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The effects of antibiotics on the microbiome throughout development and alternative approaches for therapeutic modulation
Open accessAbstract
The widespread use of antibiotics in the past 80 years has saved millions of human lives, facilitated technological progress and killed incalculable numbers of microbes, both pathogenic and commensal. Human-associated microbes perform an array of important functions, and we are now just beginning to understand the ways in which antibiotics have reshaped their ecology and the functional consequences of these changes. Mounting evidence shows that antibiotics influence the function of the immune system, our ability to resist infection, and our capacity for processing food. Therefore, it is now more important than ever to revisit how we use antibiotics. This review summarizes current research on the short-term and long-term consequences of antibiotic use on the human microbiome, from early life to adulthood, and its effect on diseases such as malnutrition, obesity, diabetes, and Clostridium difficile infection. Motivated by the consequences of inappropriate antibiotic use, we explore recent progress in the development of antivirulence approaches for resisting infection while minimizing resistance to therapy. We close the article by discussing probiotics and fecal microbiota transplants, which promise to restore the microbiota after damage of the microbiome. Together, the results of studies in this field emphasize the importance of developing a mechanistic understanding of gut ecology to enable the development of new therapeutic strategies and to rationally limit the use of antibiotic compounds.
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Cites
An obesity-associated gut microbiome with increased capacity for energy harvest
Turnbaugh, P. J., Ley, R. E., Mahowald, M. A., Magrini, V., Mardis, E. R., & Gordon, J. I. (2006) · Nature · doi:10.1038/nature05414 · Cited by 12,444
Structure, function and diversity of the healthy human microbiome
The Human Microbiome Project Consortium (2012) · Nature · doi:10.1038/nature11234 · Cited by 11,726
Hill (2014) · doi:10.1038/nrgastro.2014.66 · Cited by 9,592
Human gut microbiome viewed across age and geography
Yatsunenko, T., Rey, F. E., Manary, M. J., Trehan, I., Dominguez-Bello, M. G., Contreras, M., Magris, M., Hidalgo, G., Baldassano, R. N., Anokhin, A. P., et al. (2012) · Nature · doi:10.1038/nature11053 · Cited by 7,815
Dethlefsen, L., Huse, S., Sogin, M. L., & Relman, D. A. (2008) · PLoS Biology · doi:10.1371/journal.pbio.0060280 · Cited by 2,361
Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile
Buffie, C. G., Bucci, V., Stein, R. R., McKenney, P. T., Ling, L., Gobourne, A., No, D., Liu, H., Kinnebrew, M., Viale, A., et al. (2015) · Nature · doi:10.1038/nature13828 · Cited by 1,872
Metagenomic microbial community profiling using unique clade-specific marker genes
Segata, N., Waldron, L., Ballarini, A., Narasimhan, V., Jousson, O., & Huttenhower, C. (2012) · Nature Methods · doi:10.1038/nmeth.2066 · Cited by 1,776
Antibiotics in early life alter the murine colonic microbiome and adiposity
Cho, I., Yamanishi, S., Cox, L., Methé, B. A., Zavadil, J., Li, K., Gao, Z., Mahana, D., Raju, K., Teitler, I., et al. (2012) · Nature · doi:10.1038/nature11400 · Cited by 1,613
Persistent gut microbiota immaturity in malnourished Bangladeshi children
Subramanian, S., Huq, S., Yatsunenko, T., Haque, R., Mahfuz, M., Alam, M. A., Benezra, A., DeStefano, J., Meier, M. F., Muegge, B. D., et al. (2014) · Nature · doi:10.1038/nature13421 · Cited by 1,270
Gut Microbiomes of Malawian Twin Pairs Discordant for Kwashiorkor
Smith, M. I., Yatsunenko, T., Manary, M. J., Trehan, I., Mkakosya, R., Cheng, J., Kau, A. L., Rich, S. S., Concannon, P., Mychaleckyj, J. C., et al. (2013) · Science · doi:10.1126/science.1229000 · Cited by 1,173
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Environment dominates over host genetics in shaping human gut microbiota
Rothschild, D., Weissbrod, O., Barkan, E., Kurilshikov, A., Korem, T., Zeevi, D., Costea, P. I., Godneva, A., Kalka, I. N., Bar, N., et al. (2018) · Nature · doi:10.1038/nature25973 · Cited by 2,859
Human gut microbiota/microbiome in health and diseases: a review
Gomaa, E. Z. (2020) · Antonie van Leeuwenhoek · doi:10.1007/s10482-020-01474-7 · Cited by 1,294
The microbiome in early life: Implications for health outcomes
Tamburini, S., Shen, N., Wu, H. C., & Clemente, J. C. (2016) · Nature Medicine · doi:10.1038/nm.4142 · Cited by 1,213
The Human Gut Microbiome: From Association to Modulation
Schmidt, T. S. B., Raes, J., & Bork, P. (2018) · Cell · doi:10.1016/j.cell.2018.02.044 · Cited by 845
Development of the gut microbiota in infancy and its impact on health in later life
Tanaka, M., & Nakayama, J. (2017) · Allergology International · doi:10.1016/j.alit.2017.07.010 · Cited by 639
The influence of the microbiome on respiratory health
Wypych, T. P., Wickramasinghe, L. C., & Marsland, B. J. (2019) · Nature Immunology · doi:10.1038/s41590-019-0451-9 · Cited by 611
Microbiota-gut-brain axis: Modulator of host metabolism and appetite
van de Wouw, M., Schellekens, H., Dinan, T. G., & Cryan, J. F. (2017) · The Journal of Nutrition · doi:10.3945/jn.116.240481 · Cited by 461
Antibiotic use in food animals worldwide, with a focus on Africa: Pluses and minuses
Van, T. T. H., Yidana, Z., Smooker, P. M., & Coloe, P. J. (2020) · Journal of Global Antimicrobial Resistance · doi:10.1016/j.jgar.2019.07.031 · Cited by 451
Microbiome in healthy skin, update for dermatologists
Dréno, B., Araviiskaia, E., Berardesca, E., Gontijo, G., Sanchez Viera, M., Xiang, L. F., Martin, R., & Bieber, T. (2016) · Journal of the European Academy of Dermatology and Venereology · doi:10.1111/jdv.13965 · Cited by 292
Minter, M. R., Hinterleitner, R., Meisel, M., Zhang, C., Leone, V., Zhang, X., Oyler-Castrillo, P., Zhang, X., Musch, M. W., Shen, X., et al. (2017) · Scientific Reports · doi:10.1038/s41598-017-11047-w · Cited by 292
Zhou, T., Hu, R., Wang, L., Qiu, Y., Zhang, G., Deng, Q., Zhang, H., Yin, P., Situ, B., Zhan, C., et al. (2020) · Angewandte Chemie International Edition · doi:10.1002/anie.201916704 · Cited by 265
Systematic review: human gut dysbiosis induced by non-antibiotic prescription medications
Le Bastard, Q., Al‐Ghalith, G. A., Grégoire, M., Chapelet, G., Javaudin, F., Dailly, E., Batard, E., Knights, D., & Montassier, E. (2018) · Alimentary Pharmacology & Therapeutics · doi:10.1111/apt.14451 · Cited by 263
Intestinal microbiota in early life and its implications on childhood health
Zhuang, L., Chen, H., Zhang, S., Zhuang, J., Li, Q., & Feng, Z. (2019) · Genomics, Proteomics & Bioinformatics · doi:10.1016/j.gpb.2018.10.002 · Cited by 219
Epigenetic Regulation at the Interplay Between Gut Microbiota and Host Metabolism
Miro-Blanch, J., & Yanes, O. (2019) · Frontiers in Genetics · doi:10.3389/fgene.2019.00638 · Cited by 195
El Hage, R., Hernandez-Sanabria, E., & Van de Wiele, T. (2017) · Frontiers in Microbiology · doi:10.3389/fmicb.2017.01889 · Cited by 185
Schepper, J. D., Collins, F. L., Rios-Arce, N. D., Raehtz, S., Schaefer, L., Gardinier, J. D., Britton, R. A., Parameswaran, N., & McCabe, L. R. (2019) · Journal of Bone and Mineral Research · doi:10.1002/jbmr.3635 · Cited by 182
Intestinal Microbiota Influences Non-intestinal Related Autoimmune Diseases
Opazo, M. C., Ortega-Rocha, E. M., Coronado-Arrázola, I., Bonifaz, L. C., Boudin, H., Neunlist, M., Bueno, S. M., Kalergis, A. M., & Riedel, C. A. (2018) · Frontiers in Microbiology · doi:10.3389/fmicb.2018.00432 · Cited by 179
Disruption of the gut ecosystem by antibiotics.
