Meng, Q., Ji, J., Yu, Z., & Chen, X. (2025) · Frontiers in Microbiology · doi:10.3389/fmicb.2025.1556827 · Cited by 37
Mohr, A. E., Mach, N., Pugh, J. N., Grosicki, G. J., Allen, J. M., Karl, J. P., & Whisner, C. M. (2025) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuaf037 · Cited by 37
Phage lysins for intestinal microbiome modulation: current challenges and enabling techniques
Pottie, I., Vázquez, R., de Wiele, T. V., & Briers, Y. (2024) · Gut Microbes · doi:10.1080/19490976.2024.2387144 · Cited by 33
Lee, S., Park, J. S., Hong, J. H., Woo, H., Lee, C., Yoon, D. S., Lee, K.-B., Chung, S. H., Yoon, D. S., & Lee, J. H. (2025) · Biosensors and Bioelectronics · doi:10.1016/j.bios.2025.117399 · Cited by 37
Comprehensive management of pneumonia in older patients
Putot, A., Garin, N., Rello, J., & Prendki, V. (2025) · European Journal of Internal Medicine · doi:10.1016/j.ejim.2025.02.025 · Cited by 32
Yang, Y., Li, R., Qiang, Z., Guo, Y., Wu, R., Chen, H., Zhou, R., Ye, R., Dąbrowska, K., Prajsnar, T. K., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-65498-1 · Cited by 32
“metabolic transformations 5 .”
Taj, T., Kaushik, M., Islam, A., Das, J., Kumar, B., Hussain, M. S., Ramzan, M., Ashique, S., Tariq, M., Sridhar, S. B., et al. (2025) · Biomedicine & Pharmacotherapy · doi:10.1016/j.biopha.2025.118861 · Cited by 35
Phage-based delivery of CRISPR-associated transposases for targeted bacterial editing
Roberts, A., Adler, B. A., Cress, B. F., Doudna, J. A., & Barrangou, R. (2025) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2504853122 · Cited by 33
“Antibiotics, too, may be applied to selectively modify or perturb microbial communities based on existing or developed resistances ( 7 ).”
Huang, J., Lin, Y., Ding, X., Lin, S., Li, X., Yan, W., & Chen, M. (2024) · Microbial Pathogenesis · doi:10.1016/j.micpath.2024.106647 · Cited by 32
Zhou, L., Chen, S.-Z., Li, Y., Xue, R.-Y., Duan, X., Lin, X.-Y., Chen, S., Zhou, D., & Li, H. (2025) · Environmental Science & Technology · doi:10.1021/acs.est.5c00817 · Cited by 25
Lim, M. Y., Hong, S., & Nam, Y. (2025) · Frontiers in Immunology · doi:10.3389/fimmu.2024.1512683 · Cited by 25
Zhao, C., Chen, G., Huang, Y., Zhang, Y., Li, S., Jiang, Z., Peng, H., Wang, J., Li, D., Hou, R., et al. (2024) · Journal of Hazardous Materials · doi:10.1016/j.jhazmat.2024.134858 · Cited by 22
Lu, H., Guo, S., Yang, Y., Zhao, Z., Xie, Q., Wu, Q., Sun, C., Luo, H., An, B., & Wang, Q. (2025) · Microbiome · doi:10.1186/s40168-025-02109-7 · Cited by 22
The transfer of antibiotic resistance genes between evolutionarily distant bacteria
Parras-Moltó, M., Lund, D., Ebmeyer, S., Larsson, D. G. J., Johnning, A., & Kristiansson, E. (2025) · mSphere · doi:10.1128/msphere.00114-25 · Cited by 24
“Strong selection pressures have been shown to promote horizontal gene transfer (45), suggesting that the IPTs seen between bacteria present in the host-associated bacterial communities may be a consequence of the last 80 years of mass consumption of antibiotics.”
Decoding the Gut Microbiome in Companion Animals: Impacts and Innovations
Shah, H., Trivedi, M. H., Gurjar, T., Sahoo, D. K., Jergens, A. E., Yadav, V. K., Patel, A., & Pandya, P. (2024) · Microorganisms · doi:10.3390/microorganisms12091831 · Cited by 30
“…that metabolic transformations due to antibiotic treatment are linked to noticeable reductions in the presence of key members from the Bacteroidetes, Firmicutes, and Actinobacteria, particularly Faecal-ibacterium [27,83,84], as they play a vital role in the gut microbiome’s metabolic processes.”
BackgroundGut Microbiome Integration in Drug Discovery and Development of Small Molecules
Jimonet, P., Druart, C., Blanquet‐Diot, S., Boucinha, L., Kourula, S., Vacon, F. L., Maubant, S., Rabot, S., de Wiele, T. V., Schuren, F. H. J., et al. (2024) · Drug Metabolism and Disposition · doi:10.1124/dmd.123.001605 · Cited by 23
Advanced Bioinspired Multifunctional Platforms Focusing on Gut Microbiota Regulation
Li, M., Wang, L., Lin, D., Liu, Z., Wang, H., Yang, Y., Sun, C., Ye, J., & Liu, Y. (2024) · ACS Nano · doi:10.1021/acsnano.4c05013 · Cited by 24
Zhao, S., Lu, Z., Zhao, F., Tang, S., Zhang, L., & Feng, C. (2025) · Frontiers in Immunology · doi:10.3389/fimmu.2025.1538969 · Cited by 24
Xie, H., Zhang, H., Zhou, L., Chen, J., Yao, S., He, Q., Li, Z., & Zhou, Z. (2025) · Journal of Translational Medicine · doi:10.1186/s12967-025-06232-9 · Cited by 20
“However, antibiotics are known to induce significant changes beyond microbiota depletion, including increased gut permeability, altered immune responses, and potential systemic effects, which may influence the spinal microenvironment [49, 50].”
The Lung Microbiome in COPD and Lung Cancer: Exploring the Potential of Metal-Based Drugs
O’Shaughnessy, M., Sheils, O. M., & Baird, A. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms241512296 · Cited by 22
Zhang, C., Chen, Y., Duan, R., Zhang, Y., Zheng, H., Zhang, J., Zhang, T., Xu, J., Li, K., Pei, F., et al. (2025) · iMeta · doi:10.1002/imt2.70012 · Cited by 19
“One possible explanation for this is that following the antibiotic ‐ induced disruption of the maternal gut microbiota, bacteria ‐ carrying resistance genes were selectively enriched [34].”
Pan, Z., Ma, T., Steele, M. A., & Guan, L. L. (2024) · ISME Communications · doi:10.1093/ismeco/ycae044 · Cited by 21
“Antibiotics were used to treat diarrhea for both CON and SCB calves in this study [22], and the usage of antibiotics is capable of reshaping the gut microbiome [63].”
MethodTao, Y., Zheng, D., Zou, W., Guo, T., Liao, G., & Zhou, W. (2024) · European Journal of Medicinal Chemistry · doi:10.1016/j.ejmech.2024.116461 · Cited by 19
Role of sulfidogenic members of the gut microbiota in human disease
Pimenta, A. I., Bernardino, R. M., & Pereira, I. A. C. (2024) · Advances in microbial physiology/Advances in Microbial Physiology · doi:10.1016/bs.ampbs.2024.04.003 · Cited by 18
Sun, L., Cheng, Z., Wang, M., Wei, C., Liu, H., & Yang, Y. (2024) · Ecotoxicology and Environmental Safety · doi:10.1016/j.ecoenv.2024.117447 · Cited by 19
Deciphering Multidrug-Resistant Pseudomonas aeruginosa: Mechanistic Insights and Environmental Risks
Yang, P., Hamar, P., & Pei, D. (2025) · Toxics · doi:10.3390/toxics13040303 · Cited by 19
“For example, antibiotic use may lead to an imbalance in the gut micro-biome [20], allowing pathogenic bacteria like P. aeruginosa to more easily infect the host.”
Prolonged delays in human microbiota transmission after a controlled antibiotic perturbationPreprint
Xue, K. S., Walton, S. J., Goldman, D. A., Morrison, M. L., Verster, A. J., Parrott, A. B., Yu, F. B., Neff, N. F., Rosenberg, N. A., Ross, B. D., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.09.26.559480 · Cited by 22
“…samples at a mixture of weekly and daily intervals for two months, and in the middle of the study, one subject in each household took the broad-spectrum antibiotic ciprofloxacin orally for five days as a controlled perturbation to open niches in the established, adult gut microbiome 23,34,35 .”
