Microbiota-mediated colonization resistance: mechanisms and regulation
Open accessAbstract
A dense and diverse microbial community inhabits the gut and many epithelial surfaces. Referred to as the microbiota, it co-evolved with the host and is beneficial for many host physiological processes. A major function of these symbiotic microorganisms is protection against pathogen colonization and overgrowth of indigenous pathobionts. Dysbiosis of the normal microbial community increases the risk of pathogen infection and overgrowth of harmful pathobionts. The protective mechanisms conferred by the microbiota are complex and include competitive microbial-microbial interactions and induction of host immune responses. Pathogens, in turn, have evolved multiple strategies to subvert colonization resistance conferred by the microbiota. Understanding the mechanisms by which microbial symbionts limit pathogen colonization should guide the development of new therapeutic approaches to prevent or treat disease.
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The gut microbiota protects against intestinal colonization by pathogens via colonization resistance through both direct and indirect mechanisms.
“The gut microbiota protects against intestinal colonization by pathogens via colonization resistance through both direct and indirect mechanisms.”
From Role of the gut microbiota in nutrient competition and protection against intestinal pathogen colonization (2023) · cites this paper as [34]
Examples of direct mechanisms of colonization resistance include nutrient competition between gut commensals and pathogens, production of inhibitory metabolites by gut commensals, production of bacteriocins by gut commensals, and the presence of bacteriophages.
“Examples of direct mechanisms of colonization resistance include nutrient competition between gut commensals and pathogens, production of inhibitory metabolites by gut commensals, production of bacteriocins by gut commensals, and the presence of bacteriophages [33, 34].”
From Role of the gut microbiota in nutrient competition and protection against intestinal pathogen colonization (2023) · cites this paper as [34]
Examples of indirect mechanisms of colonization resistance include interactions between the gut microbiota and the host immune response, changes in the gut microbiota that influence oxygen availability, modulation of the mucus layer by the gut microbiota, and promotion of cytokine release by the gut microbiota.
“Indirect mechanisms of colonization resistance include interactions between the gut microbiota and the host immune response, changes in the gut microbiota that influence oxygen availability, modulation of the mucus layer by the gut microbiota, and promotion of cytokine release by the gut microbiota [34].”
From Role of the gut microbiota in nutrient competition and protection against intestinal pathogen colonization (2023) · cites this paper as [34]
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Cites
A core gut microbiome in obese and lean twins
Turnbaugh, P. J., Hamady, M., Yatsunenko, T., Cantarel, B. L., Duncan, A., Ley, R. E., Sogin, M. L., Jones, W. J., Roe, B. A., Affourtit, J. P., et al. (2009) · Nature · doi:10.1038/nature07540 · Cited by 7,823 · see citing works
Dominguez-Bello, M. G., Costello, E. K., Contreras, M., Magris, M., Hidalgo, G., Fierer, N., & Knight, R. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1002601107 · Cited by 4,774 · 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
Vaginal microbiome of reproductive-age women
Ravel, J., Gajer, P., Abdo, Z., Schneider, G. M., Koenig, S. S. K., McCulle, S. L., Karlebach, S., Gorle, R., Russell, J., Tacket, C. O., et al. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1002611107 · Cited by 4,254 · see citing works
The impact of the gut microbiota on human health: an integrative view
Clemente, J. C., Ursell, L. K., Parfrey, L. W., & Knight, R. (2012) · Cell · doi:10.1016/j.cell.2012.01.035 · Cited by 3,710 · see citing works
Duodenal Infusion of Donor Feces for Recurrent <i>Clostridium difficile</i>
van Nood, E., Vrieze, A., Nieuwdorp, M., Fuentes, S., Zoetendal, E. G., de Vos, W. M., Visser, C. E., Kuijper, E. J., Bartelsman, J. F. W. M., Tijssen, J. G. P., et al. (2013) · New England Journal of Medicine · doi:10.1056/nejmoa1205037 · Cited by 3,708 · see citing works
Dynamics and Stabilization of the Human Gut Microbiome during the First Year of Life
Bäckhed, F., Roswall, J., Peng, Y., Feng, Q., Jia, H., Kovatcheva-Datchary, P., Li, Y., Xia, Y., Xie, H., Zhong, H., et al. (2015) · Cell Host & Microbe · doi:10.1016/j.chom.2015.04.004 · Cited by 3,315 · see citing works
Topographical and Temporal Diversity of the Human Skin Microbiome
Grice, E. A., Kong, H. H., Conlan, S., Deming, C. B., Davis, J., Young, A. C., Program, N. C. S., Bouffard, G. G., Blakesley, R. W., Murray, P. R., et al. (2009) · Science · doi:10.1126/science.1171700 · Cited by 2,953 · see citing works
Desai, M. S., Seekatz, A. M., Koropatkin, N. M., Kamada, N., Hickey, C. A., Wolter, M., Pudlo, N. A., Kitamoto, S., Terrapon, N., Muller, A., et al. (2016) · Cell · doi:10.1016/j.cell.2016.10.043 · Cited by 2,805 · see citing works
Self-citationThe NIH Human Microbiome ProjectPreprint
The NIH HMP Working Group, Peterson, J. L., Garges, S., Giovanni, M. Y., McInnes, P., Wang, L., Schloss, J. A., Bonazzi, V. R., McEwen, J. E., Wetterstrand, K. A., et al. (2009) · Genome Research · doi:10.1101/gr.096651.109 · Cited by 2,104 · see citing works
Interleukin-22 mediates early host defense against attaching and effacing bacterial pathogens
Zheng, Y., Valdez, P. A., Danilenko, D. M., Hu, Y., Susan, M. L., Gong, Q., Abbas, A. R., Modrusan, Z. D., Ghilardi, N., de Sauvage, F. J., et al. (2008) · Nature Medicine · doi:10.1038/nm1720 · Cited by 1,910 · see citing works
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 · see citing works
Nod2-Dependent Regulation of Innate and Adaptive Immunity in the Intestinal Tract
Kobayashi, K. S., Chamaillard, M., Ogura, Y., Henegariu, O., Inohara, N., Núñez, G., & Flavell, R. A. (2005) · Science · doi:10.1126/science.1104911 · Cited by 1,776 · see citing works
Self-citationKelly, C. J., Zheng, L., Campbell, E. L., Saeedi, B., Scholz, C. C., Bayless, A. J., Wilson, K. E., Glover, L. E., Kominsky, D. J., Magnuson, A., et al. (2015) · Cell Host & Microbe · doi:10.1016/j.chom.2015.03.005 · Cited by 1,716 · see citing works
Gut microbiota: Role in pathogen colonization, immune responses, and inflammatory disease
Pickard, J. M., Zeng, M. Y., Caruso, R., & Núñez, G. (2017) · Immunological Reviews · doi:10.1111/imr.12567 · Cited by 1,699 · see citing works
Self-citationControl of pathogens and pathobionts by the gut microbiota
Kamada, N., Chen, G. Y., Inohara, N., & Núñez, G. (2013) · Nature Immunology · doi:10.1038/ni.2608 · Cited by 1,625 · 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
Vaishnava, S., Yamamoto, M., Severson, K. M., Ruhn, K. A., Yu, X., Koren, O., Ley, R., Wakeland, E. K., & Hooper, L. V. (2011) · Science · doi:10.1126/science.1209791 · Cited by 1,412 · see citing works
Molecular Identification of Bacteria Associated with Bacterial Vaginosis
Fredricks, D. N., Fiedler, T. L., & Marrazzo, J. M. (2005) · New England Journal of Medicine · doi:10.1056/nejmoa043802 · Cited by 1,303 · 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
Microbiota-activated PPAR-γ signaling inhibits dysbiotic Enterobacteriaceae expansion
Byndloss, M. X., Olsan, E. E., Rivera-Chávez, F., Tiffany, C. R., Cevallos, S. A., Lokken, K. L., Torres, T. P., Byndloss, A. J., Faber, F., Gao, Y., et al. (2017) · Science · doi:10.1126/science.aam9949 · Cited by 1,237 · see citing works
A Primitive T Cell-Independent Mechanism of Intestinal Mucosal IgA Responses to Commensal Bacteria
Macpherson, A. J., Gatto, D., Sainsbury, E., Harriman, G. R., Hengartner, H., & Zinkernagel, R. M. (2000) · Science · doi:10.1126/science.288.5474.2222 · Cited by 1,113 · see citing works
Nakatsuji, T., Chen, T. H., Narala, S., Chun, K. A., Two, A. M., Yun, T., Shafiq, F., Kotol, P. F., Bouslimani, A., Melnik, A. V., et al. (2017) · Science Translational Medicine · doi:10.1126/scitranslmed.aah4680 · Cited by 1,095 · see citing works
Compartmentalized Control of Skin Immunity by Resident Commensals
Naik, S., Bouladoux, N., Wilhelm, C., Molloy, M. J., Salcedo, R., Kastenmuller, W., Deming, C., Quinones, M., Koo, L., Conlan, S., et al. (2012) · Science · doi:10.1126/science.1225152 · Cited by 1,092 · see citing works
Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth
Shao, Y., Forster, S. C., Tsaliki, E., Vervier, K., Strang, A., Simpson, N., Kumar, N., Stares, M. D., Rodger, A., Brocklehurst, P., et al. (2019) · Nature · doi:10.1038/s41586-019-1560-1 · Cited by 1,088 · see citing works
Microbiota-liberated host sugars facilitate post-antibiotic expansion of enteric pathogens
Ng, K. M., Ferreyra, J. A., Higginbottom, S. K., Lynch, J. B., Kashyap, P. C., Gopinath, S., Naidu, N., Choudhury, B., Weimer, B. C., Monack, D. M., et al. (2013) · Nature · doi:10.1038/nature12503 · Cited by 1,035 · see citing works
Host-Derived Nitrate Boosts Growth of <i>E. coli</i> in the Inflamed Gut
Winter, S. E., Winter, M. G., Xavier, M. N., Thiennimitr, P., Poon, V., Keestra, A. M., Laughlin, R. C., Gomez, G., Wu, J., Lawhon, S. D., et al. (2013) · Science · doi:10.1126/science.1232467 · Cited by 1,019 · see citing works
Iwase, T., Uehara, Y., Shinji, H., Tajima, A., Seo, H., Takada, K., Agata, T., & Mizunoe, Y. (2010) · Nature · doi:10.1038/nature09074 · Cited by 991 · see citing works
(1958) · PubMed · Cited by 978 · see citing works
Theriot, C. M., Koenigsknecht, M. J., Carlson, P. E., Hatton, G. E., Nelson, A. M., Li, B., Huffnagle, G. B., Z. Li, J., & Young, V. B. (2014) · Nature Communications · doi:10.1038/ncomms4114 · Cited by 974 · see citing works
Quorum Sensing in Staphylococci
Novick, R. P., & Geisinger, E. (2008) · Annual Review of Genetics · doi:10.1146/annurev.genet.42.110807.091640 · Cited by 953 · see citing works
Human commensals producing a novel antibiotic impair pathogen colonization
Zipperer, A., Konnerth, M. C., Laux, C., Berscheid, A., Janek, D., Weidenmaier, C., Burian, M., Schilling, N. A., Slavetinsky, C., Marschal, M., et al. (2016) · Nature · doi:10.1038/nature18634 · Cited by 938 · see citing works
A Type VI Secretion System of Pseudomonas aeruginosa Targets a Toxin to Bacteria
Hood, R. D., Singh, P., Hsu, F., Güvener, T., Carl, M. A., Trinidad, R. R. S., Silverman, J. M., Ohlson, B. B., Hicks, K. B., Plemel, R. L., et al. (2010) · Cell Host & Microbe · doi:10.1016/j.chom.2009.12.007 · Cited by 937 · see citing works
Colonization resistance of the digestive tract in conventional and antibiotic-treated mice
van der Waaij, D., Vries, J. M. B.-D., & der Wees, J. E. C. L.-V. (1971) · Journal of Hygiene · doi:10.1017/s0022172400021653 · Cited by 907 · see citing works
Rivera-Chávez, F., Zhang, L. F., Faber, F., Lopez, C. A., Byndloss, M. X., Olsan, E. E., Xu, G., Velazquez, E. M., Lebrilla, C. B., Winter, S. E., et al. (2016) · Cell Host & Microbe · doi:10.1016/j.chom.2016.03.004 · Cited by 864 · see citing works
Bacterial Interference Caused by Autoinducing Peptide Variants
Ji, G., Beavis, R. C., & Novick, R. P. (1997) · Science · doi:10.1126/science.276.5321.2027 · Cited by 820 · see citing works
Skin microbiota–host interactions
Chen, Y. E., Fischbach, M. A., & Belkaid, Y. (2018) · Nature · doi:10.1038/nature25177 · Cited by 788 · see citing works
Review: microbial transformations of human bile acids
Guzior, D. V., & Quinn, R. A. (2021) · Microbiome · doi:10.1186/s40168-021-01101-1 · Cited by 762 · see citing works
Regulated virulence controls the ability of a pathogen to compete with the gut microbiota
Kamada, N., Kim, Y.-G., Sham, H. P., Vallance, B. A., Puente, J. L., Martens, E. C., & Núñez, G. (2012) · Science · doi:10.1126/science.1222195 · Cited by 682 · see citing works
Self-citationDysbiotic Proteobacteria expansion: a microbial signature of epithelial dysfunction
Litvak, Y., Byndloss, M. X., Tsolis, R. M., & Bäumler, A. J. (2017) · Current Opinion in Microbiology · doi:10.1016/j.mib.2017.07.003 · Cited by 658 · see citing works
Global Causes of Diarrheal Disease Mortality in Children <5 Years of Age: A Systematic Review
Lanata, C. F., Fischer-Walker, C. L., Olascoaga, A. C., Torres, C. X., Aryee, M. J., & Black, R. E. (2013) · PLoS ONE · doi:10.1371/journal.pone.0072788 · Cited by 654 · see citing works
Gut microbiota utilize immunoglobulin A for mucosal colonization
Donaldson, G. P., Ladinsky, M. S., Yu, K. B., Sanders, J. G., Yoo, B. B., Chou, W., Conner, M. E., Earl, A. M., Knight, R. D., Björkman, P. J., et al. (2018) · Science · doi:10.1126/science.aaq0926 · Cited by 633 · 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
Bacterial colonization factors control specificity and stability of the gut microbiota
Lee, S. M., Donaldson, G. P., Mikulski, Z., Boyajian, S., Ley, K. F., & Mazmanian, S. K. (2013) · Nature · doi:10.1038/nature12447 · Cited by 629 · 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
Intestinal inflammation allows Salmonella to use ethanolamine to compete with the microbiota
Thiennimitr, P., Winter, S., Winter, M. G., Byndloss, M. X., Tolstikov, V., Huseby, D. L., Sterzenbach, T., Tsolis, R. M., Roth, J. R., & Bäumler, A. J. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1107857108 · Cited by 611 · see citing works
A Model of Host-Microbial Interactions in an Open Mammalian Ecosystem
Bry, L., Falk, P. G., Midtvedt, T., & Gordon, J. I. (1996) · Science · doi:10.1126/science.273.5280.1380 · Cited by 607 · see citing works
Deshmukh, H. S., Liu, Y., Menkiti, O. R., Mei, J., Dai, N., O'Leary, C. E., Oliver, P. M., Kolls, J. K., Weiser, J. N., & Worthen, G. S. (2014) · Nature Medicine · doi:10.1038/nm.3542 · Cited by 579 · see citing works
Kristensen, N. B., Bryrup, T., Allin, K. H., Nielsen, T., Hansen, T. H., & Pedersen, O. (2016) · Genome Medicine · doi:10.1186/s13073-016-0300-5 · Cited by 561 · see citing works
Innate and Adaptive Humoral Responses Coat Distinct Commensal Bacteria with Immunoglobulin A
Bunker, J. J., Flynn, T. M., Koval, J., Shaw, D. G., Meisel, M., McDonald, B. D., Ishizuka, I. E., Dent, A. L., Wilson, P. C., Jabrì, B., et al. (2015) · Immunity · doi:10.1016/j.immuni.2015.08.007 · Cited by 557 · see citing works
Probiotic Bacteria Reduce Salmonella Typhimurium Intestinal Colonization by Competing for Iron
Deriu, E., Liu, J. Z., Pezeshki, M., Edwards, R. A., Ochoa, R. J., Contreras, H., Libby, S. J., Fang, F. C., & Raffatellu, M. (2013) · Cell Host & Microbe · doi:10.1016/j.chom.2013.06.007 · Cited by 550 · see citing works
Normalization of host intestinal mucus layers requires long-term microbial colonization
Johansson, M. E. V., Jakobsson, H. E., Holmén-Larsson, J., Schütte, A., Ermund, A., Rodríguez-Piñeiro, A. M., Arike, L., Wising, C., Svensson, F., Bäckhed, F., et al. (2015) · Cell Host & Microbe · doi:10.1016/j.chom.2015.10.007 · Cited by 549 · see citing works
Microcins mediate competition among Enterobacteriaceae in the inflamed gut
Sassone-Corsi, M., Nuccio, S.-P., Liu, H., Hernandez, D., Vu, C. T., Takahashi, A. A., Edwards, R. A., & Raffatellu, M. (2016) · Nature · doi:10.1038/nature20557 · Cited by 549 · see citing works
Zheng, L., Kelly, C. J., Battista, K. D., Schaefer, R., Lanis, J. M., Alexeev, E. E., Wang, R. X., Onyiah, J. C., Kominsky, D. J., & Colgan, S. P. (2017) · The Journal of Immunology · doi:10.4049/jimmunol.1700105 · Cited by 549 · see citing works
Rapid fucosylation of intestinal epithelium sustains host–commensal symbiosis in sickness
Pickard, J. M., Maurice, C. F., Kinnebrew, M. A., Abt, M. C., Schenten, D., Golovkina, T. V., Bogatyrev, S. R., Ismagilov, R. F., Pamer, E. G., Turnbaugh, P. J., et al. (2014) · Nature · doi:10.1038/nature13823 · Cited by 535 · see citing works
Self-citationRaffatellu, M., George, M. D., Akiyama, Y., Hornsby, M. J., Nuccio, S.-P., Paixao, T. A., Butler, B. P., Chu, H., Santos, R. L., Berger, T., et al. (2009) · Cell Host & Microbe · doi:10.1016/j.chom.2009.03.011 · Cited by 525 · see citing works
An enteric virus can replace the beneficial function of commensal bacteria
Kernbauer, E., Ding, Y., & Cadwell, K. (2014) · Nature · doi:10.1038/nature13960 · Cited by 513 · see citing works
Theriot, C. M., Bowman, A. A., & Young, V. B. (2016) · mSphere · doi:10.1128/msphere.00045-15 · Cited by 481 · see citing works
Bajaj, V., Lucas, R. L., Hwang, C., & Lee, C. A. (1996) · Molecular Microbiology · doi:10.1046/j.1365-2958.1996.d01-1718.x · Cited by 477 · see citing works
Natural polyreactive IgA antibodies coat the intestinal microbiota
Bunker, J. J., Erickson, S. A., Flynn, T. M., Henry, C., Koval, J., Meisel, M., Jabrì, B., Antonopoulos, D. A., Wilson, P. C., & Bendelac, A. S. (2017) · Science · doi:10.1126/science.aan6619 · Cited by 470 · see citing works
Sorbara, M. T., & Pamer, E. G. (2022) · Nature Reviews Microbiology · doi:10.1038/s41579-021-00667-9 · Cited by 468 · see citing works
Brugiroux, S., Beutler, M., Pfann, C., Garzetti, D., Ruscheweyh, H., Ring, D., Diehl, M., Herp, S., Loetscher, Y., Hussain, S., et al. (2016) · Nature Microbiology · doi:10.1038/nmicrobiol.2016.215 · Cited by 463 · see citing works
Kommineni, S., Bretl, D. J., Lam, V., Chakraborty, R., Hayward, M., Simpson, P., Cao, Y., Bousounis, P., Kristich, C. J., & Salzman, N. H. (2015) · Nature · doi:10.1038/nature15524 · Cited by 458 · see citing works
Bacterial Community Mapping of the Mouse Gastrointestinal Tract
Gu, S., Chen, D., Zhang, J., Lv, X., Wang, K., Duan, L.-P., Nie, Y., & Wu, X. (2013) · PLoS ONE · doi:10.1371/journal.pone.0074957 · Cited by 443 · see citing works
Cogen, A. L., Yamasaki, K., Sanchez, K. M., Dorschner, R. A., Lai, Y., MacLeod, D. T., Torpey, J. W., Otto, M., Nizet, V., Kim, J. E., et al. (2010) · Journal of Investigative Dermatology · doi:10.1038/jid.2009.243 · Cited by 432 · see citing works
Challenges in infant immunity: implications for responses to infection and vaccines
PrabhuDas, M., Adkins, B., Gans, H. A., King, C. L., Levy, O., Ramilo, O., & Siegrist, C. (2011) · Nature Immunology · doi:10.1038/ni0311-189 · Cited by 430 · see citing works
Stecher, B., Chaffron, S., Käppeli, R., Hapfelmeier, S., Freedrich, S., Weber, T. C., Kirundi, J., Suar, M., McCoy, K. D., von Mering, C., et al. (2010) · PLoS Pathogens · doi:10.1371/journal.ppat.1000711 · Cited by 421 · see citing works
Control of the Microbial Flora of the Vagina by H202-Generating Lactobacilli
Klebanoff, S. J., Hillier, S. L., Eschenbach, D. A., & Waltersdorph, A. M. (1991) · The Journal of Infectious Diseases · doi:10.1093/infdis/164.1.94 · Cited by 420 · see citing works
Contact-Dependent Inhibition of Growth in Escherichia coli
Aoki, S. K., Pamma, R., Hernday, A. D., Bickham, J. E., Braaten, B. A., & Low, D. A. (2005) · Science · doi:10.1126/science.1115109 · Cited by 417 · see citing works
Zeng, M. Y., Cisalpino, D., Varadarajan, S., Hellman, J., Warren, H. S., Cascalho, M., Inohara, N., & Núñez, G. (2016) · Immunity · doi:10.1016/j.immuni.2016.02.006 · Cited by 417 · see citing works
Self-citationSmillie, C. S., Sauk, J. S., Gevers, D., Friedman, J., Sung, J., Youngster, I., Hohmann, E. L., Staley, C. M., Khoruts, A., Sadowsky, M. J., et al. (2018) · Cell Host & Microbe · doi:10.1016/j.chom.2018.01.003 · Cited by 417 · see citing works
High-avidity IgA protects the intestine by enchaining growing bacteria
Moor, K., Diard, M., Sellin, M. E., Felmy, B., Wotzka, S. Y., Toska, A., Bakkeren, E., Arnoldini, M., Bansept, F., Co, A. D., et al. (2017) · Nature · doi:10.1038/nature22058 · Cited by 411 · see citing works
The microbiome-shaping roles of bacteriocins
Heilbronner, S., Krismer, B., Brötz‐Oesterhelt, H., & Peschel, A. (2021) · Nature Reviews Microbiology · doi:10.1038/s41579-021-00569-w · Cited by 398 · see citing works
Franchi, L., Kamada, N., Nakamura, Y., Burberry, A., Kuffa, P., Suzuki, S., Shaw, M. H., Kim, Y., & Núñez, G. (2012) · Nature Immunology · doi:10.1038/ni.2263 · Cited by 394 · see citing works
Self-citationBrandl, K., Plitas, G., Schnabl, B., DeMatteo, R. P., & Pamer, E. G. (2007) · The Journal of Experimental Medicine · doi:10.1084/jem.20070563 · Cited by 385 · see citing works
Importance and regulation of the colonic mucus barrier in a mouse model of colitis
Petersson, J., Schreiber, O., Hansson, G. C., Gendler, S. J., Velcich, A., Lundberg, J. O., Roos, S., Holm, L., & Phillipson, M. (2010) · American Journal of Physiology-Gastrointestinal and Liver Physiology · doi:10.1152/ajpgi.00422.2010 · Cited by 384 · see citing works
A Type VI Secretion-Related Pathway in Bacteroidetes Mediates Interbacterial Antagonism
Russell, A. B., Wexler, A. G., Harding, B. N., Whitney, J. C. C., Bohn, A., Goo, Y. A., Tran, B. Q., Barry, N. A., Zheng, H., Peterson, S. B., et al. (2014) · Cell Host & Microbe · doi:10.1016/j.chom.2014.07.007 · Cited by 369 · see citing works
An exclusive metabolic niche enables strain engraftment in the gut microbiota
Shepherd, E. S., DeLoache, W. C., Pruss, K. M., Whitaker, W. R., & Sonnenburg, J. L. (2018) · Nature · doi:10.1038/s41586-018-0092-4 · Cited by 367 · see citing works
Effect of Streptomycin on Susceptibility of Intestinal Tract to Experimental Salmonella Infection.
Bohnhoff, M., Drake, B. L., & Miller, C. P. (1954) · Experimental Biology and Medicine · doi:10.3181/00379727-86-21030 · Cited by 354 · see citing works
Freter, R., Brickner, H., Botney, M. D., Cleven, D., & Aranki, A. (1983) · Infection and Immunity · doi:10.1128/iai.39.2.676-685.1983 · Cited by 340 · see citing works
Bomar, L., Brugger, S. D., Yost, B. H., Davies, S. S., & Lemon, K. P. (2016) · mBio · doi:10.1128/mbio.01725-15 · Cited by 332 · see citing works
Salmonella Typhimurium utilizes a T6SS-mediated antibacterial weapon to establish in the host gut
Sana, T. G., Flaugnatti, N., Lugo, K., Lam, L. H., Jacobson, A. R., Baylot, V., Durand, É., Journet, L., Cascalès, E., & Monack, D. M. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1608858113 · Cited by 329 · see citing works
Liu, J. Z., Jellbauer, S., Poe, A. J., Ton, V., Pesciaroli, M., Kehl-Fie, T. E., Restrepo, N. A., Hosking, M. P., Edwards, R. A., Battistoni, A., et al. (2012) · Cell Host & Microbe · doi:10.1016/j.chom.2012.01.017 · Cited by 328 · see citing works
Modulation of Shigella virulence in response to available oxygen in vivo
Marteyn, B., West, N. P., Browning, D. F., Cole, J. A., Shaw, J. G., Palm, F., Mounier, J., Prévost, M., Sansonetti, P. J., & Tang, C. M. (2010) · Nature · doi:10.1038/nature08970 · Cited by 323 · see citing works
Mucispirillum schaedleri Antagonizes Salmonella Virulence to Protect Mice against Colitis
Herp, S., Brugiroux, S., Garzetti, D., Ring, D., Jochum, L. M., Beutler, M., Eberl, C., Hussain, S., Walter, S., Gerlach, R. G., et al. (2019) · Cell Host & Microbe · doi:10.1016/j.chom.2019.03.004 · Cited by 312 · see citing works
A widespread family of polymorphic contact-dependent toxin delivery systems in bacteria
Aoki, S. K., Diner, E. J., de Roodenbeke, C. T., Burgess, B. R., Poole, S. J., Braaten, B. A., Jones, A. M., Webb, J., Hayes, C. S., Cotter, P. A., et al. (2010) · Nature · doi:10.1038/nature09490 · Cited by 308 · see citing works
Cooperating Commensals Restore Colonization Resistance to Vancomycin-Resistant Enterococcus faecium
Caballero, S., Kim, S., Carter, R. A., Leiner, I. M., Sušac, B., