Shifting the balance: antibiotic effects on host–microbiota mutualism
Abstract
Antibiotics have been used effectively as a means to treat bacterial infections in humans and animals for over half a century. However, through their use, lasting alterations are being made to a mutualistic relationship that has taken millennia to evolve: the relationship between the host and its microbiota. Host-microbiota interactions are dynamic; therefore, changes in the microbiota as a consequence of antibiotic treatment can result in the dysregulation of host immune homeostasis and an increased susceptibility to disease. A better understanding of both the changes in the microbiota as a result of antibiotic treatment and the consequential changes in host immune homeostasis is imperative, so that these effects can be mitigated.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The human gut microbiome is influenced by diet and medication use.
“The human gut microbiome is itself shaped by a wide variety of environmental exposures, including diet (8, 9) and medication use (10–13)”
From Dietary fiber and probiotics influence the gut microbiome and melanoma immunotherapy response (2021) · cites this paper as [12]
Cites
Diversity of the Human Intestinal Microbial Flora
Eckburg, P. B., Bik, E. M., Bernstein, C. N., Purdom, E., Dethlefsen, L., Sargent, M., Gill, S. R., Nelson, K. E., & Relman, D. A. (2005) · Science · doi:10.1126/science.1110591 · Cited by 7,913 · see citing works
The gut microbiota shapes intestinal immune responses during health and disease
Round, J. L., & Mazmanian, S. K. (2009) · Nature Reviews Immunology · doi:10.1038/nri2515 · Cited by 5,029 · see citing works
Cani, P. D., Bibiloni, R., Knauf, C., Waget, A., Neyrinck, A. M., Delzenne, N. M., & Burcelin, R. (2008) · Diabetes · doi:10.2337/db07-1403 · Cited by 4,819 · see citing works
Metagenomic Analysis of the Human Distal Gut Microbiome
Gill, S. R., Pop, M., DeBoy, R. T., Eckburg, P. B., Turnbaugh, P. J., Samuel, B. S., Gordon, J. I., Relman, D. A., Fraser-Liggett, C. M., & Nelson, K. E. (2006) · Science · doi:10.1126/science.1124234 · Cited by 4,699 · see citing works
Induction of Intestinal Th17 Cells by Segmented Filamentous Bacteria
Ivanov, I. I., Atarashi, K., Manel, N., Brodie, E. L., Shima, T., Karaoz, U., Wei, D., Goldfarb, K. C., Santee, C. A., Lynch, S. V., et al. (2009) · Cell · doi:10.1016/j.cell.2009.09.033 · Cited by 4,554 · see citing works
Induction of Colonic Regulatory T Cells by Indigenous <i>Clostridium</i> Species
Atarashi, K., Tanoue, T., Shima, T., Imaoka, A., Kuwahara, T., Momose, Y., Cheng, G., Yamasaki, S., Saito, T., Ohba, Y., et al. (2011) · Science · doi:10.1126/science.1198469 · Cited by 3,752 · see citing works
Review article: the role of butyrate on colonic function
HAMER, H. M., JONKERS, D., VENEMA, K., VANHOUTVIN, S., TROOST, F. J., & BRUMMER, R. ‐. (2008) · Alimentary Pharmacology & Therapeutics · doi:10.1111/j.1365-2036.2007.03562.x · Cited by 2,721 · see citing works
Dethlefsen, L., & Relman, D. A. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1000087107 · Cited by 2,421 · see citing works
Dethlefsen, L., Huse, S., Sogin, M. L., & Relman, D. A. (2008) · PLoS Biology · doi:10.1371/journal.pbio.0060280 · Cited by 2,361 · see citing works
Round, J. L., & Mazmanian, S. K. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0909122107 · Cited by 2,233 · see citing works
The inner of the two Muc2 mucin-dependent mucus layers in colon is devoid of bacteria
Johansson, M. E. V., Phillipson, M., Petersson, J., Velcich, A., Holm, L., & Hansson, G. C. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0803124105 · Cited by 2,200 · see citing works
Peng, L., Li, Z.-R., Green, R. S., Holzmanr, I. R., & Lin, J. (2009) · The Journal of Nutrition · doi:10.3945/jn.109.104638 · Cited by 2,130 · see citing works
Ivanov, I. I., Frutos, R. D. L., Manel, N., Yoshinaga, K., Rifkin, D. B., Sartor, R. B., Finlay, B. B., & Littman, D. R. (2008) · Cell Host & Microbe · doi:10.1016/j.chom.2008.09.009 · Cited by 1,770 · see citing works
Self-citationSymbiotic bacteria direct expression of an intestinal bactericidal lectin
Cash, H. L., Whitham, C. V., Behrendt, C. L., & Hooper, L. V. (2006) · Science · doi:10.1126/science.1127119 · Cited by 1,432 · see citing works
Abreu, M. T. (2010) · Nature Reviews Immunology · doi:10.1038/nri2707 · Cited by 1,288 · see citing works
Gut inflammation provides a respiratory electron acceptor for Salmonella
Winter, S., Thiennimitr, P., Winter, M. G., Butler, B. P., Huseby, D. L., Crawford, R. W., Russell, J. M., Bevins, C. L., Adams, L. G., Tsolis, R. M., et al. (2010) · Nature · doi:10.1038/nature09415 · Cited by 1,271 · see citing works
Sobel, J. D. (2007) · The Lancet · doi:10.1016/s0140-6736(07)60917-9 · Cited by 1,270 · see citing works
Jakobsson, H. E., Jernberg, C., Andersson, A. F., Sjölund-Karlsson, M., Jansson, J. K., & Engstrand, L. (2010) · PLoS ONE · doi:10.1371/journal.pone.0009836 · Cited by 1,160 · see citing works
Recognition of peptidoglycan from the microbiota by Nod1 enhances systemic innate immunity
Clarke, T. B., Davis, K. M., Lysenko, E. S., Zhou, A. Y., Yu, Y., & Weiser, J. N. (2010) · Nature Medicine · doi:10.1038/nm.2087 · Cited by 1,154 · see citing works
Symbiotic gut microbes modulate human metabolic phenotypes
Li, M., Wang, B., Zhang, M., Rantalainen, M., Wang, S., Zhou, H., Zhang, Y., Shen, J., Pang, X., Zhang, M., et al. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0712038105 · Cited by 1,144 · see citing works
Long-term ecological impacts of antibiotic administration on the human intestinal microbiota
Jernberg, C., Löfmark, S., Edlund, C., & Jansson, J. K. (2007) · The ISME Journal · doi:10.1038/ismej.2007.3 · Cited by 1,134 · see citing works
Malaviya, R., Ikeda, T., Ross, E., & Abraham, S. N. (1996) · Nature · doi:10.1038/381077a0 · Cited by 1,123 · see citing works
Lymphoid tissue genesis induced by commensals through NOD1 regulates intestinal homeostasis
Bouskra, D., Brézillon, C., Bérard, M., Werts, C., Varona, R., Boneca, I. G., & Eberl, G. (2008) · Nature · doi:10.1038/nature07450 · Cited by 1,107 · see citing works
Stecher, B., Robbiani, R., Walker, A. W., Westendorf, A. M., Barthel, M., Kremer, M., Chaffron, S., Macpherson, A. J., Buer, J., Parkhill, J., et al. (2007) · PLoS Biology · doi:10.1371/journal.pbio.0050244 · Cited by 1,048 · see citing works
Barthel, M., Hapfelmeier, S., Quintanilla-Martínez, L., Kremer, M., Rohde, M., Hogardt, M., Pfeffer, K., Rüssmann, H., & Hardt, W.-D. (2003) · Infection and Immunity · doi:10.1128/iai.71.5.2839-2858.2003 · Cited by 1,020 · see citing works
Kelly, D., Campbell, J. I., King, T. P., Grant, G., Jansson, E. Å., Coutts, A., Pettersson, S., & Conway, S. (2003) · Nature Immunology · doi:10.1038/ni1018 · Cited by 997 · see citing works
Ubeda, C., Taur, Y., Jenq, R. R., Equinda, M. J., Son, T., Samstein, M., Viale, A., Socci, N. D., van den Brink, M. R. M., Kamboj, M., et al. (2010) · Journal of Clinical Investigation · doi:10.1172/jci43918 · Cited by 943 · see citing works
Belenguer, A., Duncan, S. H., Calder, A. G., Holtrop, G., Louis, P., Lobley, G. E., & Flint, H. J. (2006) · Applied and Environmental Microbiology · doi:10.1128/aem.72.5.3593-3599.2006 · Cited by 856 · see citing works
The germless theory of allergic disease: revisiting the hygiene hypothesis
Wills-Karp, M. A., Santeliz, J., & Karp, C. L. (2001) · Nature reviews. Immunology · doi:10.1038/35095579 · Cited by 788 · see citing works
Gastrointestinal Microflora Studies in Late‐Onset Autism
Finegold, S. M., Molitoris, D., Song, Y., Liu, C., Vaisanen, M., Bolte, E., McTeague, M., Sandler, R., Wexler, H., Marlowe, E. M., et al. (2002) · Clinical Infectious Diseases · doi:10.1086/341914 · Cited by 742 · see citing works
Mechanisms of Action and Clinical Application of Macrolides as Immunomodulatory Medications
Kanoh, S., & Rubin, B. K. (2010) · Clinical Microbiology Reviews · doi:10.1128/cmr.00078-09 · Cited by 710 · see citing works
A humanized gnotobiotic mouse model of host-archaeal-bacterial mutualism
Samuel, B. S., & Gordon, J. I. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0602187103 · Cited by 674 · see citing works
Khoruts, A., Dicksved, J., Jansson, J. K., & Sadowsky, M. J. (2010) · Journal of Clinical Gastroenterology · doi:10.1097/mcg.0b013e3181c87e02 · Cited by 649 · see citing works
Rapid and Noninvasive Metabonomic Characterization of Inflammatory Bowel Disease
Marchesi, J. R., Holmes, E. C., Khan, F. M. A., Kochhar, S., Scanlan, P. D., Shanahan, F., Wilson, I. D., & Wang, Y. (2007) · Journal of Proteome Research · doi:10.1021/pr060470d · Cited by 632 · see citing works
Vancomycin-resistant enterococci exploit antibiotic-induced innate immune deficits
Brandl, K., Plitas, G., Mihu, C. N., Ubeda, C., Jia, T., Fleisher, M., Schnabl, B., DeMatteo, R. P., & Pamer, E. G. (2008) · Nature · doi:10.1038/nature07250 · Cited by 631 · see citing works
Bergstrom, K. S. B., Kissoon-Singh, V., Gibson, D. L., Ma, C., Montero, M., Sham, H. P., Ryz, N., Huang, T., Velcich, A., Finlay, B. B., et al. (2010) · PLoS Pathogens · doi:10.1371/journal.ppat.1000902 · Cited by 625 · see citing works
Self-citationShort-Term Benefit From Oral Vancomycin Treatment of Regressive-Onset Autism
Sandler, R. H., Finegold, S. M., Bolte, E. R., Buchanan, C. P., Maxwell, A. P., Väisänen, M.-L., Nelson, M. N., & Wexler, H. M. (2000) · Journal of Child Neurology · doi:10.1177/088307380001500701 · Cited by 614 · see citing works
Clindamycin-Associated Colitis
Tedesco, F. J., BARTON, R. W., & ALPERS, D. H. (1974) · Annals of Internal Medicine · doi:10.7326/0003-4819-81-4-429 · Cited by 611 · see citing works
Critical Roles of Activation-Induced Cytidine Deaminase in the Homeostasis of Gut Flora
Fagarasan, S., Muramatsu, M., Suzuki, K., Nagaoka, H., Hiai, H., & Honjo, T. (2002) · Science · doi:10.1126/science.1077336 · Cited by 590 · see citing works
Role of Gut Commensal Microflora in the Development of Experimental Autoimmune Encephalomyelitis
Ochoa-Repáraz, J., Mielcarz, D. W., Ditrio, L. E., Burroughs, A. R., Foureau, D. M., Haque-Begum, S., & Kasper, L. H. (2009) · The Journal of Immunology · doi:10.4049/jimmunol.0900747 · Cited by 590 · see citing works
Reproducible Community Dynamics of the Gastrointestinal Microbiota following Antibiotic Perturbation
Antonopoulos, D. A., Huse, S. M., Morrison, H. G., Schmidt, T. M., Sogin, M. L., & Young, V. B. (2009) · Infection and Immunity · doi:10.1128/iai.01520-08 · Cited by 545 · see citing works
Bacterial contributions to mammalian gut development
Hooper, L. (2004) · Trends in Microbiology · doi:10.1016/j.tim.2004.01.001 · Cited by 541 · cited 1× · see citing works
“These mutualists contribute substantially to host phenotype, so extensively, in fact, that mammals have been described as 'superorganisms', and terms such as 'ecological development' have been coined to signify that development is a product of both host genetics and interactions with the microbiot”
BackgroundUpdated Meta-analysis of Probiotics for Preventing Necrotizing Enterocolitis in Preterm Neonates
Deshpande, G. C., Rao, S. C., Patole, S., & Bulsara, M. K. (2010) · PEDIATRICS · doi:10.1542/peds.2009-1301 · Cited by 530 · see citing works
Metabolomics Reveals Metabolic Biomarkers of Crohn's Disease
Jansson, J. K., Willing, B. P., Lucio, M., Fekete, A., Dicksved, J., Halfvarson, J., Tysk, C., & Schmitt‐Kopplin, P. (2009) · PLoS ONE · doi:10.1371/journal.pone.0006386 · Cited by 512 · see citing works
Self-citationA mouse model of clostridium difficile-associated disease
Chen, X., Katchar, K., Goldsmith, J. D., Nanthakumar, N., Cheknis, A., Gerding, D. N., & Kelly, C. P. (2008) · Gastroenterology · doi:10.1053/j.gastro.2008.09.002 · Cited by 510 · see citing works
Ochoa-Repáraz, J., Mielcarz, D. W., Wang, Y., Begum-Haque, S., Dasgupta, S., Kasper, D. L., & Kasper, L. H. (2010) · Mucosal Immunology · doi:10.1038/mi.2010.29 · Cited by 507 · see citing works
Hall, J. A., Bouladoux, N. J., Sun, C., Wohlfert, E. A., Blank, R. B., Zhu, Q., Grigg, M. E., Berzofsky, J. A., & Belkaid, Y. (2008) · Immunity · doi:10.1016/j.immuni.2008.08.009 · Cited by 490 · see citing works
Sekirov, I., Tam, N. M., Jogova, M., Robertson, M. L., Li, Y., Lupp, C., & Finlay, B. B. (2008) · Infection and Immunity · doi:10.1128/iai.00319-08 · Cited by 483 · see citing works
Self-citationSmith, D. L., Harris, A. D., Johnson, J. A., Silbergeld, E. K., & Morris, J. G. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.082188899 · Cited by 462 · see citing works
Butyrate and other short-chain fatty acids as modulators of immunity: What relevance for health?
Meijer, K., de Vos, P., & Priebe, M. G. (2010) · Current Opinion in Clinical Nutrition and Metabolic Care · doi:10.1097/mco.0b013e32833eebe5 · Cited by 443 · see citing works
Hill, D. A., Hoffmann, C., Abt, M. C., Du, Y., Kobuley, D. E., Kirn, T. J., Bushman, F. D., & Artis, D. (2009) · Mucosal Immunology · doi:10.1038/mi.2009.132 · Cited by 425 · see citing works
Woodmansey, E. J., McMurdo, M. E. T., Macfarlane, G. T., & Macfarlane, S. (2004) · Applied and Environmental Microbiology · doi:10.1128/aem.70.10.6113-6122.2004 · Cited by 418 · see citing works
Mechanisms controlling pathogen colonization of the gut
Stecher, B., & Hardt, W. (2010) · Current Opinion in Microbiology · doi:10.1016/j.mib.2010.10.003 · Cited by 415 · see citing works
Nathan, C. (2004) · Nature · doi:10.1038/431899a · Cited by 412 · see citing works
The ‘microflora hypothesis’ of allergic diseases
Noverr, M. C., & Huffnagle, G. B. (2005) · Clinical & Experimental Allergy · doi:10.1111/j.1365-2222.2005.02379.x · Cited by 394 · see citing works
