Antibiotic perturbations to the gut microbiome

Fishbein, Skye R. S.; Mahmud, Bejan; Dantas, Gautam

doi:10.1038/s41579-023-00933-y

Cited by 440Gut microbiota and healthOral microbiology and periodontitis researchMicrobial Community Ecology and Physiology

Antibiotic perturbations to the gut microbiome

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Fishbein, Skye R. S., Mahmud, Bejan, Dantas, Gautam·2023·Nature Reviews Microbiology

DOI 10.1038/s41579-023-00933-yPMC PMC12087466

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Abstract

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 time to pathogen identification with standard techniques is approximately 96 h.
“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]
The passages from “Species and community determinants of susceptibility during antibiotic exposure” discuss susceptibility testing, but give no time to pathogen identification. Searches for a 96-hour median and diagnostic turnaround time found no passage addressing that figure. Page numbers were not available in our copy. (LLM, conf=0.73)
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Antibiotic-Associated Diarrhea Accompanied by Large-Scale Alterations in the Composition of the Fecal Microbiota
Young, V. B., & Schmidt, T. M. (2004) · Journal of Clinical Microbiology · doi:10.1128/jcm.42.3.1203-1206.2004 · Cited by 337 · see citing works
Elevated rates of horizontal gene transfer in the industrialized human microbiome
Groussin, M., Poyet, M., Sistiaga, A., Kearney, S. M., Moniz, K., Noel, M., Hooker, J., Gibbons, S. M., Ségurel, L., Froment, A., et al. (2021) · Cell · doi:10.1016/j.cell.2021.02.052 · Cited by 331 · cited 1× · see citing works
“Overall, higher rates of horizontal transfer of ARGs are found in populations with higher reported clinical use and environmental antibiotic exposure 139 .”
Background
Understanding Competition and Cooperation within the Mammalian Gut Microbiome
Coyte, K. Z., & Rakoff-Nahoum, S. (2019) · Current Biology · doi:10.1016/j.cub.2019.04.017 · Cited by 329 · see citing works
Key bacterial taxa and metabolic pathways affecting gut short-chain fatty acid profiles in early life
Tsukuda, N., Yahagi, K., Hara, T., Watanabe, Y., Matsumoto, H., Mori, H., Higashi, K., Tsuji, H., Matsumoto, S., Kurokawa, K., et al. (2021) · The ISME Journal · doi:10.1038/s41396-021-00937-7 · Cited by 324 · see citing works
Short- and long-term effects of oral vancomycin on the human intestinal microbiota
Isaac, S., Scher, J. U., Djuković, A., Jiménez‐Hernández, N., Littman, D. R., Abramson, S. B., Pamer, E. G., & Úbeda, C. (2016) · Journal of Antimicrobial Chemotherapy · doi:10.1093/jac/dkw383 · Cited by 320 · cited 1× · see citing works
“animals) results in distinct loss of several Gram-negative gut microbiome commensals including Bacteroides, Prevotella and Alistipes spp.(97).”
Background
Dietary fat intake and risk of cardiovascular disease and all-cause mortality in a population at high risk of cardiovascular disease
Guasch-Ferré, M., Babio, N., Martínez-González, M. A., Corella, D., Ros, E., Martín-Peláez, S., Estruch, R., Arós, F., Gómez-Gracia, E., Fiol, M., et al. (2015) · The American Journal of Clinical Nutrition · doi:10.3945/ajcn.115.116046 · Cited by 313 · cited 1× · see citing works
“Investigations into ‘Western-style’ diets (high in fat and simple sugars) have revealed that these diets correlate with an increased risk for obesity and heart disease, among other poor health outcomes 103,104 .”
Background
Role of dietary fiber in the recovery of the human gut microbiome and its metabolome
Tanes, C., Bittinger, K. L., Gao, Y., Friedman, E. S., Nessel, L. A., Paladhi, U. R., Chau, L., Panfen, E., Fischbach, M. A., Braun, J. G., et al. (2021) · Cell Host & Microbe · doi:10.1016/j.chom.2020.12.012 · Cited by 306 · cited 1× · see citing works
“Specifically, fibre-containing diets encouraged a rapid restoration of stool butyrate levels and a return of Firmicutes with distinct amino acid metabolism 108 .”
Background
Persistent metagenomic signatures of early-life hospitalization and antibiotic treatment in the infant gut microbiota and resistome
Gasparrini, A. J., Wang, B., Sun, X., Kennedy, E. A., Hernandez-Leyva, A. J., Ndao, I. M., Tarr, P. I., Warner, B. B., & Dantas, G. A. (2019) · Nature Microbiology · doi:10.1038/s41564-019-0550-2 · Cited by 305 · cited 2× · see citing works
“Specifically, it is imperative for future models of antibiotic-mediated damage to the gut community to control for and test the predictive capacities of broader sets of host and microbial variables to yield more predictive models of the community dynamics 52,59,126 .”
BackgroundSelf-citation
Minimizing treatment-induced emergence of antibiotic resistance in bacterial infections
Stracy, M., Snitser, O., Yelin, I., Amer, Y., Parizade, M., Katz, R., Rimler, G., Wolf, T., Herzel, E., Koren, G., et al. (2022) · Science · doi:10.1126/science.abg9868 · Cited by 305 · cited 1× · see citing works
“Notably, the presence of ARG-encoding pathobionts in the gut is a risk factor for recurrent resistant infections post-treatment 30 .”
Background
Triclosan at environmentally relevant concentrations promotes horizontal transfer of multidrug resistance genes within and across bacterial genera
Lu, J., Wang, Y., Li, J., Mao, L., Nguyen, S. H., Duarte, T. P. S., Coin, L., Bond, P. L., Yuan, Z., & Guo, J. (2018) · Environment International · doi:10.1016/j.envint.2018.10.040 · Cited by 290 · cited 1× · see citing works
“Increased rates of conjugation can result from the antibiotic-mediated induction of the bacterial SOS response and increased membrane permeability 153–157 , which may stem from the DNA damage inflicted by certain antibiotics.”
Background
Antibiotics as a selective driver for conjugation dynamics
Lopatkin, A. J., Huang, S., Smith, R. P., Srimani, J. K., Sysoeva, T. A., Bewick, S. A., Karig, D., & You, L. (2016) · Nature Microbiology · doi:10.1038/nmicrobiol.2016.44 · Cited by 289 · see citing works
Bile Acid Recognition by the Clostridium difficile Germinant Receptor, CspC, Is Important for Establishing Infection
Francis, M. B., Allen, C. A., Shrestha, R., & Sorg, J. A. (2013) · PLoS Pathogens · doi:10.1371/journal.ppat.1003356 · Cited by 284 · cited 1× · see citing works
“Importantly, SER-109 improves the production of secondary bile acids, which presumably prevent C. difficile germination 190,191 .”
Background
What Antimicrobial Resistance Has Taught Us About Horizontal Gene Transfer
Barlow, M. (2009) · Methods in molecular biology · doi:10.1007/978-1-60327-853-9_23 · Cited by 283 · cited 1× · see citing works
“Antibiotics can reportedly facilitate all three mechanisms of HGT: transformation 141–143 , transduction 144 and conjugation 145,146 , the last being the best-studied form of horizontal transfer of ARGs 138,147–152 (Box 2).”
Background
Recovery of the Gut Microbiota after Antibiotics Depends on Host Diet, Community Context, and Environmental Reservoirs
Ng, K. M., Aranda-Díaz, A., Tropini, C., Frankel, M. R., Treuren, W. V., O’Loughlin, C. T., Merrill, B. D., Yu, F. B., Pruss, K. M., Oliveira, R. A., et al. (2019) · Cell Host & Microbe · doi:10.1016/j.chom.2019.10.011 · Cited by 270 · cited 2× · see citing works
“Without fibre, mice with a conventional microbiome or a humanized microbiome have a delayed recovery in alpha diversity after ciprofloxacin treatment 96 .”
Background
Salmonella persisters promote the spread of antibiotic resistance plasmids in the gut
Bakkeren, E., Huisman, J. S., Fattinger, S. A., Hausmann, A., Furter, M., Egli, A., Slack, E. M. C., Sellin, M. E., Bonhoeffer, S., Regoes, R. R., et al. (2019) · Nature · doi:10.1038/s41586-019-1521-8 · Cited by 258 · cited 1× · see citing works
“Apart from spore-mediated persistence, many gut microorganisms can tolerate antibiotics through various resiliency mechanisms, including persister cell formation, perhaps in a mucin-embedded biofilm or deeper tissue niche where they can resist antibiotics 84–87 .”
Background
Probiotics impact the antibiotic resistance gene reservoir along the human GI tract in a person-specific and antibiotic-dependent manner
Montassier, E., Valdés-Mas, R., Batard, E., Zmora, N., Dori-Bachash, M., Suez, J., & Elinav, E. (2021) · Nature Microbiology · doi:10.1038/s41564-021-00920-0 · Cited by 256 · see citing works
Microbiota-accessible carbohydrates suppress Clostridium difficile infection in a murine model
Hryckowian, A. J., Treuren, W. V., Smits, S. A., Davis, N. M., Gardner, J. O., Bouley, D. M., & Sonnenburg, J. L. (2018) · Nature Microbiology · doi:10.1038/s41564-018-0150-6 · Cited by 249 · cited 1× · see citing works
“…can be used to restore the production of these molecules; this restoration is largely associated with colonization resistance against pathogens 49,177,178 or prebiotic administration, which may facilitate the growth of commensal members of the microbiome and/or prevent the colonization of…”
Antibiotic use and the development of inflammatory bowel disease: a national case-control study in Sweden
Nguyen, L. H., Örtqvist, A. K., Cao, Y., Simon, T. G., Roelstraete, B., Song, M., Joshi, A. D., Staller, K. D., Chan, A. T., Khalili, H., et al. (2020) · The Lancet. Gastroenterology & hepatology · doi:10.1016/s2468-1253(20)30267-3 · Cited by 248 · cited 2× · see citing works
“…and metabolic pathway architecture of the gut microbial community (referred to as dysbiosis) have been associated with an increased risk of numerous human pathologies, including inflammatory bowel disease 5 , obesity 6 , colorectal cancer 7,8 and numerous gastrointestinal infections 9–11 .”
BackgroundInfluential
On the antibacterial action of cultures of a penicillium, with special reference to their use in the isolation of B. influenzae. 1929.
Fleming, A. (2001) · PubMed Central · Cited by 242 · see citing works
A review of the role of antibiotic policies in the control of antibiotic resistance
Gould, I. M. (1999) · Journal of Antimicrobial Chemotherapy · doi:10.1093/jac/43.4.459 · Cited by 242 · cited 2× · see citing works
“…a greater understanding of the mechanisms by which antibiotics perturb the human microbiome is critical to maximizing the therapeutic benefits of these agents while reducing both the damage imposed on the commensal gut microbiome and the broader spread of antimicrobial resistant pathogens 23,24 .”
Background
Transmission of human-associated microbiota along family and social networks
Brito, I., Gurry, T., Zhao, S., Huang, K. H., Young, S., Shea, T. P., Naisilisili, W., Jenkins, A., Jupiter, S. D., Gevers, D., et al. (2019) · Nature Microbiology · doi:10.1038/s41564-019-0409-6 · Cited by 239 · cited 1× · see citing works
“those incorporating long-read metagenomic sequencing, can provide increased strain-level resolution 70–72 .”
Background
Antibiotic-induced replication stress triggers bacterial competence by increasing gene dosage near the origin
Slager, J., Kjos, M., Attaiech, L., & Veening, J.-W. (2014) · Cell · doi:10.1016/j.cell.2014.01.068 · Cited by 237 · see citing works
Multimodal interactions of drugs, natural compounds and pollutants with the gut microbiota
Lindell, A. E., Zimmermann‐Kogadeeva, M., & Patil, K. R. (2022) · Nature Reviews Microbiology · doi:10.1038/s41579-022-00681-5 · Cited by 232 · cited 1× · see citing works
“The interactions between these non-antibiotic factors and the microbiome have been reviewed elsewhere 109 .”
Background
Clusters of Antibiotic Resistance Genes Enriched Together Stay Together in Swine Agriculture
Johnson, T. A., Stedtfeld, R. D., Wang, Q., Cole, J. R., Hashsham, S. A., Looft, T. P., Zhu, Y., & Tiedje, J. M. (2016) · mBio · doi:10.1128/mbio.02214-15 · Cited by 231 · see citing works
Acute and persistent effects of commonly used antibiotics on the gut microbiome and resistome in healthy adults
Anthony, W., Wang, B., Sukhum, K. V., D’Souza, A. W., Hink, T., Cass, C., Seiler, S. M., Reske, K. A., Coon, C., Dubberke, E. R., et al. (2022) · Cell Reports · doi:10.1016/j.celrep.2022.110649 · Cited by 231 · cited 7× · see citing works
“Antibiotics expectedly enrich for ARGs that confer resistance to the treatment agent 33,34,51,62–66 ,114,115, 117, 119– 123 through selection of bacterial strains Importantly, the effects of antibiotics on the gut resistome vary substantially depending on the nature of the administered drug…”
BackgroundInfluentialSelf-citation
The distribution of antibiotic use and its association with antibiotic resistance
Olesen, S. W., Barnett, M. L., MacFadden, D. R., Brownstein, J. S., Hernández–Dı́az, S., Lipsitch, M., & Grad, Y. H. (2018) · eLife · doi:10.7554/elife.39435 · Cited by 227 · see citing works
Gut microbiome alterations in high-fat-diet-fed mice are associated with antibiotic tolerance
Liu, Y., Yang, K., Jia, Y., Shi, J., Tong, Z., Fang, D., Yang, B., Su, C., Li, R., Xiao, X., et al. (2021) · Nature Microbiology · doi:10.1038/s41564-021-00912-0 · Cited by 227 · see citing works
Widespread transfer of mobile antibiotic resistance genes within individual gut microbiomes revealed through bacterial Hi-C
Kent, A. G., Vill, A. C., Shi, Q., Satlin, M. J., & Brito, I. L. (2020) · Nature Communications · doi:10.1038/s41467-020-18164-7 · Cited by 216 · cited 5× · see citing works
“These limitations can be addressed through Hi-C, a technique in which crosslinking before cell lysis preserves interacting DNA molecules and the information regarding the MGE–bacterial host associations 138 .”
BackgroundMethodInfluential
Global transcriptional control by glucose and carbon regulator CcpA in Clostridium difficile
Antunes, A., Camiade, É., Monot, M., Courtois, E., Barbut, F., Sernova, N. V., Rodionov, D. A., Martin‐Verstraete, I., & Dupuy, B. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks864 · Cited by 205 · see citing works
Antibiotic Administration Routes Significantly Influence the Levels of Antibiotic Resistance in Gut Microbiota
Zhang, L., Huang, Y., Zhou, Y., Buckley, T., & Wang, H. H. (2013) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.00670-13 · Cited by 203 · see citing works
Metabolism of Bile Salts in Mice Influences Spore Germination in Clostridium difficile
Giel, J. L., Sorg, J. A., Sonenshein, A. L., & Zhu, J. (2010) · PLoS ONE · doi:10.1371/journal.pone.0008740 · Cited by 195 · see citing works
Inhibiting Growth of Clostridioides difficile by Restoring Valerate, Produced by the Intestinal Microbiota
McDonald, J. A. K., Mullish, B. H., Pechlivanis, A., Liu, Z., Brignardello, J., Kao, D. H., Holmes, E. C., Li, J. V., Clarke, T. B., Thursz, M. R., et al. (2018) · Gastroenterology · doi:10.1053/j.gastro.2018.07.014 · Cited by 189 · cited 1× · see citing works
“…be used to restore the production of these molecules; this restoration is largely associated with colonization resistance against pathogens 49,177,178 or prebiotic administration, which may facilitate the growth of commensal members of the microbiome and/or prevent the colonization of pathogenic…”
Method
THE TREASURE CALLED ANTIBIOTICS.
Adedeji, W. A. (2016) · PubMed · Cited by 189 · see citing works
High-Fat Diet and Antibiotics Cooperatively Impair Mitochondrial Bioenergetics to Trigger Dysbiosis that Exacerbates Pre-inflammatory Bowel Disease
Lee, J., Cevallos, S. A., Byndloss, M. X., Tiffany, C. R., Olsan, E. E., Butler, B. P., Young, B. M., Rogers, A. W. L., Nguyen, H., Kim, K., et al. (2020) · Cell Host & Microbe · doi:10.1016/j.chom.2020.06.001 · Cited by 189 · cited 1× · see citing works
“Antibiotic treatment of mice on a high-fat diet pro-vokes pathological inflammation at the gut mucosa and increased levels of Enterobacterales, a taxonomic order that contains common pathobionts of the microbiome 105 .”
Background
Strain-level characterization of broad host range mobile genetic elements transferring antibiotic resistance from the human microbiome
Forster, S. C., Liu, J., Kumar, N., Gulliver, E. L., Gould, J. A., Escobar‐Zepeda, A., Mkandawire, T. T., Pike, L. J., Shao, Y., Stares, M. D., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-29096-9 · Cited by 189 · cited 1× · see citing works
“However, the spread of ARGs is not exclusively attributed to their primary bacterial hosts: ARGs are commonly encoded within mobile genetic elements (MGEs) 28 , which enable their acquisition by new hosts, including pathobionts 29 .”
Background
An assay for determining minimal concentrations of antibiotics that drive horizontal transfer of resistance
Jutkina, J., Rutgersson, C., Flach, C., & Larsson, D. G. J. (2016) · The Science of The Total Environment · doi:10.1016/j.scitotenv.2016.01.044 · Cited by 186 · see citing works
Salmonella typhimurium intercepts Escherichia coli signaling to enhance antibiotic tolerance
Vega, N. M., Allison, K. R., Samuels, A. N., Klempner, M. S., & Collins, J. J. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1308085110 · Cited by 185 · see citing works
Antibiotic-Induced Disruption of Gut Microbiota Alters Local Metabolomes and Immune Responses
Sun, L., Zhang, X., Zhang, Y., Zheng, K., Xiang, Q., Chen, N., Chen, Z., Zhang, N., Zhu, J., & He, Q. (2019) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2019.00099 · Cited by 183 · see citing works
Genomic insights into the 2016–2017 cholera epidemic in Yemen
Weill, F., Domman, D., Njamkepo, E., Almesbahi, A. A., Naji, M., Nasher, S. S., Rakesh, A., Assiri, A. M., Sharma, N. C., Kariuki, S., et al. (2018) · Nature · doi:10.1038/s41586-018-0818-3 · Cited by 182 · cited 1× · see citing works
“Although clinical studies of bacterial infections often emphasize the species and/or strain of opportunistic pathogens or pathobionts 53,54 , literature describing commensal fluctuations during antibiotic exposure is currently limited to the taxonomic resolution of genus or species.”
Background
Macrolide and Nonmacrolide Resistance with Mass Azithromycin Distribution
Doan, T. A., Worden, L., Hinterwirth, A. J., Arzika, A. M., Maliki, R., Abdou, A., Zhong, L., Chen, C., Cook, C. A., Lebas, E., et al. (2020) · New England Journal of Medicine · doi:10.1056/nejmoa2002606 · Cited by 182 · see citing works
Probiotics interaction with foodborne pathogens: a potential alternative to antibiotics and future challenges
Wan, M. L. Y., Forsythe, S. J., & El-Nezami, H. S. (2018) · Critical Reviews in Food Science and Nutrition · doi:10.1080/10408398.2018.1490885 · Cited by 180 · cited 2× · see citing works
“Nonetheless, probiotic organisms have been extensively used therapeutically against various pathogens, commonly achieving their native anti-infective activity through competitive exclusion, sequestration and release of antimicrobial compounds (constitutive or induced), as reviewed elsewhere 166 .”
Background
Necrotizing enterocolitis is preceded by increased gut bacterial replication, Klebsiella, and fimbriae-encoding bacteria
Olm, M., Bhattacharya, N., Crits-Christoph, A., Firek, B., Baker, R., Song, Y. S., Morowitz, M., & Banfield, J. (2019) · Science Advances · doi:10.1126/sciadv.aax5727 · Cited by 177 · see citing works
Clindamycin-induced enrichment and long-term persistence of resistant Bacteroides spp. and resistance genes
Löfmark, S., Jernberg, C., Jansson, J. K., & Edlund, C. (2006) · Journal of Antimicrobial Chemotherapy · doi:10.1093/jac/dkl420 · Cited by 175 · see citing works
The Gut Microbiome as a Reservoir for Antimicrobial Resistance
Anthony, W., Burnham, C. D., Dantas, G. A., & Kwon, J. H. (2020) · The Journal of Infectious Diseases · doi:10.1093/infdis/jiaa497 · Cited by 171 · cited 1× · see citing works
“17)), including drug-resistant Enterobacteriaceae, Clostridioides difficile , vancomycin-resistant Enterococcus and Salmonella spp., are responsible for a substantial amount of gastrointestinal disease 18 .”