BackgroundThe rise, fall, and resurgence of phage therapy for urinary tract infection
Zulk, J. J., Patras, K. A., & Maresso, A. W. (2024) · EcoSal Plus · doi:10.1128/ecosalplus.esp-0029-2023 · Cited by 18
Challenges of antimicrobial stewardship among older adults
Alves, J., Prendki, V., Chedid, M., Yahav, D., Bosetti, D., & Rello, J. (2024) · European Journal of Internal Medicine · doi:10.1016/j.ejim.2024.01.009 · Cited by 18
Daisley, B. A., & Allen‐Vercoe, E. (2024) · Annals of the New York Academy of Sciences · doi:10.1111/nyas.15237 · Cited by 17
Antibiotic-associated changes in Akkermansia muciniphila alter its effects on host metabolic health
Han, Y., Teng, T. M., Han, J., & Kim, H. S. (2025) · Microbiome · doi:10.1186/s40168-024-02023-4 · Cited by 22
Wang, M., Liu, Y., Zhong, L., Wu, F., & Wang, J. (2025) · Frontiers in Immunology · doi:10.3389/fimmu.2025.1533343 · Cited by 17
Zhao, L., Xu, J. Z., Li, X., Liu, S., Du, J., Jia, X., Wang, Z., Ge, L., Cui, K., Ga, Y., et al. (2025) · Environment International · doi:10.1016/j.envint.2025.109679 · Cited by 15
Iqbal, S., Begum, F., Ullah, I., Jalal, N., & Shaw, P. M. (2024) · Critical Reviews in Microbiology · doi:10.1080/1040841x.2024.2319669 · Cited by 21
“…Mitchell et al. 2020): Microbial ecology; Microbes found in general habitats like fresh-waters (tran et al. 2021), soils (Yi et al. 2021), and gut (Fishbein et al. 2023), taxonomy; tens of millions of microorganisms are known, spanning multiple domains (Sunagawa et al. 2015; Biteen et al. 2016;…”
An intratumor bacteria-targeted DNA nanocarrier for multifaceted tumor microenvironment intervention
Wang, Y., Fu, X., Zhu, Y., Lin, M., Cai, R.-D., Zhu, Y., & Wu, T. (2024) · Materials Today Bio · doi:10.1016/j.mtbio.2024.101144 · Cited by 17
Favaron, A., Abdalla, Y., McCoubrey, L. E., Nandiraju, L. P., Shorthouse, D., Gaisford, S., Basit, A. W., & Orlu, M. (2024) · European Journal of Pharmaceutical Sciences · doi:10.1016/j.ejps.2024.106845 · Cited by 17
Antioxidant Potential of Xanthohumol in Disease Prevention: Evidence from Human and Animal Studies
Piekara, J., & Piasecka‐Kwiatkowska, D. (2024) · Antioxidants · doi:10.3390/antiox13121559 · Cited by 16
Parodi, E. L., Novi, M., Bottino, P., Porta, E. L., Merlotti, G., Castello, L. M., Gotta, F., Rocchetti, A., & Quaglia, M. (2025) · Microorganisms · doi:10.3390/microorganisms13020445 · Cited by 16
“As discussed in Section 4.5.2 the use of antibiotics generally alters GM, reducing physiological populations such as Firmicutes and creating an inflammatory environment with a rise of pathobionts [88].”
InfluentialIntestinal host–microbe interactions fuel pulmonary inflammation in cigarette smoke exposed mice
Yang-Jensen, S. K., Nägele, N. S., Sonne, S. B., Koeninger, L., Pineault, M., Tremblay, F., Kristensen, N. N., Bay, L., Aubin, S., Morissette, M. C., et al. (2025) · Gut Microbes · doi:10.1080/19490976.2025.2519699 · Cited by 16
Xiang, Y., Li, Z., Liu, C., Wei, Z., Mo, X., Zhong, Y., He, R., Liang, Z., He, Y., & He, J. (2025) · Frontiers in Veterinary Science · doi:10.3389/fvets.2025.1603107 · Cited by 14
“…studies have already provided compelling evidence regarding the disruption of the gut microbiome by hormones and antibacterial drugs, mainly focusing on aspects such as the composition, diversity, and abundance of the gut microbiota and the reduction in the number of beneficial bacteria (39–41).”