Wlodarska, M., Willing, B., Keeney, K. M., Menendez, A., Bergstrom, K. S., Gill, N., Russell, S. L., Vallance, B. A., & Finlay, B. B. (2011) · Infection and Immunity · doi:10.1128/iai.01104-10 · Cited by 382 · see citing works
Short-chain fatty acids act as antiinflammatory mediatorsby regulating prostaglandin E2 and cytokines
Cox, M. A., Jackson, J., Stanton, M., Rojas-Triana, A., Bober, L., Laverty, M., Yang, X., Zhu, F., Liu, J., Wang, S., et al. (2009) · World Journal of Gastroenterology · doi:10.3748/wjg.15.5549 · Cited by 377 · see citing works
Ochoa-Repáraz, J., Mielcarz, D. W., Ditrio, L. E., Burroughs, A. R., Begum-Haque, S., Dasgupta, S., Kasper, D. L., & Kasper, L. H. (2010) · The Journal of Immunology · doi:10.4049/jimmunol.1001443 · Cited by 367 · see citing works
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
Resilience of the Dominant Human Fecal Microbiota upon Short-Course Antibiotic Challenge
Cochetiere, M. F. D. L., Durand, T., Lepage, P., Bourreille, A., Galmiche, J. P., & Dore, J. M. (2005) · Journal of Clinical Microbiology · doi:10.1128/jcm.43.11.5588-5592.2005 · Cited by 333 · see citing works
Brugman, S., Klatter, F., Visser, J. T. J., Wildeboer-Veloo, A. C. M., Harmsen, H. J. M., Rozing, J., & Bos, N. A. (2006) · Diabetologia · doi:10.1007/s00125-006-0334-0 · Cited by 332 · see citing works
Reshaping the gut microbiome with bacterial transplantation and antibiotic intakePreprint
Manichanh, C., Reeder, J., Gibert, P., Varela, E., Llopis, M., Antolı́n, M., Guigó, R., Knight, R. D., & Guarner, F. (2010) · Genome Research · doi:10.1101/gr.107987.110 · Cited by 332 · see citing works
Role of Antibiotics and Fungal Microbiota in Driving Pulmonary Allergic Responses
Noverr, M. C., Noggle, R. M., Toews, G. B., & Huffnagle, G. B. (2004) · Infection and Immunity · doi:10.1128/iai.72.9.4996-5003.2004 · Cited by 330 · see citing works
Mechanisms of Disease: the hygiene hypothesis revisited
Guarner, F., Bourdet‐Sicard, R., Brandtzæg, P., Gill, H. S., McGuirk, P., van Eden, W., Versalovic, J. A., Weinstock, J. V., & Rook, G. A. W. (2006) · Nature Clinical Practice Gastroenterology & Hepatology · doi:10.1038/ncpgasthep0471 · Cited by 315 · see citing works
Usami, M., Kishimoto, K., Ohata, A., Miyoshi, M., Aoyama, M., Fueda, Y., & Kotani, J. (2008) · Nutrition Research · doi:10.1016/j.nutres.2008.02.012 · Cited by 309 · see citing works
Secreted enteric antimicrobial activity localises to the mucus surface layer
Meyer‐Hoffert, U., Hornef, M. W., Henriques‐Normark, B., Axelsson, L.-G., Midtvedt, T., Pütsep, K., & Andersson, M. (2008) · Gut · doi:10.1136/gut.2007.141481 · Cited by 304 · see citing works
Antibiotic Use in Children Is Associated With Increased Risk of Asthma
Marra, F., Marra, C. A., Richardson, K., Lynd, L. D., Kozyrskyj, A. L., Patrick, D. M., Bowie, W., & FitzGerald, J. M. (2009) · PEDIATRICS · doi:10.1542/peds.2008-1146 · Cited by 286 · see citing works
Noverr, M. C., Falkowski, N. R., McDonald, R. A., McKenzie, A. N. J., & Huffnagle, G. B. (2004) · Infection and Immunity · doi:10.1128/iai.73.1.30-38.2005 · Cited by 279 · see citing works
Increased risk of childhood asthma from antibiotic use in early life
Kozyrskyj, A. L., Ernst, P., & Becker, A. B. (2007) · Chest · doi:10.1378/chest.06-3008 · Cited by 272 · see citing works
Croswell, A., Amir, E., Teggatz, P., Barman, M., & Salzman, N. H. (2009) · Infection and Immunity · doi:10.1128/iai.00006-09 · Cited by 272 · see citing works
Does the shape of lipid A determine the interaction of LPS with Toll-like receptors?
Netea, M. G., van Deuren, M., Kullberg, B. J., Cavaillon, J., & van der Meer, J. W. M. (2002) · Trends in Immunology · doi:10.1016/s1471-4906(01)02169-x · Cited by 268 · see citing works
Clindamycin-Associated Colitis
Cohen, L. E. (1973) · JAMA · doi:10.1001/jama.1973.03220120045012 · Cited by 267 · see citing works
Schauber, J., Dorschner, R. A., Yamasaki, K., Brouha, B., & Gallo, R. L. (2006) · Immunology · doi:10.1111/j.1365-2567.2006.02399.x · Cited by 263 · see citing works
Iimura, M., Gallo, R. L., Hase, K., Miyamoto, Y., Eckmann, L., & Kagnoff, M. F. (2005) · The Journal of Immunology · doi:10.4049/jimmunol.174.8.4901 · Cited by 236 · see citing works
Kinnebrew, M. A., Ubeda, C., Zenewicz, L. A., Smith, N., Flavell, R. A., & Pamer, E. G. (2010) · The Journal of Infectious Diseases · doi:10.1086/650203 · Cited by 236 · see citing works
Yap, I. K. S., Li, J. V., Saric, J., Martin, F., Davies, H., Wang, Y., Wilson, I. D., Nicholson, J. K., Utzinger, J., Marchesi, J. R., et al. (2008) · Journal of Proteome Research · doi:10.1021/pr700864x · Cited by 231 · see citing works
Duan, J., Chung, H., Troy, E. B., & Kasper, D. L. (2010) · Cell Host & Microbe · doi:10.1016/j.chom.2010.01.005 · Cited by 224 · see citing works
MILLARD, A. L., MERTES, P. M., ITTELET, D., VILLARD, F., JEANNESSON, P., & BERNARD, J. (2002) · Clinical and Experimental Immunology · doi:10.1046/j.0009-9104.2002.01977.x · Cited by 220 · see citing works
Sougioultzis, S., Simeonidis, S., Bhaskar, K. R., Chen, X., Anton, P. M., Keates, S. E., Pothoulakis, C., & Kelly, C. P. (2006) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2006.02.080 · Cited by 205 · see citing works
Freter, R. (1955) · The Journal of Infectious Diseases · doi:10.1093/infdis/97.1.57 · Cited by 194 · see citing works
Sakito, O., Kadota, J.-I., Kohno, S., et al. (2009) · Respiration · doi:10.1159/000196514 · Cited by 186 · see citing works
Host Susceptibility to the Attaching and Effacing Bacterial PathogenCitrobacter rodentium
Vallance, B. A., Deng, W., Jacobson, K., & Finlay, B. B. (2003) · Infection and Immunity · doi:10.1128/iai.71.6.3443-3453.2003 · Cited by 180 · see citing works
Self-citationLöfmark, S., Jernberg, C., Jansson, J. K., & Edlund, C. (2006) · Journal of Antimicrobial Chemotherapy · doi:10.1093/jac/dkl420 · Cited by 175 · see citing works
Kummeling, I., Stelma, F. F., Dagnelie, P. C., Snijders, B. E. P., Penders, J., Huber, M., van Ree, R., van den Brandt, P. A., & Thijs, C. T. (2007) · PEDIATRICS · doi:10.1542/peds.2006-0896 · Cited by 173 · see citing works
Butyrate enemas upregulate Muc genes expression but decrease adherent mucus thickness in mice colon
Gaudier, E. A., Rival, M., Buisine, M., Robineau, I., & Hoebler, C. (2009) · Physiological Research · doi:10.33549/physiolres.931271 · Cited by 165 · see citing works
Antibiotic administration alters the community structure of the gastrointestinal microbiota
Robinson, C. J., & Young, V. B. (2010) · Gut Microbes · doi:10.4161/gmic.1.4.12614 · Cited by 161 · see citing works
Schumann, A., Nutten, S., Donnicola, D., Comelli, E. M., Mansourian, R., Cherbut, C., Corthesy-Theulaz, I. E., & García‐Ródenas, C. L. (2005) · Physiological Genomics · doi:10.1152/physiolgenomics.00057.2005 · Cited by 156 · see citing works
Update on the changing epidemiology of Clostridium difficile-associated disease
McFarland, L. V. (2008) · Nature Clinical Practice Gastroenterology & Hepatology · doi:10.1038/ncpgasthep1029 · Cited by 153 · see citing works
Effects of short chain fatty acids on effector mechanisms of neutrophils
Vinolo, M. A. R., Hatanaka, E., Lambertucci, R. H., Newsholme, P., & Curi, R. (2008) · Cell Biochemistry and Function · doi:10.1002/cbf.1533 · Cited by 132 · see citing works
Gen, R., Demir, M. E., & Ataseven, H. (2010) · Southern Medical Journal · doi:10.1097/smj.0b013e3181cf373f · Cited by 129 · see citing works
Therapy and epidemiology of autism–clostridial spores as key elements
Finegold, S. M. (2007) · Medical Hypotheses · doi:10.1016/j.mehy.2007.07.019 · Cited by 116 · see citing works
Romick‐Rosendale, L. E., Goodpaster, A. M., Hanwright, P. J., Patel, N. B., Wheeler, E. T., Chona, D. L., & Kennedy, M. A. (2009) · Magnetic Resonance in Chemistry · doi:10.1002/mrc.2511 · Cited by 106 · see citing works
Dessein, R., Gironella, M., Vignal, C., Peyrin‐Biroulet, L., Sokol, H., Sécher, T., Lacas‐Gervais, S., Gratadoux, J.-J., Lafont, F., Dagorn, J.-C., et al. (2009) · Gut · doi:10.1136/gut.2008.168443 · Cited by 106 · see citing works
三浦, 智., Durand, T., Lalande, V., Petit, J., Potel, G., & Beaugerie, L. (2008) · Microbial Ecology · doi:10.1007/s00248-007-9356-5 · Cited by 105 · see citing works
Role of Lactobacillus in the Prevention of Antibiotic‐Associated Diarrhea: A Meta‐analysis
Kale-Pradhan, P. B., Jassaly, H. K., & Wilhelm, S. M. (2010) · Pharmacotherapy The Journal of Human Pharmacology and Drug Therapy · doi:10.1592/phco.30.2.119 · Cited by 105 · see citing works
The role of innate signaling in the homeostasis of tolerance and immunity in the intestine
Wells, J. M., Loonen, L. M. P., & Karczewski, J. M. (2009) · International Journal of Medical Microbiology · doi:10.1016/j.ijmm.2009.08.008 · Cited by 105 · see citing works
Effect of broad-spectrum parenteral antibiotics on composition of intestinal microflora of humans
Giuliano, M., Barza, M. J., Jacobus, N. V., & Gorbach, S. L. (1987) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.31.2.202 · Cited by 95 · see citing works
Høverstad, T., Carlstedt‐Duke, B., Lingaas, E., et al. (1986) · Scandinavian Journal of Gastroenterology · doi:10.3109/00365528609003109 · Cited by 91 · see citing works
Marcone, V., Calzolari, E., & Bertini, M. (2008) · PubMed · Cited by 77 · see citing works
Janczyk, P., Pieper, R., Souffrant, W. B., et al. (2007) · The ISME Journal · doi:10.1038/ismej.2007.29 · Cited by 76 · see citing works
Verhulst, S. L., Vael, C., Beunckens, C., Nelen, V., Goossens, H., & Desager, K. (2008) · Journal of Asthma · doi:10.1080/02770900802339734 · Cited by 70 · see citing works
Desvignes, C., Bour, H., Nicolas, J., et al. (1996) · European Journal of Immunology · doi:10.1002/eji.1830260814 · Cited by 68 · see citing works
Julia, V., McSorley, S. J., Malherbe, L. P., et al. (2000) · The Journal of Immunology · doi:10.4049/jimmunol.165.10.5637 · Cited by 68 · see citing works
Woo, J., Shinohara, C., SAKAI, K., Hasumi, K., & Endo, A. (1992) · European Journal of Biochemistry · doi:10.1111/j.1432-1033.1992.tb17061.x · Cited by 58 · see citing works
Schreiber, O., Petersson, J., Phillipson, M., Perry, M. A., Roos, S., & Holm, L. (2009) · American Journal of Physiology-Gastrointestinal and Liver Physiology · doi:10.1152/ajpgi.90470.2008 · Cited by 58 · see citing works
Leung, C., Lam, W. Y., Ma, D., Gullen, E. A., & Cheng, Y. (2009) · European Journal of Immunology · doi:10.1002/eji.200939454 · Cited by 56 · see citing works
Metronidazole effects on microbiota and mucus layer thickness in the rat gut
Pélissier, M. A., Vasquez, N., Ramadass, B., Pereira, E., Dossou-Yovo, F., Suau, A., Pochart, P., & Magne, F. (2010) · FEMS Microbiology Ecology · doi:10.1111/j.1574-6941.2010.00916.x · Cited by 54 · see citing works
Schultz, M. J. (2000) · Journal of Antimicrobial Chemotherapy · doi:10.1093/jac/46.2.235 · Cited by 51 · see citing works
Xu, X. M., Weksler‐Zangen, S., Pikarsky, A. J., Pappo, O., Wengrower, D., Bischoff, S. C., Pines, M., Rivkind, A., Goldin, E., & Levi‐Schaffer, F. (2002) · Scandinavian Journal of Gastroenterology · doi:10.1080/003655202317284246 · Cited by 50 · see citing works
Comelli, E. M., Simmering, R., Faure, M., Donnicola, D., Mansourian, R., Rochat, F., Corthesy-Theulaz, I. E., & Cherbut, C. (2007) · Genomics · doi:10.1016/j.ygeno.2007.09.006 · Cited by 49 · see citing works
Hossain, Z., Konishi, M., Hosokawa, M., et al. (2005) · Cell Biochemistry and Function · doi:10.1002/cbf.1202 · Cited by 44 · see citing works
van Ogtrop, M. L., Guiot, H. F. L., Mattie, H., et al. (1991) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.35.5.976 · Cited by 39 · see citing works
Dufour, V., Millon, L., Faucher, J., et al. (2005) · International Immunopharmacology · doi:10.1016/j.intimp.2005.01.007 · Cited by 37 · see citing works
Toll-like receptor 4 is protective against neonatal murine ischemia-reperfusion intestinal injury
Tatum, P. M., Harmon, C. M., Lorenz, R. G., & Dimmitt, R. A. (2010) · Journal of Pediatric Surgery · doi:10.1016/j.jpedsurg.2010.02.093 · Cited by 31 · see citing works
Gentamicin suppresses endotoxin-driven TNF-α production in human and mouse proximal tubule cells
Zager, R. A., Johnson, A. C. M., & Geballe, A. P. (2007) · American Journal of Physiology-Renal Physiology · doi:10.1152/ajprenal.00333.2007 · Cited by 28 · see citing works
Gut microbes extend reach to systemic innate immunity
Philpott, D. J., & Girardin, S. E. (2010) · Nature Medicine · doi:10.1038/nm0210-160 · Cited by 18 · see citing works
Watanabe, J., Fujiwara, R., Sasajima, N., Ito, S., & Sonoyama, K. (2010) · Bioscience Biotechnology and Biochemistry · doi:10.1271/bbb.90709 · Cited by 17 · see citing works
Enerb�ck, L., L�whagen, G.-B., L�whagen, O., et al. (1981) · Cell and Tissue Research · doi:10.1007/bf00249208 · Cited by 15 · see citing works
Umenai, T., Hirai, H., Shime, N., Nakaya, T., Asahara, T., Nomoto, K., Kita, M., Tanaka, Y., & Imanishi, J. (2010) · European Journal of Clinical Microbiology & Infectious Diseases · doi:10.1007/s10096-010-0905-3 · Cited by 13 · see citing works
Yaguchi, Y., Fukatsu, K., Moriya, T., et al. (2006) · Journal of Parenteral and Enteral Nutrition · doi:10.1177/0148607106030005395 · Cited by 9 · see citing works
Apoptosis induced by butyrate is independent of Jak/STAT signaling in a fibrosarcoma cell line
Rabelo, F. L. A., Ramos, M. G., Brumatti, G., et al. (2003) · Biochemical and Biophysical Research Communications · doi:10.1016/s0006-291x(03)00072-x · Cited by 5 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
Bacteriocins—A viable alternative to antibiotics?
Cotter, P. D., Ross, R. P., & Hill, C. (2013) · Nature Reviews Microbiology · doi:10.1038/nrmicro2937 · Cited by 1,793 · see citing works
Kang, D.-W., Adams, J. B., Gregory, A. C., Borody, T., Chittick, L., Fasano, A., Khoruts, A., Geis, E., Maldonado, J., McDonough-Means, S., et al. (2017) · Microbiome · doi:10.1186/s40168-016-0225-7 · Cited by 1,391 · see citing works
Kelly, J. R., Kennedy, P. J., Cryan, J. F., Dinan, T. G., Clarke, G., & Hyland, N. P. (2015) · Frontiers in Cellular Neuroscience · doi:10.3389/fncel.2015.00392 · Cited by 1,110 · see citing works
Microbes, Metabolites, and the Gut-Lung Axis
Dang, A. T., & Marsland, B. J. (2019) · Mucosal Immunology · doi:10.1038/s41385-019-0160-6 · Cited by 1,028 · see citing works
Immunological aspects of intestinal mucus and mucins
Johansson, M. E. V., & Hansson, G. C. (2016) · Nature Reviews Immunology · doi:10.1038/nri.2016.88 · Cited by 1,007 · see citing works
Reduced incidence of Prevotella and other fermenters in intestinal microflora of autistic children
Kang, D.-W., Park, J. G., Ilhan, Z. E., Wallstrom, G., LaBaer, J., Adams, J. B., & Krajmalnik-Brown, R. (2013) · PLoS ONE · doi:10.1371/journal.pone.0068322 · Cited by 976 · see citing works
The microbiota-gut-brain axis: from motility to mood
Margolis, K. G., Cryan, J. F., & Mayer, E. A. (2021) · Gastroenterology · doi:10.1053/j.gastro.2020.10.066 · Cited by 999 · see citing works
Dietary fiber and probiotics influence the gut microbiome and melanoma immunotherapy response
Spencer, C. N., McQuade, J. L., Gopalakrishnan, V., McCulloch, J. A., Vetizou, M., Cogdill, A. P., Khan, M. A. W., Zhang, X., White, M. G., Peterson, C. B., et al. (2021) · Science · doi:10.1126/science.aaz7015 · Cited by 966 · see citing works
Early life antibiotic‐driven changes in microbiota enhance susceptibility to allergic asthma
Russell, S. L., Gold, M. J., Hartmann, M., Willing, B. P., Thorson, L., Wlodarska, M., Gill, N., Blanchet, M., Mohn, W. W., McNagny, K. M., et al. (2012) · The EMBO Reports · doi:10.1038/embor.2012.32 · Cited by 883 · see citing works
Self-citationBäckhed, F., Fraser, C. M., Ringel, Y., Sanders, M. E., Sartor, R. B., Sherman, P. M., Versalovic, J., Young, V., & Finlay, B. B. (2012) · Cell Host & Microbe · doi:10.1016/j.chom.2012.10.012 · Cited by 836 · see citing works
Self-citationRegulation of intestinal inflammation by microbiota following allogeneic bone marrow transplantation
Jenq, R. R., Ubeda, C., Taur, Y., Menezes, C. C., Khanin, R., Dudakov, J. A., Liu, C., West, M. L., Singer, N. V., Equinda, M. J., et al. (2012) · Journal of Experimental Medicine · doi:10.1084/jem.20112408 · Cited by 626 · see citing works
Gut barrier disruption and chronic disease
Martel, J., Chang, S.-H., Ko, Y.-F., Hwang, T.-L., Young, J. D., & Ojcius, D. M. (2022) · Trends in Endocrinology & Metabolism · doi:10.1016/j.tem.2022.01.002 · Cited by 514 · see citing works
A role for the gut microbiota in IBS
Collins, S. M. (2014) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/nrgastro.2014.40 · Cited by 351 · see citing works
Zhao, N., Chen, J., Carroll, I. M., Ringel-Kulka, T., Epstein, M. P., Zhou, H., Zhou, J. J., Ringel, Y., Li, H., & Wu, M. C. (2015) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2015.04.003 · Cited by 306 · see citing works
Heiss, C. N., & Olofsson, L. E. (2019) · Journal of Neuroendocrinology · doi:10.1111/jne.12684 · Cited by 304 · see citing works
Microbiome dynamics of human epidermis following skin barrier disruption
Zeeuwen, P. L., Boekhorst, J., van den Bogaard, E. H., de Koning, H. D., van de Kerkhof, P. M., Saulnier, D. M., van Swam, I. I., van Hijum, S. A., Kleerebezem, M., Schalkwijk, J., et al. (2012) · Genome Biology · doi:10.1186/gb-2012-13-11-r101 · Cited by 274 · see citing works
Microbiota effects on cancer: From risks to therapies
Rea, D., Coppola, G., Palma, G., Barbieri, A., Luciano, A., Del Prete, P., Rossetti, S., Berretta, M., Facchini, G., Perdonà, S., et al. (2018) · Oncotarget · doi:10.18632/oncotarget.24681 · Cited by 208 · see citing works
Differential Effects of Antibiotic Therapy on the Structure and Function of Human Gut Microbiota
Pérez-Cobas, A. E., Artacho, A., Knecht, H., Ferrús, M. L., Friedrichs, A., Ott, S. J., Moya, A., Latorre, A., & Gosalbes, M. J. (2013) · PLoS ONE · doi:10.1371/journal.pone.0080201 · Cited by 212 · see citing works
van den Bergh, M. R., Biesbroek, G., Rossen, J. W. A., de Steenhuijsen Piters, W. A. A., Bosch, A. A. T. M., van Gils, E. J. M., Wang, X., Boonacker, C. W. B., Veenhoven, R. H., Bruin, J. P., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0047711 · Cited by 208 · see citing works
Pettigrew, M. M., Laufer, A. S., Gent, J. F., Kong, Y., Fennie, K. P., & Metlay, J. P. (2012) · Applied and Environmental Microbiology · doi:10.1128/aem.01051-12 · Cited by 183 · see citing works
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 · see citing works
How to: establish and run a stool bank
Terveer, E. M., van Beurden, Y. H., Goorhuis, A., Seegers, J. F. M. L., Bauer, M. P., van Nood, E., Dijkgraaf, M. G. W., Mulder, C. J. J., Vandenbroucke-Grauls, C. M. J. E., Verspaget, H. W., et al. (2017) · Clinical Microbiology and Infection · doi:10.1016/j.cmi.2017.05.015 · Cited by 168 · see citing works
Impact of the gut microbiota, prebiotics, and probiotics on human health and disease
Lai, H.-C., Young, J., Lin, C.-S., Chang, C.-J., Lu, C.-C., Martel, J., Ojcius, D., & Ko, Y.-F. (2014) · Biomedical Journal · doi:10.4103/2319-4170.138314 · Cited by 153 · see citing works
Modulation of post-antibiotic bacterial community reassembly and host response by Candida albicans
Erb Downward, J. R., Falkowski, N. R., Mason, K. L., Muraglia, R., & Huffnagle, G. B. (2013) · Scientific Reports · doi:10.1038/srep02191 · Cited by 136 · see citing works
The gut microbiome: a key player in the complexity of amyotrophic lateral sclerosis (ALS)
Boddy, S. L., Giovannelli, I., Sassani, M., Cooper-Knock, J., Snyder, M. P., Segal, E., Elinav, E., Barker, L. A., Shaw, P. J., & McDermott, C. J. (2021) · BMC Medicine · doi:10.1186/s12916-020-01885-3 · Cited by 127 · see citing works
The intestinal microbiota and host immune interactions in the critically ill
Schuijt, T. J., van der Poll, T., de Vos, W. M., & Wiersinga, W. J. (2013) · Trends in Microbiology · doi:10.1016/j.tim.2013.02.001 · Cited by 123 · see citing works
Routy, B., Letendre, C., Enot, D., Chénard-Poirier, M., Mehraj, V., Séguin, N. C., Guenda, K., Gagnon, K., Woerther, P.-L., Ghez, D., et al. (2017) · OncoImmunology · doi:10.1080/2162402x.2016.1258506 · Cited by 75 · see citing works
The Yin and Yang of Bacterial Resilience in the Human Gut Microbiota
Gibson, M. K., Pesesky, M. W., & Dantas, G. (2014) · Journal of Molecular Biology · doi:10.1016/j.jmb.2014.05.029 · Cited by 71 · see citing works
Nutrients and Microbiota in Lung Diseases of Prematurity: The Placenta-Gut-Lung Triangle
Piersigilli, F., Van Grambezen, B., Hocq, C., & Danhaive, O. (2020) · Nutrients · doi:10.3390/nu12020469 · Cited by 64 · see citing works
Alteration of metabolomic markers of amino-acid metabolism in piglets with in-feed antibiotics
Mu, C., Yang, Y., Yu, K., Yu, M., Zhang, C., Su, Y., & Zhu, W. (2017) · Amino Acids · doi:10.1007/s00726-017-2379-4 · Cited by 59 · see citing works
Minichino, A., Brondino, N., Solmi, M., Del Giovane, C., Fusar-Poli, P., Burnet, P., Cipriani, A., & Lennox, B. R. (2021) · Schizophrenia Research · doi:10.1016/j.schres.2020.02.012 · Cited by 50 · see citing works
Ostrem Loss, E., Thompson, J., Cheung, P. L. K., Qian, Y., & Venturelli, O. S. (2023) · Nature Ecology & Evolution · doi:10.1038/s41559-022-01930-9 · Cited by 38 · see citing works
Jenkins, S. V., Robeson, M. S., Griffin, R. J., Quick, C. M., Siegel, E. R., Cannon, M. J., Vang, K. B., & Dings, R. P. M. (2019) · Cancer Research · doi:10.1158/0008-5472.can-18-4108 · Cited by 41 · see citing works
Modulation of urinary siderophores by the diet, gut microbiota and inflammation in mice
Xiao, X., Yeoh, B. S., Saha, P., Tian, Y., Singh, V., Patterson, A. D., & Vijay-Kumar, M. (2017) · The Journal of Nutritional Biochemistry · doi:10.1016/j.jnutbio.2016.11.014 · Cited by 16 · see citing works
The Seven Methods for the Evaluation of Nutritional Status—ABCDEFG: Narrative Review
Zambrano-Villacres, R., Arteaga-Pazmiño, C., Guevara Castillo, W. D., Herrera-Fontana, M. E., Domínguez Brito, L. D., Becerra Granados, L. M., Recoba-Obregón, P. E., Rodríguez-Veintimilla, D., Bressi, V., Andrade-Molina, D., et al. (2026) · Applied Sciences · doi:10.3390/app16020845 · Cited by 5 · see citing works
- Authors
- Willing, B. P., Russell, S. L., & Finlay, B. B.
- Affiliations
- University of British Columbia (CA)
- Corresponding author
- Finlay, B. Brett
- Venue
- Nature Reviews Microbiology
- Published
- 2011-02-28
- Volume
- 9
- Issue
- 4
- Pages
- 233-243
- ISSN
- 1740-1526 (ISSN-L)
- 1740-1534
- OpenAlex
- W2134985690
- Cited by
- 747
- References
- 121
- Citations by year
- 2026: 24 · 2025: 56 · 2024: 68 · 2023: 45 · 2022: 77 · 2021: 62 · 2020: 86 · 2019: 47 · 2018: 38 · 2017: 42 · 2016: 36 · 2015: 31 · 2014: 53 · 2013: 32 · 2012: 37
- FWCI
- 3.92
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- Locations
- Nature Reviews Microbiology (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Canadian Institutes of Health Research
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Life Sciences › Immunology and Microbiology › Applied Microbiology and Biotechnology › Antibiotic Use and Resistance
- Health Sciences › Dentistry › Periodontics › Oral microbiology and periodontitis research
- Keywords
- antibiotics, host-microbiota interactions, gut microbiota, immune homeostasis, dysbiosis, disease susceptibility, antibiotic resistance
- MeSH terms
- Animals, Anti-Bacterial Agents, Bacteria, Bacterial Infections, Disease Susceptibility, Enterocolitis, Pseudomembranous, Fatty Acids, Volatile, Homeostasis, Humans, Biomass, Immunity, Mucosal, Gastrointestinal Tract, Host-Pathogen Interactions, Metagenome, Microbial Interactions
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review