BackgroundSelf-citation
Antibiotic effects on gut microbiota and metabolism are host dependent
Fujisaka, S., Ussar, S., Clish, C. B., Devkota, S., Dreyfuss, J. M., Sakaguchi, M., Soto, M., Konishi, M., Softic, S., Altındiş, E., et al. (2016) · Journal of Clinical Investigation · doi:10.1172/jci86674 · Cited by 166 · see citing works
Protection of the Human Gut Microbiome From Antibiotics
de Gunzburg, J., Ghozlane, A., Ducher, A., Chatelier, E. L., Duval, X., Ruppé, É., Armand-Lefèvre, L., Sablier-Gallis, F., Burdet, C., Alavoine, L., et al. (2017) · The Journal of Infectious Diseases · doi:10.1093/infdis/jix604 · Cited by 166 · see citing works
Efficacy of Hospital Cleaning Agents and Germicides Against EpidemicClostridium difficileStrains
Fawley, W. N., Underwood, S., Freeman, J., Baines, S. D., Saxton, K., Stephenson, K., Owens, R. C., & Wilcox, M. H. (2007) · Infection Control and Hospital Epidemiology · doi:10.1086/519201 · Cited by 165 · see citing works
Distinct impact of antibiotics on the gut microbiome and resistome: a longitudinal multicenter cohort study
Willmann, M., Vehreschild, M. J. G. T., Biehl, L. M., Vogel, W., Dörfel, D., Hamprecht, A. G., Seifert, H., Autenrieth, I. B., & Peter, S. (2019) · BMC Biology · doi:10.1186/s12915-019-0692-y · Cited by 162 · cited 6× · see citing works
“Recent investigations of the gut resistome have primarily relied on whole-metagenome shotgun sequencing with subsequent alignment of sequencing reads or annotated open reading frames from assembled contigs against one or a few of the available databases of known ARGs 32–34 ,59 ,62 ,114, 117– 119”
BackgroundMethodInfluential
Antibiotic-induced decreases in the levels of microbial-derived short-chain fatty acids correlate with increased gastrointestinal colonization of Candida albicans
Guinan, J., Wang, S., Hazbun, T. R., Yadav, H., & Thangamani, S. (2019) · Scientific Reports · doi:10.1038/s41598-019-45467-7 · Cited by 158 · cited 1× · see citing works
“…can be used to restore the production of these molecules; this restoration is largely associated with colonization resistance against pathogens 49,177,178 or prebiotic administration, which may facilitate the growth of commensal members of the microbiome and/or prevent the colonization of…”
Effect of various antibiotics on modulation of intestinal microbiota and bile acid profile in mice
Zhang, Y., Limaye, P. B., Renaud, H. J., & Klaassen, C. D. (2014) · Toxicology and Applied Pharmacology · doi:10.1016/j.taap.2014.03.009 · Cited by 155 · see citing works
Metagenome-assembled genome binning methods with short reads disproportionately fail for plasmids and genomic islands
Maguire, F., Jia, B., Gray, K. L., Lau, W. Y. V., Beiko, R. G., & Brinkman, F. S. L. (2020) · Microbial Genomics · doi:10.1099/mgen.0.000436 · Cited by 152 · see citing works
Impact of microbial derived secondary bile acids on colonization resistance against Clostridium difficile in the gastrointestinal tract
Winston, J. A., & Theriot, C. M. (2016) · Anaerobe · doi:10.1016/j.anaerobe.2016.05.003 · Cited by 150 · see citing works
Metagenomic analysis with strain-level resolution reveals fine-scale variation in the human pregnancy microbiomePreprint
Goltsman, D. S. A., Sun, C. L., Proctor, D. M., DiGiulio, D. B., Robaczewska, A., Thomas, B. C., Shaw, G. M., Stevenson, D. K., Holmes, S., Banfield, J. F., et al. (2018) · Genome Research · doi:10.1101/gr.236000.118 · Cited by 148 · cited 1× · see citing works
“those incorporating long-read metagenomic sequencing, can provide increased strain-level resolution 70–72 .”
Background
Diet, microbes, and host genetics: the perfect storm in inflammatory bowel diseases
Leone, V., Chang, E. B., & Devkota, S. (2013) · Journal of Gastroenterology · doi:10.1007/s00535-013-0777-2 · Cited by 142 · cited 1× · see citing works
“Investigations into ‘Western-style’ diets (high in fat and simple sugars) have revealed that these diets correlate with an increased risk for obesity and heart disease, among other poor health outcomes 103,104 .”
Background
Collateral damage from oral ciprofloxacin versus nitrofurantoin in outpatients with urinary tract infections: a culture-free analysis of gut microbiota
Stewardson, A. J., Gaïa, N., François, P., Malhotra-Kumar, S., Delémont, C., de Tejada, B. M., Schrenzel, J., Harbarth, S., & Lazarević, V. (2014) · Clinical Microbiology and Infection · doi:10.1016/j.cmi.2014.11.016 · Cited by 142 · cited 1× · see citing works
“…and nitrofurantoin, ciprofloxacin has been shown to cause a greater reduction in species richness (less than twofold) and beta diversity 58,59 , in addition to its effect in depleting Bifidobacterium and Ruminococcus spp. Azithromycin has been widely explored (in clinical trials of…”
Background
Cross-feeding modulates antibiotic tolerance in bacterial communities
Adamowicz, E. M., Flynn, J. M., Hunter, R. C., & Harcombe, W. R. (2018) · The ISME Journal · doi:10.1038/s41396-018-0212-z · Cited by 142 · cited 1× · see citing works
“In vitro studies of interactions between two gut commensals during antibiotic treatment indicate that symbiotic relationships can have multiple outcomes in effecting differences in antibiotic tolerance in one 99 or both members of the community 100,101 .”
Background
Antibiotic use during pregnancy alters the commensal vaginal microbiota
Stokholm, J., Schjørring, S., Eskildsen, C. E., Pedersen, L., Bischoff, A. L., Følsgaard, N. V., Carson, C. G., Chawes, B., Bønnelykke, K., Mølgaard, A., et al. (2013) · Clinical Microbiology and Infection · doi:10.1111/1469-0691.12411 · Cited by 139 · see citing works
Transfer of Carbapenem-Resistant Plasmid fromKlebsiella pneumoniaeST258 toEscherichia coliin Patient
Goren, M. G., Carmeli, Y., Schwaber, M. J., Chmelnitsky, I., Schechner, V., & Navon‐Venezia, S. (2010) · Emerging infectious diseases · doi:10.3201/eid1606.091671 · Cited by 138 · see citing works
Colonization of the live biotherapeutic product VE303 and modulation of the microbiota and metabolites in healthy volunteers
Dsouza, M., Menon, R., Crossette, E. M., Bhattarai, S. K., Schneider, J., Kim, Y., Reddy, S., Caballero, S., Felix, C. R., Cornacchione, L. P., et al. (2022) · Cell Host & Microbe · doi:10.1016/j.chom.2022.03.016 · Cited by 134 · cited 2× · see citing works
“…Biosciences), is composed of fewer members than SER-109 and demonstrates robust restoration of butyrate production and secondary bile acid production in dysbiotic human microbiomes engrafted into mice; this community is well tolerated when administered with vancomycin to healthy volunteers 189 .”
Background
Engineered Probiotic for the Inhibition of Salmonella via Tetrathionate-Induced Production of Microcin H47
Palmer, J. D., Piattelli, E., McCormick, B. A., Silby, M. W., Brigham, C. J., & Bucci, V. (2018) · ACS Infectious Diseases · doi:10.1021/acsinfecdis.7b00114 · Cited by 133 · see citing works
Clinical Relevance of Macrolide-Resistant Streptococcus pneumoniae for Community-Acquired Pneumonia
Lynch, J. P., & Martínez, F. J. (2002) · Clinical Infectious Diseases · doi:10.1086/324527 · Cited by 132 · cited 1× · see citing works
“…and metabolic pathway architecture of the gut microbial community (referred to as dysbiosis) have been associated with an increased risk of numerous human pathologies, including inflammatory bowel disease 5 , obesity 6 , colorectal cancer 7,8 and numerous gastrointestinal infections 9–11 .”
Background
Antibiotic perturbation of the preterm infant gut microbiome and resistome
Gasparrini, A. J., Crofts, T. S., Gibson, M. K., Tarr, P. I., Warner, B. B., & Dantas, G. A. (2016) · Gut Microbes · doi:10.1080/19490976.2016.1218584 · Cited by 130 · cited 1× · see citing works
“Enrichment for AMR often begins within the gut microbiome of the patient, with antibiotics increasing the abundance of resident bacteria that carry antibiotic resistance genes (ARGs) and altering ARG content within the gut microbiome (termed the ‘resistome’) 26,27 .”
BackgroundSelf-citation
Gut microbiome alteration in MORDOR I: a community-randomized trial of mass azithromycin distribution
Doan, T. A., Hinterwirth, A. J., Worden, L., Arzika, A. M., Maliki, R., Abdou, A., Kane, S., Zhong, L., Cummings, M. E., Sakar, S., et al. (2019) · Nature Medicine · doi:10.1038/s41591-019-0533-0 · Cited by 130 · see citing works
Antimicrobial Probiotics Reduce Salmonella enterica in Turkey Gastrointestinal Tracts
Forkus, B., Ritter, S. C., Vlysidis, M., Geldart, K., & Kaznessis, Y. N. (2017) · Scientific Reports · doi:10.1038/srep40695 · Cited by 128 · cited 1× · see citing works
“Probiotics can also be engineered to express and release pathogen-specific antimicrobial agents 201 .”
Background
Microbial Metabolism Modulates Antibiotic Susceptibility within the Murine Gut Microbiome
Cabral, D. J., Penumutchu, S., Reinhart, E. M., Zhang, C., Korry, B. J., Wurster, J. I., Nilson, R., Guang, A., Sano, W. H., Rowan-Nash, A. D., et al. (2019) · Cell Metabolism · doi:10.1016/j.cmet.2019.08.020 · Cited by 127 · cited 2× · see citing works
“Antibiotic susceptibility of a gut commensal may thus be determined by its surrounding nutrient milieu (Box 1), a concept that remains difficult to investigate in vivo 88–92 .”
Background
Cephalosporinases associated with outer membrane vesicles released by Bacteroides spp. protect gut pathogens and commensals against β-lactam antibiotics
Stentz, R., Horn, N., Cross, K. L., Salt, L. J., Brearley, C. A., Livermore, D. M., & Carding, S. R. (2014) · Journal of Antimicrobial Chemotherapy · doi:10.1093/jac/dku466 · Cited by 124 · cited 1× · see citing works
“As proof of principle, gut commensal Bacteroides spp. can release cephalosporinases that protect susceptible members of the community from lethal doses of cefotaxime 171 .”
Background
Maternal propensity for infections and risk of childhood asthma: a registry-based cohort study
Stokholm, J., Sevelsted, A., Bønnelykke, K., & Bisgaard, H. F. (2014) · The Lancet Respiratory Medicine · doi:10.1016/s2213-2600(14)70152-3 · Cited by 120 · see citing works
Induction of competence for genetic transformation by antibiotics: convergent evolution of stress responses in distant bacterial species lacking SOS?
Charpentier, X., Polard, P., & Claverys, J. P. (2012) · Current Opinion in Microbiology · doi:10.1016/j.mib.2012.08.001 · Cited by 118 · cited 1× · see citing works
“Antibiotics can reportedly facilitate all three mechanisms of HGT: transformation 141–143 , transduction 144 and conjugation 145,146 , the last being the best-studied form of horizontal transfer of ARGs 138,147–152 (Box 2).”
Background
Macrolide Resistance in MORDOR I — A Cluster-Randomized Trial in Niger
Doan, T. A., Arzika, A. M., Hinterwirth, A. J., Maliki, R., Zhong, L., Cummings, S., Sarkar, S., Chen, C., Porco, T. C., Keenan, J. D., et al. (2019) · New England Journal of Medicine · doi:10.1056/nejmc1901535 · Cited by 115 · see citing works
Mucus-degrading Bacteroides link carbapenems to aggravated graft-versus-host disease
Hayase, E., Hayase, T., Jamal, M. A., Miyama, T., Chang, C., Ortega, M. R., Ahmed, S., Karmouch, J. L., Sanchez, C. A., Brown, A. N., et al. (2022) · Cell · doi:10.1016/j.cell.2022.09.007 · Cited by 115 · cited 1× · see citing works
“In addition to enrichment of overtly pathogenic organisms following antibiotic exposure, antibiotics are increasingly considered key contributors to more complex immunological manifestations such as graft-versus-host disease, inflammatory bowel disease and even allergies in the host 5,19–21 .”
BackgroundInfluential
Comparison of different modes of antibiotic delivery on gut microbiota depletion efficiency and body composition in mouse
Tirelle, P., Breton, J., Riou, G., Déchelotte, P., Coëffier, M., & Ribet, D. (2020) · BMC Microbiology · doi:10.1186/s12866-020-02018-9 · Cited by 113 · see citing works
Selective pressure affects transfer and establishment of a Lactobacillus plantarum resistance plasmid in the gastrointestinal environment
Feld, L., Schjørring, S., Hammer, K., Licht, T. R., Danielsen, M., Krogfelt, K. A., & Wilcks, A. (2008) · Journal of Antimicrobial Chemotherapy · doi:10.1093/jac/dkn033 · Cited by 112 · cited 1× · see citing works
“However, the effects of antibiotics on the rates of HGT (particularly conjugation) are contested, with other studies demonstrating highest plasmid transfer rates in the absence of antibiotics 158–161 .”
Result
Engineering probiotics to inhibit Clostridioides difficile infection by dynamic regulation of intestinal metabolism
Koh, E., Hwang, I. Y., Lee, H. L., Sotto, R. D., Lee, J. W. J., Lee, Y. S., March, J. C., & Chang, M. W. (2022) · Nature Communications · doi:10.1038/s41467-022-31334-z · Cited by 111 · cited 5× · see citing works
“The engineered probiotic reduced the germination of C. difficile endospores, resulting in 100% survival and improved clinical symptoms in murine models of C. difficile infection 168 .”
BackgroundInfluential
Inter-species interactions alter antibiotic efficacy in bacterial communities
Bottery, M. J., Matthews, J. L., Wood, A. J., Johansen, H. K., Pitchford, J. W., & Friman, V. (2021) · The ISME Journal · doi:10.1038/s41396-021-01130-6 · Cited by 109 · see citing works
Ecology determines how low antibiotic concentration impacts community composition and horizontal transfer of resistance genes
Cairns, J., Ruokolainen, L., Hultman, J., Tamminen, M. V., Virta, M., & Hiltunen, T. (2018) · Communications Biology · doi:10.1038/s42003-018-0041-7 · Cited by 106 · cited 2× · see citing works
“Low doses of antibiotics have been reported to facilitate plasmid conjugation within bacterial communities 145,146 .”
Background
Machine Learning Leveraging Genomes from Metagenomes Identifies Influential Antibiotic Resistance Genes in the Infant Gut Microbiome
Rahman, S. F., Olm, M. R., Morowitz, M. J., & Banfield, J. F. (2018) · mSystems · doi:10.1128/msystems.00123-17 · Cited by 104 · see citing works
Gut Bacterial Microbiota and its Resistome Rapidly Recover to Basal State Levels after Short-term Amoxicillin-Clavulanic Acid Treatment in Healthy Adults
MacPherson, C. W., Mathieu, O., Tremblay, J., Champagne, J., Nantel, A., Girard, S., & Tompkins, T. A. (2018) · Scientific Reports · doi:10.1038/s41598-018-29229-5 · Cited by 104 · cited 3× · see citing works
“…antibiotic treatment in adult humans is often associated with an increase in the relative abundance of facultative anaerobes that were initially less abundant members of the community, such as Enterobacteriaceae, Enterococcus spp., Clostridium spp. and Streptococcus spp. 34,37,51,52 .”
Background
The Role of Antibiotic Resistance Genes in the Fitness Cost of Multiresistance Plasmids
Rajer, F., & Sandegren, L. (2022) · mBio · doi:10.1128/mbio.03552-21 · Cited by 104 · see citing works
An engineered live biotherapeutic for the prevention of antibiotic-induced dysbiosis
Cubillos-Ruiz, A., Alcantar, M. A., Donghia, N. M., Cárdenas, P., Ávila-Pacheco, J., & Collins, J. J. (2022) · Nature Biomedical Engineering · doi:10.1038/s41551-022-00871-9 · Cited by 104 · cited 15× · see citing works
“Such increased HGT rates are of concern owing to their potential implication in the spread of ARGs to both resident commensals and pathobionts within the gut microbiome 140 , thus increasing the future risk of opportunistic infections.”
BackgroundInfluential
Effects of Probiotic Supplementation on the Gut Microbiota and Antibiotic Resistome Development in Preterm Infants
Esaiassen, E., Hjerde, E., Cavanagh, J. P., Pedersen, T., Andresen, J. H., Rettedal, S. I., Støen, R., Nakstad, B., Willassen, N. P., & Klingenberg, C. (2018) · Frontiers in Pediatrics · doi:10.3389/fped.2018.00347 · Cited by 102 · see citing works
Effects of selective digestive decontamination (SDD) on the gut resistome
Buelow, E., Gonzalez, T. D. J. B., Versluis, D., Oostdijk, E. A. N., Ogilvie, L. A., van Mourik, M. S. M., Oosterink, E., van Passel, M. W. J., Smidt, H., D’Andrea, M. M., et al. (2014) · Journal of Antimicrobial Chemotherapy · doi:10.1093/jac/dku092 · Cited by 101 · cited 1× · see citing works
“As we have outlined here, the gut microbiome response to antibiotics is highly complex and variable 33 , driven by a multitude of factors 33,59,206,207 .”
Background
Receptor-targeted engineered probiotics mitigate lethal Listeria infection
Drolia, R., Amalaradjou, M. A. R., Ryan, V., Tenguria, S., Liu, D., Bai, X., Xu, L., Singh, A. K., Cox, A. D., Bernal-Crespo, V., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-20200-5 · Cited by 100 · see citing works
Critical evaluation of short, long, and hybrid assembly for contextual analysis of antibiotic resistance genes in complex environmental metagenomes
Brown, C., Keenum, I. M., Dai, D., Zhang, L., Vikesland, P. J., & Pruden, A. J. (2021) · Scientific Reports · doi:10.1038/s41598-021-83081-8 · Cited by 100 · cited 4× · see citing works
“The longer contigs also reveal the genetic context of ARGs and their potential localization within MGEs 151 .”
BackgroundInfluential
Platforms for elucidating antibiotic resistance in single genomes and complex metagenomes
Gupta, C. L., Tiwari, R. K., & Cytryn, E. J. (2020) · Environment International · doi:10.1016/j.envint.2020.105667 · Cited by 99 · see citing works
Shiga Toxin–Producing Escherichia coli Transmission via Fecal Microbiota Transplant
Zellmer, C., Sater, M. R. A., Huntley, M. H., Osman, M., Olesen, S. W., & Ramakrishna, B. (2021) · Clinical Infectious Diseases · doi:10.1093/cid/ciaa1486 · Cited by 98 · see citing works
Review and Comparison of Antimicrobial Resistance Gene Databases
Papp, M., & Solymosi, N. (2022) · Antibiotics · doi:10.3390/antibiotics11030339 · Cited by 96 · see citing works
Consolidating and Exploring Antibiotic Resistance Gene Data Resources
Xavier, B. B., Das, A. J., Cochrane, G., Ganck, S. D., Kumar‐Singh, S., Aarestrup, F. M., Goossens, H., & Malhotra‐Kumar, S. (2016) · Journal of Clinical Microbiology · doi:10.1128/jcm.02717-15 · Cited by 95 · cited 1× · see citing works
“There are instances of the same gene annotated by different names across databases 133 , which further impedes accurate comparative analysis of corresponding resistome studies.”
Background
Antibiotics as Instigators of Microbial Dysbiosis: Implications for Asthma and Allergy
Wypych, T. P., & Marsland, B. J. (2018) · Trends in Immunology · doi:10.1016/j.it.2018.02.008 · Cited by 94 · see citing works
Mucin-derived O -glycans supplemented to diet mitigate diverse microbiota perturbations
Pruss, K. M., Marcobal, A. M., Southwick, A. M., Dahan, D., Smits, S. A., Ferreyra, J. A., Higginbottom, S. K., Sonnenburg, E. D., Kashyap, P., Choudhury, B., et al. (2020) · The ISME Journal · doi:10.1038/s41396-020-00798-6 · Cited by 94 · see citing works
Changes in the life history traits of Daphnia magna are associated with the gut microbiota composition shaped by diet and antibiotics
Akbar, S., Gu, L., Sun, Y., Zhou, Q., Zhang, L., Lyu, K., Huang, Y., & Yang, Z. (2019) · The Science of The Total Environment · doi:10.1016/j.scitotenv.2019.135827 · Cited by 93 · see citing works
Systemic absorption of oral vancomycin in patients with Clostridium difficile infection
Rao, S., Kupfer, Y. Y., Pagala, M. K. D., Chapnick, E. K., & Tessler, S. (2011) · Scandinavian Journal of Infectious Diseases · doi:10.3109/00365548.2010.544671 · Cited by 92 · see citing works
Predominantly Antibiotic-resistant Intestinal Microbiome Persists in Patients With Pouchitis Who Respond to Antibiotic Therapy
Dubinsky, V., Reshef, L., Bar, N., Keizer, D., Golan, N., Rabinowitz, K. M., Godny, L., Yadgar, K., Zonensain, K., Tulchinsky, H., et al. (2019) · Gastroenterology · doi:10.1053/j.gastro.2019.10.001 · Cited by 92 · cited 4× · see citing works
“…by significant decreases in the relative abundance of important members of the phyla Firmicutes, Bacteroidetes and Actinobacteria, most notably Faecalibacterium prausnitzii , Eubacterium spp., Roseburia spp., Bifidobacterium spp., Dorea spp., Anaerostipes spp. and Ruminococcus spp. 32,34,38,39 .”
BackgroundMethodInfluential
Baseline microbiota composition modulates antibiotic-mediated effects on the gut microbiota and host
Lavelle, A., Hoffmann, T. W., Pham, H., Langella, P., Guédon, É., & Sokol, H. (2019) · Microbiome · doi:10.1186/s40168-019-0725-3 · Cited by 90 · see citing works
Use of ribaxamase (SYN-004), a β-lactamase, to prevent Clostridium difficile infection in β-lactam-treated patients: a double-blind, phase 2b, randomised placebo-controlled trial
Kokai‐Kun, J. F., Roberts, T., Coughlin, O., Le, C., Whalen, H., Stevenson, R. W., Wacher, V. J., & Sliman, J. A. (2019) · The Lancet Infectious Diseases · doi:10.1016/s1473-3099(18)30731-x · Cited by 89 · cited 1× · see citing works
“Similarly, oral administration of a β-lactamase concurrently with systemic β-lactam antibiotic treatment maintains the taxonomic structure of the gut community 164,172 .”
Background
Effects of stress and other environmental factors on horizontal plasmid transfer assessed by direct quantification of discrete transfer events
Johnsen, A. R., & Kroer, N. (2006) · FEMS Microbiology Ecology · doi:10.1111/j.1574-6941.2006.00230.x · Cited by 88 · see citing works
Dosing a synbiotic of human milk oligosaccharides and B. infantis leads to reversible engraftment in healthy adult microbiomes without antibiotics
Button, J. E., Autran, C. A., Reens, A. L., Cosetta, C. M., Smriga, S., Ericson, M. E., Pierce, J. V., Cook, D. N., Lee, M. L., Sun, A. K., et al. (2022) · Cell Host & Microbe · doi:10.1016/j.chom.2022.04.001 · Cited by 85 · see citing works
Durable reduction of Clostridioides difficile infection recurrence and microbiome restoration after treatment with RBX2660: results from an open-label phase 2 clinical trial
Orenstein, R., Dubberke, E. R., Khanna, S., Lee, C., Yoho, D. S., Johnson, S., Hecht, G. A., DuPont, H. L., Gerding, D. N., Blount, K., et al. (2022) · BMC Infectious Diseases · doi:10.1186/s12879-022-07256-y · Cited by 83 · cited 1× · see citing works
“In the context of rCDI, several microbial communities (derived from human donor stool or from defined bacterial culture) have shown promise in providing decreased risk of recurrent episodes 186–189 .”
Background
Combined treatment with the antibiotics kanamycin and streptomycin promotes the conjugation ofEscherichia coli
Zhang, P.-Y., Xu, P., Xia, Z., Wang, J., Xiong, J., & Li, Y. (2013) · FEMS Microbiology Letters · doi:10.1111/1574-6968.12282 · Cited by 82 · see citing works
The effect of a microbial ecosystem therapeutic (MET-2) on recurrent Clostridioides difficile infection: a phase 1, open-label, single-group trial
Kao, D., Wong, K., Franz, R., Cochrane, K., Sherriff, K., Chui, L., Lloyd, C., Roach, B., Bai, A. D., Petrof, E. O., et al. (2021) · The Lancet Gastroenterology & Hepatology · doi:10.1016/s2468-1253(21)00007-8 · Cited by 81 · see citing works
Activity of vancomycin against epidemic Clostridium difficile strains in a human gut model
Baines, S. D., O'Connor, R., Saxton, K., Freeman, J., & Wilcox, M. H. (2008) · Journal of Antimicrobial Chemotherapy · doi:10.1093/jac/dkn502 · Cited by 79 · see citing works
Surveying Gut Microbiome Research in Africans: Toward Improved Diversity and Representation
Brewster, R., Tamburini, F. B., Asiimwe, E., Oduaran, O. H., Hazelhurst, S., & Bhatt, A. S. (2019) · Trends in Microbiology · doi:10.1016/j.tim.2019.05.006 · Cited by 79 · cited 1× · see citing works
“Thus, our current models of microbiome dynamics are critically limited in their scope and application 209 .”
Method
Biofilms harbour Clostridioides difficile, serving as a reservoir for recurrent infection
Normington, C., Moura, I. B., Bryant, J. A., Ewin, D. J., Clark, E., Kettle, M. J., Harris, H. C., Spittal, W. D., Davis, G. L., Henn, M. R., et al. (2021) · npj Biofilms and Microbiomes · doi:10.1038/s41522-021-00184-w · Cited by 79 · cited 1× · see citing works
“These spores survive antibiotic exposure in the gastrointestinal tract, and the presence of free nutrients and primary bile acids (as discussed above) provides molecular signals for spore germination and subsequent pathogenesis 82,83 .”
Background
Repurposing a Two-Component System-Based Biosensor for the Killing of Vibrio cholerae
Jayaraman, P., Holowko, M. B., Yeoh, J. W., Lim, S., & Poh, C. L. (2017) · ACS Synthetic Biology · doi:10.1021/acssynbio.7b00058 · Cited by 76 · cited 1× · see citing works
“To further reduce the off-target effects of the treatment, the release of antimicrobials can be engineered to be induced on sensing of external stimuli produced by the target pathogen 202,203 .”
Background
Antibiotic Treatment Drives the Diversification of the Human Gut Resistome
Li, J., Rettedal, E. A., van der Helm, E., Ellabaan, M. M. H., Panagiotou, G., & Sommer, M. O. A. (2019) · Genomics Proteomics & Bioinformatics · doi:10.1016/j.gpb.2018.12.003 · Cited by 75 · see citing works
Bacterial interspecies interactions modulate pH-mediated antibiotic tolerance
Aranda-Díaz, A., Obadia, B., Dodge, R., Thomsen, T., Hallberg, Z. F., Güvener, Z. T., Ludington, W. B., & Huang, K. C. (2020) · eLife · doi:10.7554/elife.51493 · Cited by 75 · cited 1× · see citing works
“In vitro studies of interactions between two gut commensals during antibiotic treatment indicate that symbiotic relationships can have multiple outcomes in effecting differences in antibiotic tolerance in one 99 or both members of the community 100,101 .”
Background
Cotrimoxazole Prophylaxis Increases Resistance Gene Prevalence and α-Diversity but Decreases β-Diversity in the Gut Microbiome of Human Immunodeficiency Virus–Exposed, Uninfected Infants
D’Souza, A. W., Moodley-Govender, E., Berla, B. M., Kelkar, T., Wang, B., Sun, X., Daniels, B. B., Coutsoudis, A., Trehan, I., & Dantas, G. A. (2019) · Clinical Infectious Diseases · doi:10.1093/cid/ciz1186 · Cited by 74 · see citing works
Self-citation
The gut microbiome of healthy long-living people
Deng, F., Li, Y., & Zhao, J. (2019) · Aging · doi:10.18632/aging.101771 · Cited by 73 · cited 1× · see citing works
“The gastrointestinal tract requires a high, diverse microbial load to carry out requisite microbiome functions 163 .”
Background
Spatial analysis of gut microbiome reveals a distinct ecological niche associated with the mucus layer
Duncan, K., Carey-Ewend, K., & Vaishnava, S. (2021) · Gut Microbes · doi:10.1080/19490976.2021.1874815 · Cited by 73 · see citing works
Dissecting the effects of antibiotics on horizontal gene transfer: analysis suggests a critical role of selection dynamics
Lopatkin, A. J., Sysoeva, T. A., & You, L. (2016) · BioEssays · doi:10.1002/bies.201600133 · Cited by 72 · cited 1× · see citing works
“3), which suggests that the reported post-antibiotic enrichments of ARG-encoding MGEs often result from the growth advantage conferred on transconjugants, not higher HGT rates per se 162 .”
Background
Targeted adsorption of molecules in the colon with the novel adsorbent‐based Medicinal Product, DAV132: A proof of concept study in healthy subjects
de Gunzburg, J., Ducher, A., Modeß, C., Wegner, D., Oswald, S., Dressman, J., Augustin, V., Féger, C., Andremont, A., Weitschies, W., et al. (2014) · The Journal of Clinical Pharmacology · doi:10.1002/jcph.359 · Cited by 71 · see citing works
Engineer probiotic bifidobacteria for food and biomedical applications - Current status and future prospective
Zuo, F., Chen, S., & Marcotte, H. (2020) · Biotechnology Advances · doi:10.1016/j.biotechadv.2020.107654 · Cited by 71 · cited 1× · see citing works
“Recent expansions of the toolsets aimed at genetic modification of bacterial and yeast probiotics 197–199 have enabled the engineering of probiotic organisms with more potent and/or targeted anti-pathogenic activities.”
Background
Host adaptation in gut Firmicutes is associated with sporulation loss and altered transmission cycle
Browne, H. P., Almeida, A., Kumar, N., Vervier, K., Adoum, A., Viciani, E., Dawson, N. J. R., Forster, S. C., Cormie, C., Goulding, D., et al. (2021) · Genome biology · doi:10.1186/s13059-021-02428-6 · Cited by 71 · cited 1× · see citing works
“Members of the Clostridium and Peptostreptococcus genera (along with several other species in the phylum Firmicutes) have the capacity to form endospores, which are non-replicating forms of the cell that are intrinsically resistant to antibiotics, heat and oxygen 78–80 .”
Background
Ceftriaxone and Cefotaxime Have Similar Effects on the Intestinal Microbiota in Human Volunteers Treated by Standard-Dose Regimens
Burdet, C., Grall, N., Linard, M., Bridier‐Nahmias, A., Benhayoun, M., Bourabha, K., Magnan, M., Clermont, O., d’Humières, C., Tenaillon, O., et al. (2019) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.02244-18 · Cited by 70 · see citing works
Antibiotic Selection Pressure Determination through Sequence-Based Metagenomics
Willmann, M., El-Hadidi, M. S., Huson, D. H., Schütz, M. S., Weidenmaier, C., Autenrieth, I. B., & Peter, S. (2015) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.01504-15 · Cited by 69 · see citing works
Harnessing CRISPR-Cas systems for precision engineering of designer probiotic lactobacilli
Goh, Y. J., & Barrangou, R. (2018) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2018.11.009 · Cited by 69 · see citing works
Gut resistomes, microbiota and antibiotic residues in Chinese patients undergoing antibiotic administration and healthy individuals
Duan, Y., Chen, Z., Tan, L., Wang, X., Xue, Y., Wang, S., Wang, Q., Das, R., Lin, H., Hou, J., et al. (2019) · The Science of The Total Environment · doi:10.1016/j.scitotenv.2019.135674 · Cited by 68 · cited 1× · see citing works
“Despite increasing the total resistome burden, antibiotics can concurrently lead to a substantial loss of specific ARGs 119 and reduced resistome diversity 116 , which is probably due to taxonomic loss.”
Background
High-throughput fitness screening and transcriptomics identify a role for a type IV secretion system in the pathogenesis of Crohn’s disease-associated Escherichia coli
Elhenawy, W., Hordienko, S., Gould, S., Oberc, A. M., Tsai, C. N., Hubbard, T. P., Waldor, M. K., & Coombes, B. K. (2021) · Nature Communications · doi:10.1038/s41467-021-22306-w · Cited by 68 · see citing works
Antibiotic Exposure Has Sex-Dependent Effects on the Gut Microbiota and Metabolism of Short-Chain Fatty Acids and Amino Acids in Mice
Gao, H., Shu, Q., Chen, J., Fan, K., Xu, P., Zhou, Q., Li, C., & Zheng, H. X. (2019) · mSystems · doi:10.1128/msystems.00048-19 · Cited by 66 · cited 2× · see citing works
“…mouse models have reproduced the superior capacity of vancomycin to decrease alpha diversity or increase pathogen susceptibility compared to more than five other antibiotic agents or combinations (including ampicillin, azithromycin, ciprofloxacin and ciprofloxacin– metronidazole) 46,56,57 .”
Background
Gut Microbiota Dysbiosis Is Associated with Altered Bile Acid Metabolism in Infantile Cholestasis
Wang, Y., Gao, X., Zhang, X., Xiao, Y., Huang, J., Yu, D., Li, X., Hu, H., Ge, T., Li, D., et al. (2019) · mSystems · doi:10.1128/msystems.00463-19 · Cited by 64 · see citing works
Cross-feeding modulates the rate and mechanism of antibiotic resistance evolution in a model microbial community of Escherichia coli and Salmonella enterica
Adamowicz, E. M., Muza, M., Chacón, J. M., & Harcombe, W. R. (2020) · PLoS Pathogens · doi:10.1371/journal.ppat.1008700 · Cited by 63 · cited 1× · see citing works
“In vitro studies of interactions between two gut commensals during antibiotic treatment indicate that symbiotic relationships can have multiple outcomes in effecting differences in antibiotic tolerance in one 99 or both members of the community 100,101 .”
Background
Impact of investigational microbiota therapeutic RBX2660 on the gut microbiome and resistome revealed by a placebo-controlled clinical trial
Kwak, S., Choi, J., Hink, T., Reske, K. A., Blount, K., Jones, C. R., Bost, M. H., Sun, X., Burnham, C. D., Dubberke, E. R., et al. (2020) · Microbiome · doi:10.1186/s40168-020-00907-9 · Cited by 62 · cited 2× · see citing works
“Nonetheless, there are noteworthy therapeutic risks, including the unintended introduction of pathogens and ARGs into the gut of the recipient 185,192 .”
BackgroundSelf-citation
Evolution of the murine gut resistome following broad-spectrum antibiotic treatment
de Nies, L., Busi, S. B., Tsenkova, M., Halder, R., Letellier, E., & Wilmes, P. (2022) · Nature Communications · doi:10.1038/s41467-022-29919-9 · Cited by 59 · see citing works
Factors That Affect Transfer of the IncI1 β-Lactam Resistance Plasmid pESBL-283 between E. coli Strains
Händel, N., Otte, S., Jonker, M. J., Brul, S., & ter Kuile, B. H. (2015) · PLoS ONE · doi:10.1371/journal.pone.0123039 · Cited by 58 · cited 1× · see citing works
“However, the effects of antibiotics on the rates of HGT (particularly conjugation) are contested, with other studies demonstrating highest plasmid transfer rates in the absence of antibiotics 158–161 .”
Result
Effect of Commonly Used Pediatric Antibiotics on Gut Microbial Diversity in Preschool Children in Burkina Faso: A Randomized Clinical Trial
Oldenburg, C. E., Sié, A., Coulibaly, B., Ouèrmi, L., Dah, C., Tapsoba, C., Bärnighausen, T., Ray, K. J., Zhong, L., Cummings, M. E., et al. (2018) · Open Forum Infectious Diseases · doi:10.1093/ofid/ofy289 · Cited by 57 · cited 1× · see citing works
“In a comparative study, azithromycin leads to a greater decrease in Simpson’s alpha diversity (less than twofold) 5 days post-treatment than amoxicillin or cotrimoxazole 67 .”
Background
Soluble plantain fibre blocks adhesion and M-cell translocation of intestinal pathogens
Roberts, C. L., Keita, Å. V., Parsons, B. N., Prorok-Hamon, M., Knight, P., Winstanley, C., O’Kennedy, N., Söderholm, J. D., Rhodes, J. M., & Campbell, B. J. (2012) · The Journal of Nutritional Biochemistry · doi:10.1016/j.jnutbio.2012.02.013 · Cited by 55 · cited 1× · see citing works
“In addition to restructuring the microbiome, it is also possible that several soluble non-starch polysaccharides could serve as a physical barrier against pathogen adherence to the epithelial barrier 181,182 .”
Background
Human Papillomavirus (HPV) Vaccine Effectiveness and Potential Herd Immunity for Reducing Oncogenic Oropharyngeal HPV-16 Prevalence in the United Kingdom: A Cross-sectional Study
Mehanna, H. M., Bryant, T. S., Babrah, J., Louie, K. S., Bryant, J., Spruce, R. J., Batis, N., Olaleye, O., Jones, J. E., Struijk, L., et al. (2018) · Clinical Infectious Diseases · doi:10.1093/cid/ciy1081 · Cited by 55 · see citing works
Impact of Oral Fidaxomicin Administration on the Intestinal Microbiota and Susceptibility to Clostridium difficile Colonization in Mice
Ajami, N. J., Cope, J. L., Wong, M. C., Petrosino, J. F., & Chesnel, L. (2018) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.02112-17 · Cited by 53 · cited 2× · see citing works
“Given that antibiotics vary in their spectrum of activity against the diverse members of the commensal gut microbiome, the choice of treatments with a narrower spectrum could result in less perturbation to the microbiome and faster community recovery 169 .”
Background
Strain-resolved microbiome sequencing reveals mobile elements that drive bacterial competition on a clinical timescale
Bishara, A., Moss, E. L., Tkachenko, E., Kang, J. B., Zlitni, S., Culver, R. N., Andermann, T. M., Weng, Z., Wood-Bouwens, C. M., Handy, C., et al. (2020) · Genome Medicine · doi:10.1186/s13073-020-00747-0 · Cited by 53 · cited 1× · see citing works
“…stool short-read shotgun metagenomics or 16S rRNA amplicon sequencing as the main techniques for determining community structure, which generally does not provide strain-level resolution of the microbiome (a requirement for understanding gut microbiome AMR composition, as discussed below) 68,69 .”
Background
Microbiome-mediated fructose depletion restricts murine gut colonization by vancomycin-resistant Enterococcus
Isaac, S., Flor‐Duro, A., Carruana, G., Puchades‐Carrasco, L., Quirant, A., López‐Nogueroles, M., Pineda‐Lucena, A., Garcia‐Garcerà, M., & Úbeda, C. (2022) · Nature Communications · doi:10.1038/s41467-022-35380-5 · Cited by 53 · cited 3× · see citing works
“…mouse models have reproduced the superior capacity of vancomycin to decrease alpha diversity or increase pathogen susceptibility compared to more than five other antibiotic agents or combinations (including ampicillin, azithromycin, ciprofloxacin and ciprofloxacin– metronidazole) 46,56,57 .”
Background
Humans are animals, but are animals human enough? A systematic review and meta-analysis on interspecies differences in renal drug clearance
Jansen, K., Casellas, C. P., Groenink, L., Wever, K. E., & Masereeuw, R. (2020) · Drug Discovery Today · doi:10.1016/j.drudis.2020.01.018 · Cited by 51 · see citing works
Strain-Dependent Inhibition of Clostridioides difficile by Commensal Clostridia Carrying the Bile Acid-Inducible ( bai ) Operon
Reed, A. D., Nethery, M. A., Stewart, A. K., Barrangou, R., & Theriot, C. M. (2020) · Journal of Bacteriology · doi:10.1128/jb.00039-20 · Cited by 49 · see citing works
An open randomized multicentre Phase 2 trial to assess the safety of DAV132 and its efficacy to protect gut microbiota diversity in hospitalized patients treated with fluoroquinolones
Vehreschild, M. J. G. T., Ducher, A., Louie, T., Cornely, O. A., Féger, C., Dane, A. L., Varastet, M., Vitry, F., de Gunzburg, J., Andremont, A., et al. (2021) · Journal of Antimicrobial Chemotherapy · doi:10.1093/jac/dkab474 · Cited by 49 · cited 2× · see citing works
“The most notable example is DAV132, an adsorbent based on activated charcoal, which reduces the faecal concentrations of moxifloxacin and fluoroquinolones without altering the serum levels of the antibiotics 165,174 .”
Background
THE EFFECT OF ANTIBACTERIAL DRUGS ON THE FECAL FLORA OF MICE
Dubos, R. J., Schaedler, R. W., & Stephens, M. (1963) · The Journal of Experimental Medicine · doi:10.1084/jem.117.2.231 · Cited by 44 · see citing works
Early Parenteral Administration of Ceftiofur has Gender-Specific Short- and Long-Term Effects on the Fecal Microbiota and Growth in Pigs from the Suckling to Growing Phase
Ruczizka, U., Metzler-Zebeli, B. U., Unterweger, C., Mann, E., Schwarz, L., Knecht, C., & Hennig‐Pauka, I. (2019) · Animals · doi:10.3390/ani10010017 · Cited by 44 · see citing works
Impact of azithromycin mass drug administration on the antibiotic-resistant gut microbiome in children: a randomized, controlled trial
Pickering, H. C., Hart, J., Burr, S. E., Stabler, R. A., Maleta, K. M., Kalua, K., Bailey, R. L., & Holland, M. J. (2022) · Gut Pathogens · doi:10.1186/s13099-021-00478-6 · Cited by 43 · cited 3× · see citing works
“Antibiotics expectedly enrich for ARGs that confer resistance to the treatment agent 33,34,51,62–66 ,114,115, 117, 119– 123 through selection of bacterial strains Importantly, the effects of antibiotics on the gut resistome vary substantially depending on the nature of the administered drug…”
Background
Consumption of a Western-Style Diet Modulates the Response of the Murine Gut Microbiome to Ciprofloxacin
Cabral, D. J., Wurster, J. I., Korry, B. J., Penumutchu, S., & Belenky, P. A. (2020) · mSystems · doi:10.1128/msystems.00317-20 · Cited by 42 · cited 1× · see citing works
“From several other mouse studies using both dietary and chemical interventions to simulate the effects of a Western-style diet, it is clear that the combination of both diet and antibiotics changes microbial and host metabolism 106 .”
Background
The potential utility of fecal (or intestinal) microbiota transplantation in controlling infectious diseases
Ghani, R., Mullish, B. H., Roberts, L. A., Davies, F., & Marchesi, J. R. (2022) · Gut Microbes · doi:10.1080/19490976.2022.2038856 · Cited by 42 · cited 1× · see citing works
“Originally designed for its use in the treatment of recurrent C. difficile infection (rCDI), the use of FMTs has expanded to other infectious diseases, including the treatment of enteric infections, MDR bacterial colonization and viral infections (as reviewed elsewhere) 184 .”
Background
Dietary Xanthan Gum Alters Antibiotic Efficacy against the Murine Gut Microbiota and Attenuates Clostridioides difficile Colonization
Schnizlein, M. K., Vendrov, K. C., Edwards, S. J., Martens, E. C., & Young, V. B. (2020) · mSphere · doi:10.1128/msphere.00708-19 · Cited by 41 · cited 1× · see citing works
“In another study, dietary xanthan gum demonstrated a capacity to increase fibre-degrading taxa, although without significantly altering alpha diversity, and prevented C. difficile colonization, probably owing to the maintenance of the commensal microbiota during antibiotic treatment 180 .”
Background
Effects of Antibiotics on the Intestinal Microbiota of Mice
Hertz, F. B., Budding, A. E., van der Lugt-Degen, M., Savelkoul, P. H. M., Løbner‐Olesen, A., & Frimodt‐Møller, N. (2020) · Antibiotics · doi:10.3390/antibiotics9040191 · Cited by 41 · see citing works
SYN-004 (ribaxamase), an oral beta-lactamase, mitigates antibiotic-mediated dysbiosis in a porcine gut microbiome model
Connelly, S., Bristol, J. A., Hubert, S., Subramanian, P., Hasan, N. A., Colwell, R. R., & Kaleko, M. (2017) · Journal of Applied Microbiology · doi:10.1111/jam.13432 · Cited by 40 · cited 3× · see citing works
“Thus, efforts towards the maintenance or restoration of richness and diversity in the gut micro biome on antibiotic exposure are of extreme medical importance 113,164,165 .”
Background
Distinct consequences of amoxicillin and ertapenem exposure in the porcine gut microbiome
Connelly, S., Subramanian, P., Hasan, N. A., Colwell, R. R., & Kaleko, M. (2018) · Anaerobe · doi:10.1016/j.anaerobe.2018.04.012 · Cited by 37 · cited 1× · see citing works
“Bioavailability of antibiotics and their administration route have been rarely examined as influential variables in comparative studies of microbiome perturbation 75,76 .”
Background
Role of Microbiome in Carcinogenesis Process and Epigenetic Regulation of Colorectal Cancer
Farhana, L., Banerjee, H. N., Verma, M., & Majumdar, A. P. N. (2018) · Methods in molecular biology · doi:10.1007/978-1-4939-8751-1_3 · Cited by 37 · cited 1× · see citing works
“…and metabolic pathway architecture of the gut microbial community (referred to as dysbiosis) have been associated with an increased risk of numerous human pathologies, including inflammatory bowel disease 5 , obesity 6 , colorectal cancer 7,8 and numerous gastrointestinal infections 9–11 .”
Background
Randomized Controlled Trial of Oral Vancomycin Treatment in Clostridioides difficile-Colonized Patients
Fishbein, S. R. S., Hink, T., Reske, K. A., Cass, C., Struttmann, E. L., Iqbal, Z. H., Seiler, S. M., Kwon, J. H., Burnham, C. D., Dantas, G. A., et al. (2021) · mSphere · doi:10.1128/msphere.00936-20 · Cited by 37 · cited 1× · see citing works
“Most notably, treatment-induced disturbance of the gut community enables the growth of potentially infectious pathobi-onts (opportunistic microorganisms that proliferate on microbiome perturbation) with the capacity to cause disease 15,16 .”
BackgroundSelf-citation
A Solution to Antifolate Resistance in Group B Streptococcus : Untargeted Metabolomics Identifies Human Milk Oligosaccharide-Induced Perturbations That Result in Potentiation of Trimethoprim
Chambers, S. A., Moore, R. E., Craft, K. M., Thomas, H. C., Das, R. K., Manning, S. D., Codreanu, S. G., Sherrod, S. D., Aronoff, D. M., MCLEAN, J. A. J., et al. (2020) · mBio · doi:10.1128/mbio.00076-20 · Cited by 36 · cited 1× · see citing works
“Human milk oligosaccharides cause changes to membrane permeability, sensitizing Streptococcus agalactiae to trimethoprim 89”
Background
Antibiotic-driven intestinal dysbiosis in pediatric short bowel syndrome is associated with persistently altered microbiome functions and gut-derived bloodstream infections
Thänert, R., Thänert, A., Ou, J., Bajinting, A., Burnham, C. D., Engelstad, H. J., Tecos, M. E., Ndao, I. M., Hall-Moore, C. M., Rouggly-Nickless, C., et al. (2021) · Gut Microbes · doi:10.1080/19490976.2021.1940792 · Cited by 35 · cited 1× · see citing works
“in acutely increased ARG burden (as measured by changes in relative abundance) in the gut microbiome 33,51,114–118 .”
BackgroundSelf-citation
Fast growth can counteract antibiotic susceptibility in shaping microbial community resilience to antibiotics
Amor, D. R., & Gore, J. (2022) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2116954119 · Cited by 34 · see citing works

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Sorted by citations

The interplay between gut microbiota, short-chain fatty acids, and implications for host health and disease
Hays, K. E., Pfaffinger, J. M., & Ryznar, R. J. (2024) · Gut Microbes · doi:10.1080/19490976.2024.2393270 · Cited by 502 · see citing works
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 135 · see citing works
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 128 · see citing works
“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].”
Background
Unraveling 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 108 · see citing works
“[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.”
Effects of Helicobacter pylori infection on intestinal microbiota, immunity and colorectal cancer risk
Engelsberger, V., Gerhard, M., & Mejías‐Luque, R. (2024) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2024.1339750 · Cited by 109 · see citing works
“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).”
BackgroundInfluential
Ten 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 100 · see citing works
“Actually, it is increasingly evident that prescribing oral antibiotics could influence gut microbiome dynamics, promoting more strongly AMR [206].”
Background
Puerarin alleviates atherosclerosis via the inhibition of Prevotella copri and its trimethylamine production
Li, Z. H. (2024) · Gut · doi:10.1136/gutjnl-2024-331880 · Cited by 76 · see citing works
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 74 · see citing works
The use of probiotics and prebiotics in decolonizing pathogenic bacteria from the gut; a systematic review and meta-analysis of clinical outcomes
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 70 · see citing works
“…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.”
Background
Antibiotics are associated with worse outcomes in lung cancer patients treated with chemotherapy and immunotherapy
Elkrief, 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 · see citing works
Mechanisms and Clinical Implications of Human Gut Microbiota-Drug Interactions in the Precision Medicine Era
Wang, S., Ju, D., & Zeng, X. L. (2024) · Biomedicines · doi:10.3390/biomedicines12010194 · Cited by 60 · see citing works
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 63 · see citing works
The microbiota-gut-brain axis and central nervous system diseases: from mechanisms of pathogenesis to therapeutic strategies
Xu, J., & Lu, Y. (2025) · Frontiers in Microbiology · doi:10.3389/fmicb.2025.1583562 · Cited by 67 · see citing works
Intermittent fasting, calorie restriction, and a ketogenic diet improve mitochondrial function by reducing lipopolysaccharide signaling in monocytes during obesity: A randomized clinical trial
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 41 · see citing works
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 42 · see citing works
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 39 · see citing works
“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 .”
Influential
Poria cocos polysaccharides alleviate obesity-related adipose tissue insulin resistance via gut microbiota-derived short-chain fatty acids activation of FGF21/PI3K/AKT signaling
Liu, 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 · see citing works
Dissecting microbial communities with single-cell transcriptome analysis
Pountain, A. W., & Yanai, I. (2025) · Science · doi:10.1126/science.adp6252 · Cited by 37 · see citing works
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 · see citing works
“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 38 · see citing works
Unpacking Food Fermentation: Clinically Relevant Tools for Fermented Food Identification and Consumption
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 34 · see citing works
“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].”
Fecal microbiota transplantation: application scenarios, efficacy prediction, and factors impacting donor-recipient interplay
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 · see citing works
Mechanisms underlying alterations of the gut microbiota by exercise and their role in shaping ecological resilience
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 34 · see citing works
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 · see citing works
Artificial intelligence in bacterial diagnostics and antimicrobial susceptibility testing: Current advances and future prospects
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 36 · see citing works
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 · see citing works
In situ gut microbiota editing: enhancing therapeutic efficacy for bacterial colitis by compatible oral hydrogel microspheres with phages
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 · see citing works
“metabolic transformations 5 .”
Microbiota-brain interaction: The role of gut-derived proteins in addressing various neurological disorders including Parkinson’s (PD) and Alzheimer’s diseases (AD)
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 33 · see citing works
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 · see citing works
“Antibiotics, too, may be applied to selectively modify or perturb microbial communities based on existing or developed resistances ( 7 ).”
Alteration of the gut microbiome in patients with heart failure: A systematic review and meta-analysis
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 29 · see citing works
Gut Dysbiosis Exacerbates Intestinal Absorption of Cadmium and Arsenic from Cocontaminated Rice in Mice Due to Impaired Intestinal Barrier Functions
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 · see citing works
Understanding the role of the gut microbiome in solid tumor responses to immune checkpoint inhibitors for personalized therapeutic strategies: a review
Lim, M. Y., Hong, S., & Nam, Y. (2025) · Frontiers in Immunology · doi:10.3389/fimmu.2024.1512683 · Cited by 24 · see citing works
Alleviation of fluoride-induced colitis by tea polysaccharides: Insights into the role of Limosilactobacillus vaginalis and butyric acid
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 · see citing works
Bikaverin as a molecular weapon: enhancing Fusarium oxysporum pathogenicity in bananas via rhizosphere microbiome manipulation
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 · see citing works
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 22 · see citing works
“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 22 · see citing works
“…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.”
Background
Gut 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 22 · see citing works
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 22 · see citing works
Assessing the impact of probiotics on immunotherapy effectiveness and antibiotic-mediated resistance in cancer: a systematic review and meta-analysis
Zhao, S., Lu, Z., Zhao, F., Tang, S., Zhang, L., & Feng, C. (2025) · Frontiers in Immunology · doi:10.3389/fimmu.2025.1538969 · Cited by 21 · see citing works
Fecal microbiota transplantation promotes functional recovery in mice with spinal cord injury by modulating the spinal cord microenvironment
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 · see citing works
“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 20 · see citing works
Preconception maternal gut dysbiosis affects enteric nervous system development and disease susceptibility in offspring via the GPR41–GDNF/RET/SOX10 signaling pathway
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 · see citing works
“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].”
Varied microbial community assembly and specialization patterns driven by early life microbiome perturbation and modulation in young ruminants
Pan, Z., Ma, T., Steele, M. A., & Guan, L. L. (2024) · ISME Communications · doi:10.1093/ismeco/ycae044 · Cited by 19 · see citing works
“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].”
Method
Targeting the cysteine biosynthesis pathway in microorganisms: Mechanism, structure, and drug discovery
Tao, 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 · see citing works
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 · see citing works
A multi-levels analysis to evaluate the toxicity of microplastics on aquatic insects: A case study with damselfly larvae (Ischnura elegans)
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 18 · see citing works
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 · see citing works
“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 19 · see citing works
“…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 .”
Background
The 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 · see citing works
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 · see citing works
Microbes as medicine
Daisley, B. A., & Allen‐Vercoe, E. (2024) · Annals of the New York Academy of Sciences · doi:10.1111/nyas.15237 · Cited by 17 · see citing works
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 20 · see citing works
Advancements in the investigation of gut microbiota-based strategies for stroke prevention and treatment
Wang, M., Liu, Y., Zhong, L., Wu, F., & Wang, J. (2025) · Frontiers in Immunology · doi:10.3389/fimmu.2025.1533343 · Cited by 17 · see citing works
Antibiotic exposure at environmental concentrations under high-fat diet: Impacts on gut microbiota and metabolism
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 · see citing works
Peeling off the layers from microbial dark matter (MDM): recent advances, future challenges, and opportunities
Iqbal, S., Begum, F., Ullah, I., Jalal, N., & Shaw, P. M. (2024) · Critical Reviews in Microbiology · doi:10.1080/1040841x.2024.2319669 · Cited by 18 · see citing works
“…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 15 · see citing works
Exploring the interactions of JAK inhibitor and S1P receptor modulator drugs with the human gut microbiome: Implications for colonic drug delivery and inflammatory bowel disease.
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 15 · see citing works
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 15 · see citing works
The Complex Role of Gut Microbiota in Systemic Lupus Erythematosus and Lupus Nephritis: From Pathogenetic Factor to Therapeutic Target
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 15 · see citing works
“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].”
Influential
Intestinal 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 · see citing works
Pulsatilla chinensis extract alleviate Staphylococcus aureus induced mastitis in mice by regulating the inflammatory response and gut microbiota
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 · see citing works
“…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 14 · see citing works
“…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 14 · see citing works
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 16 · see citing works
“In the complex gut microbiome, antibiotics often target both harmful and bene ﬁ cial bacteria indiscriminately [149].”
Cariogenic Microbiota and Emerging Antibacterial Materials to Combat Dental Caries: A Literature Review
Cao, J., Ma, Q., Shi, J., Wang, X., Ye, D., Liang, J., & Zou, J. (2025) · Pathogens · doi:10.3390/pathogens14020111 · Cited by 14 · see citing works
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 14 · see citing works
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 · see citing works
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 · see citing works
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 · see citing works
GMrepo v3: a curated human gut microbiome database with expanded disease coverage and enhanced cross-dataset biomarker analysis
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 13 · see citing works
“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 ].”
Unveiling the covert interaction between gut microbiota and neutrophils to drive colorectal cancer metastasis
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 · see citing works
Deciphering the Intricate Interplay in the Framework of Antibiotic-Drug Interactions: A Narrative Review
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 · see citing works
“…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…”
Background
Exploring dried ginger essential oil as a therapeutic strategy for 5-FU-induced mucositis: Gut microbiota and tryptophan metabolite IAA-AHR/IL-22/STAT3 signaling axis
Zhao, 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 · see citing works
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 · see citing works
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 · see citing works
“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 · see citing works
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 14 · see citing works
Dietary Fibers as Drivers of Short-Chain Fatty Acids Homeostasis: A Review of Intestinal Production, Systemic Distribution, and Inter-Individual Variation
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 12 · see citing works
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 12 · see citing works
Microbes in Health and Disease: Human Gut Microbiota
Hu, C., & Shen, H. (2024) · Applied Sciences · doi:10.3390/app142311354 · Cited by 12 · see citing works
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 · see citing works
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 · see citing works
“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.”
Shift work, gut dysbiosis, and circadian misalignment: The combined impact of nighttime light exposure, nutrients, and microbiota rhythmicity
Touitou, Y., Perlemuter, G., & Touitou, C. (2025) · Chronobiology International · doi:10.1080/07420528.2025.2540039 · Cited by 11 · see citing works
“…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).”
Chac1 deficiency confers sepsis resistance by enriching gut microbiota-derived indole-3-carboxylic acid to drive macrophage metabolic shifts.
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 · see citing works
Designing a reengineered probiotic yeast to spontaneously degrade residual antibiotics in gut during antimicrobial therapy
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 · see citing works
Short chain fatty acids mediates complement C1q pathway alleviation of perioperative neurocognitive disorders
Liu, X., Tan, X., Yu, Y., Niu, J., Zhao, B., & Wang, Q. (2024) · Neuropharmacology · doi:10.1016/j.neuropharm.2024.110266 · Cited by 11 · see citing works
Understanding the transfer and persistence of antimicrobial resistance in aquaculture using a model teleost gut system
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 · see citing works
Prophylactic antibiotic use is associated with better clinical outcomes in gastric cancer patients receiving immunotherapy
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 · see citing works
Bifidobacterium bacteriocins efficiently inhibit Clostridium perfringens and facilitate repair of infection damage: Application informed by intestinal niche
Yu, D., Wang, H., Zhang, H., Lu, W., & Chen, W. (2025) · Food Bioscience · doi:10.1016/j.fbio.2025.106298 · Cited by 11 · see citing works
Warming exacerbates the effects of pesticides on the soil collembolan gut microbiome and antibiotic resistome
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 · see citing works
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 · see citing works
“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.”
Current advances and emerging prospects of specifically targeted antimicrobial peptides: A comprehensive review
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 · see citing works
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 · see citing works
“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).”
Surface coordination induced a quasi p-n junction for efficient visible light driven degradation of tetracycline over hydroxyapatite
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 · see citing works
Pharmacovigilance Strategies to Address Resistance to Antibiotics and Inappropriate Use—A Narrative Review
Sandes, V. S., Figueras, A., & Lima, E. D. C. (2024) · Antibiotics · doi:10.3390/antibiotics13050457 · Cited by 10 · see citing works
Light‐Activated Nanocatalyst for Precise In‐Situ Antimicrobial Synthesis via Photoredox‐Catalytic Click Reaction
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 · see citing works
Environmental Driving of Adaptation Mechanism on Rumen Microorganisms of Sheep Based on Metagenomics and Metabolomics Data Analysis
He, H., Fang, C., Liu, L., Li, M., & Liu, W. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms252010957 · Cited by 10 · see citing works
“All procedures used in this study were approved by the Animal Care and Use Committee of Xinjiang Agricultural University (Approval number: 2024010).”
Method
Roseburia 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 · see citing works
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 · see citing works
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 · see citing works

Understanding Gut Microbiota and Antibiotics Complex Interplay and Clinical Implications
Karim, M. M., Paswan, S., Bhairam, M., & Mishra, S. (2024) · Zenodo (CERN European Organization for Nuclear Research) · doi:10.5281/zenodo.14635348 · Cited by 9 · see citing works
Understanding the impact of antibiotic perturbation on the human microbiome
Schwartz, D. J., Langdon, A. E., & Dantas, G. A. (2020) · Genome Medicine · doi:10.1186/s13073-020-00782-x · Cited by 329 · see citing works
Self-citation
Antibiotic-Driven Gut Microbiome Dysbiosis: Resistome Dynamics, Metabolic Disruption, and Paths to Restoration
Niculescu, A.-G., Iacob, C.-M., Brătilă, E., Tocariu, R., Coroleucă, C. A., Corcionivoschi, N., Vrâncianu, C. O., Popescu, D., Popa, G. L., Popa, M. I., et al. (2026) · Antibiotics · doi:10.3390/antibiotics15070688 · Cited by 3 · see citing works
Antibiotics and the gut microbiome: From ecological disruption to systemic dysregulation of metabolism, immunity, and infection susceptibility
AL-Saedi, M. J. R., Al-Mohammadawy, Z. H., Hasan, Z., & Al-Khikani, F. H. O. (2026) · Journal of Advanced Biotechnology and Experimental Therapeutics · doi:10.5455/jabet.2026.39
Harnessing microbial modulators to mitigate antibiotic-induced gut dysbiosis: from phytochemicals to faecal microbiota transplantation
Wang, Q., Zhong, W., Huang, H., Yang, X., Liu, X., Ren, Y., He, F., & Li, J. (2026) · Beneficial Microbes · doi:10.1163/18762891-bja00123

Authors: Fishbein, S. R. S., Mahmud, B., & Dantas, G.
Affiliations: Washington University in St. Louis (US)
Corresponding author: Dantas, Gautam
ORCID: Fishbein, Skye R. S.
Mahmud, Bejan
Dantas, Gautam
Venue: Nature Reviews Microbiology
Publisher: Springer Science and Business Media LLC
Published: 2023-07-25
Volume: 21
Issue: 12
Pages: 772-788
ISSN: 1740-1526 (ISSN-L)
1740-1534
DOI: 10.1038/s41579-023-00933-y
PMC: PMC12087466
OpenAlex: W4385240643
Cited by: 440
References: 229
Citations by year: 2026: 152 · 2025: 165 · 2024: 115 · 2023: 7 · 2017: 1
FWCI: 11.59
Type: journal article
Language: en
Open access: green
www.ncbi.nlm.nih.gov
Licence: www.springernature.com/gp/researchers/text-and-data-mining (tdm)
www.springernature.com/gp/researchers/text-and-data-mining (vor)
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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