Gut microbiome in gastrointestinal neoplasms: from mechanisms to precision therapeutic strategies
Song, J., Zhang, W., & Wang, D. (2025) · Gut Pathogens · doi:10.1186/s13099-025-00734-z · Cited by 17
“…of the antimicrobial peptide LL-37, reduce the intestinal pH environment to hinder the spore germination of pathogenic bacteria (such as Clostridium difficile ), and activate immune effector molecules such as REGIIIγ/β to enhance the clearance ability of vancomycin-resistant enterococci (VRE) [51].”
Sulfated dietary fiber protects gut microbiota from antibiotics
Wu, F., Yu, X. A., Angeles-Albores, D., Erdman, S. E., & Alm, E. J. (2025) · Microbiome · doi:10.1186/s40168-025-02176-w · Cited by 17
The emerging role of the gut microbiome in depression: implications for precision medicine
Liu, L., Wang, H., Guo, S., Liu, S., Du, Y., Wang, L. Y., He, D., Mo, X., Zhang, H., Cheng, Q., et al. (2025) · Molecular Psychiatry · doi:10.1038/s41380-025-03191-x · Cited by 17
“In the complex gut microbiome, antibiotics often target both harmful and bene fi cial bacteria indiscriminately [149].”
Cao, J., Ma, Q., Shi, J., Wang, X., Ye, D., Liang, J., & Zou, J. (2025) · Pathogens · doi:10.3390/pathogens14020111 · Cited by 16
Innovative Therapeutic Strategies for Asthma: The Role of Gut Microbiome in Airway Immunity
Liu, Y., Dai, J., Zhou, G., Chen, R., Bai, C., & Shi, F. (2025) · Journal of Asthma and Allergy · doi:10.2147/jaa.s504571 · Cited by 15
Improving Empiric Antibiotic Selection for Patients Hospitalized With Abdominal Infection
Gohil, S. K., Septimus, E. J., KLEINMAN, K. P., Varma, N., Sands, K., Avery, T. R., Mauricio, A., Sljivo, S., Rahm, R., Roemer, K., et al. (2025) · JAMA Surgery · doi:10.1001/jamasurg.2025.1108 · Cited by 14
Gut–lung axis in asthma and obesity: role of the gut microbiome
Tashiro, H., Kuwahara, Y., & Takahashi, K. (2025) · Frontiers in Allergy · doi:10.3389/falgy.2025.1618466 · Cited by 17
Gut microbiota in gastric cancer: from pathogenesis to precision medicine
Huo, S., Lv, K., Han, L., Zhao, Y., & Jiang, J. (2025) · Frontiers in Microbiology · doi:10.3389/fmicb.2025.1606924 · Cited by 13
Liu, C., Wang, X., Zhang, Z., Wang, W., Wang, T., Zhao, Y., Wang, M., & Chen, W. (2025) · Nucleic Acids Research · doi:10.1093/nar/gkaf1190 · Cited by 17
“Its composition and function are shaped by a range of host and environmental factors, including age [ 18 ], sex [ 19 ], body mass index (BMI) [ 20 ], geography [ 21 ], diet [ 4 ], antibiotic use [ 22 ], and host genetics [ 23 ].”
Shen, P., Cheng, P., Li, Y., Zong, G., Deng, R., Qian, C., Zhao, Y., Wei, Z., & Lu, Y. (2023) · European Journal of Pharmacology · doi:10.1016/j.ejphar.2023.176217 · Cited by 13
Radu, A.-F., BUNGAU, S. G., Aron, R. A. C., Tarce, A. G., Bodog, R. F., Bodog, T. M., & Radu, A.-F. (2024) · Antibiotics · doi:10.3390/antibiotics13100938 · Cited by 13
“…colonization via biofilm formation, immune system dysfunctions, genetic defects [13], the development of gut dysbiosis due to antibiotic therapy [14], delays in initiating treatment, extended intervals between doses, increased hepatic or renal clearance, inappropriate dosage adjustments…”
BackgroundZhao, X.-L., Xu, L.-Y., Li, K.-D., Tang, F., Liu, D., Zhang, J., Cao, Z.-J., Peng, C., & Ao, H. (2025) · Journal of Ethnopharmacology · doi:10.1016/j.jep.2025.119616 · Cited by 13
Leveraging strain competition to address antimicrobial resistance with microbiota therapies
Steed, D. B., Koundakjian, D., Harris, A. D., Rosato, A. E., Konstantinidis, K. T., & Woodworth, M. H. (2025) · Gut Microbes · doi:10.1080/19490976.2025.2488046 · Cited by 13
Effects of antibiotics on chicken gut microbiota: community alterations and pathogen identification
Zhan, R., Lu, Y., Xu, Y., Li, X., Wang, X., & Yu, G. (2025) · Frontiers in Microbiology · doi:10.3389/fmicb.2025.1562510 · Cited by 13
“Moreover, because the gut microbiome is a complex microbial ecological network, the impacts of different antibiotics vary, (Fishbein et al., 2023), as established herein, further indicating variations in the exposure time required for different antibiotics to alter the community structure and in…”
The gut microbiome in solid-organ and haematopoietic-stem-cell transplantation
Swarte, J. C., Zhang, S., Bakker, S. J. L., Björk, J. R., & Weersma, R. K. (2026) · Nature Reviews Microbiology · doi:10.1038/s41579-025-01271-x · Cited by 14
Principles and Practice Guidelines of Microbiota Medicine: Statements From the CHINAGUT Conference
Zhang, F., Pi, Z., Wong, H. S., Ahuja, V., Porcari, S., Ishikawa, D., Cao, H., Chen, L., Chen, N., Chen, X., et al. (2026) · Microbiota Medicine Research · doi:10.1002/mmr3.70001 · Cited by 15
Fan, S., Tu, Z., Zhang, Z., Fu, L. H., Shen, N., & Xiao, X. (2026) · Journal of Agricultural and Food Chemistry · doi:10.1021/acs.jafc.5c12022 · Cited by 16
Exploring novel microbial metabolites and drugs for inhibiting Clostridioides difficile
Abouelkhair, A. A., & Seleem, M. N. (2024) · mSphere · doi:10.1128/msphere.00273-24 · Cited by 11
Microbes in Health and Disease: Human Gut Microbiota
Hu, C., & Shen, H. (2024) · Applied Sciences · doi:10.3390/app142311354 · Cited by 17
Towards a unified approach in managing resistance to vaccines, drugs, and pesticides
Alyokhin, A., Rosenthal, B. M., Weber, D. C., & Baker, M. B. (2025) · Biological reviews/Biological reviews of the Cambridge Philosophical Society · doi:10.1111/brv.13174 · Cited by 11
The Effect of Gut Microbiome Perturbation on the Bioavailability of Glycyrrhizic Acid in Rats
Shi, T., Li, H., Zhang, Z., Zang, Y., Jiang, S., & Yuan, T. (2025) · Pharmaceutics · doi:10.3390/pharmaceutics17040457 · Cited by 11
“Furthermore, the gut microbiome has the potential to influence the host gene expression; our results indicated that probiotic intervention could significantly downregulate the relative expression of MDR1 compared to both the control and ATB groups, particularly in the ileum part.”
Touitou, Y., Perlemuter, G., & Touitou, C. (2025) · Chronobiology International · doi:10.1080/07420528.2025.2540039 · Cited by 11
“…use notably reduces microbial diversity and disrupts circadian cycling of essential functions such as short-chain fatty acid (SCFA) production, with effects often persisting beyond treatment and impairing immune and metabolic regulation (Deaver et al. 2018; Fishbein et al. 2023; Zhang et al. 2024).”
Hu, J., Feng, S.-Y., Wu, L., He, S.-Z., Chen, X.-F., Li, G., Min, Y., Xu, H.-L., Sun, Q.-S., Xie, S., et al. (2026) · Journal of Advanced Research · doi:10.1016/j.jare.2026.04.065 · Cited by 10
Qian, H., Lin, Z.-Y., Zhang, X., Qin, M., Yu, H., Liao, X., Liu, Y., Ren, H., & Sun, J. G. (2024) · Journal of Cleaner Production · doi:10.1016/j.jclepro.2024.144177 · Cited by 11
Liu, X., Tan, X., Yu, Y., Niu, J., Zhao, B., & Wang, Q. (2024) · Neuropharmacology · doi:10.1016/j.neuropharm.2024.110266 · Cited by 12
Barcan, A. S., Humble, J. L., Kasaragod, S., Sajib, M. S. I., Barcan, R. A., McGinnity, P., Welch, T. J., Robertson, B., Vamanu, E., Bacigalupo, A., et al. (2025) · Animal Microbiome · doi:10.1186/s42523-025-00377-0 · Cited by 11
Zhang, F., Ding, Z., Lian, Y., Yang, X., Hu, P., Liu, Y., Xu, L., Li, Z., & Qiu, H. (2024) · The Oncologist · doi:10.1093/oncolo/oyae362 · Cited by 11
Yu, D., Wang, H., Zhang, H., Lu, W., & Chen, W. (2025) · Food Bioscience · doi:10.1016/j.fbio.2025.106298 · Cited by 11
Wang, Y.-N., Cai, T.-G., Li, Y., Dai, W., Lin, D., Zheng, J.-J., Wang, Y.-F., & Zhu, D. (2025) · Journal of Hazardous Materials · doi:10.1016/j.jhazmat.2025.138294 · Cited by 11
Sustainable Nanotechnology Strategies for Modulating the Human Gut Microbiota
Törős, G., Gulyás, G., El-Ramady, H. R., Alibrahem, W., Muthu, A., Gangakhedkar, P. S., Atieh, R., & Prokisch, J. (2025) · International Journal of Molecular Sciences · doi:10.3390/ijms26125433 · Cited by 11
“Furthermore, disruptions in gut microbiota due to antibiotic use may facilitate the proliferation of antibiotic-resistant pathogens, complicating infection management [192], while a balanced gut microbiota is crucial for immune function and disease protection.”
Qiu, J., Wu, D., Xu, C., Zhuang, Y., Lu, Y., sun, A., Lu, X., Han, J., & Ni, L. (2025) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2025.147037 · Cited by 11
Factors influencing gut microbial colonization: A host-microbe-environment interaction perspective
Zhao, Y., Ren, Z., Xu, Q., Zhu, T., Hu, H., Fu, Y., Jiang, J., & Zhai, Q. (2026) · Current Research in Food Science · doi:10.1016/j.crfs.2026.101361 · Cited by 13
“Additionally, broad-spectrum antibiotics can drastically deplete diverse symbiotic bacteria, creating an ecological vacuum that facilitates the colonization and infection by drug-resistant pathogens such as Clostridium difficile (Fishbein et al., 2023).”
Wu, M., Fan, Q., Li, X., Wang, P., Feng, C., Wang, L., Chang, Z., Wu, W., & Chong, R. (2024) · Journal of Colloid and Interface Science · doi:10.1016/j.jcis.2024.04.077 · Cited by 10
Sandes, V. S., Figueras, A., & Lima, E. D. C. (2024) · Antibiotics · doi:10.3390/antibiotics13050457 · Cited by 12
Zhao, M., Cao, L., Bai, Q., Lu, Y., Li, B., Wu, W., Ye, J.-Z., Chen, X., Wang, Z., Liu, B., et al. (2024) · Angewandte Chemie International Edition · doi:10.1002/anie.202408918 · Cited by 10
He, H., Fang, C., Liu, L., Li, M., & Liu, W. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms252010957 · Cited by 12
“All procedures used in this study were approved by the Animal Care and Use Committee of Xinjiang Agricultural University (Approval number: 2024010).”
MethodRoseburia intestinalis: A possible target for vascular calcification
Pan, X., Song, Y., Liang, Y., Feng, G., & Wang, Z. (2024) · Heliyon · doi:10.1016/j.heliyon.2024.e39865 · Cited by 11
Acetylshikonin reduces the spread of antibiotic resistance via plasmid conjugation
Liu, W., Wang, Z., Huang, Y., Liu, Y., Li, R., Wang, M., Zhang, H., Meng, C., & Xiao, X. (2024) · International Journal of Antimicrobial Agents · doi:10.1016/j.ijantimicag.2024.107370 · Cited by 10
The microbiome and the eye: a new era in ophthalmology
Kaur, S., Patel, B. C. K., Collen, A., & Malhotra, R. (2024) · Eye · doi:10.1038/s41433-024-03517-z · Cited by 10
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
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