Yoon, M. Y., & Yoon, S. S. (2018) · Yonsei Medical Journal · doi:10.3349/ymj.2018.59.1.4 · Cited by 175
Microbiota-Centered Interventions: The Next Breakthrough in Immuno-Oncology?
Derosa, L., Routy, B., Desilets, A., Daillère, R., Terrisse, S., Kroemer, G., & Zitvogel, L. (2021) · Cancer Discovery · doi:10.1158/2159-8290.cd-21-0236 · Cited by 170
Batch effects removal for microbiome data via conditional quantile regression
Ling, W., Lu, J., Zhao, N., Lulla, A., Plantinga, A. M., Fu, W., Zhang, A., Liu, H., Song, H., Li, Z., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-33071-9 · Cited by 136
Gut microbiota composition during infancy and subsequent behavioural outcomes
Loughman, A., Ponsonby, A.-L., O'Hely, M., Symeonides, C., Collier, F., Tang, M. L. K., Carlin, J., Ranganathan, S., Allen, K., Pezic, A., et al. (2020) · EBioMedicine · doi:10.1016/j.ebiom.2020.102640 · Cited by 120
The Gut Microbiome as Therapeutic Target in Central Nervous System Diseases: Implications for Stroke
Winek, K., Dirnagl, U., & Meisel, A. (2016) · Neurotherapeutics · doi:10.1007/s13311-016-0475-x · Cited by 108
The connection between microbiome and schizophrenia
Golofast, B., & Vales, K. (2020) · Neuroscience & Biobehavioral Reviews · doi:10.1016/j.neubiorev.2019.12.011 · Cited by 92
Integrated molecular approaches for fermented food microbiome research
Walsh, A. M., Leech, J., Huttenhower, C., Delhomme-Nguyen, H., Crispie, F., Chervaux, C., & Cotter, P. D. (2023) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuad001 · Cited by 56
The shrinking human gut microbiome
Moeller, A. H. (2017) · Current Opinion in Microbiology · doi:10.1016/j.mib.2017.04.002 · Cited by 50
Langgartner, D., Vaihinger, C. A., Haffner-Luntzer, M., Kunze, J. F., Weiss, A.-L. J., Foertsch, S., Bergdolt, S., Ignatius, A., & Reber, S. O. (2018) · Frontiers in Behavioral Neuroscience · doi:10.3389/fnbeh.2018.00252 · Cited by 45
Targeting the human gut microbiome with small-molecule inhibitors
Woo, A. Y. M., Aguilar Ramos, M. A., Narayan, R., Richards-Corke, K. C., Wang, M. L., Sandoval-Espinola, W. J., & Balskus, E. P. (2023) · Nature Reviews Chemistry · doi:10.1038/s41570-023-00471-4 · Cited by 42
An enterococcal phage protein inhibits type IV restriction enzymes involved in antiphage defense
Bullen, N. P., Johnson, C. N., Andersen, S. E., Arya, G., Marotta, S. R., Lee, Y.-J., Weigele, P. R., Whitney, J. C., & Duerkop, B. A. (2024) · Nature Communications · doi:10.1038/s41467-024-51346-1 · Cited by 13
Li, S., Zhang, H., Xiao, J., Yuan, T., Shu, Z., Min, Y., Xu, W., Yin, Y., & Zhang, X. (2020) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2020.00358 · Cited by 8
Metadata
- Authors
- Langdon, A., Crook, N., & Dantas, G.
- Venue
- Genome Medicine
- Published
- 2016-04-13
- Volume
- 8
- Issue
- 1
- Pages
- 39-39
- ISSN
- 1756-994X (ISSN-L)
- OpenAlex
- W2336105168
- Cited by
- 912
- References
- 28
- FWCI
- 43.94
- Type
- journal article
- Language
- en
- Open access
- gold
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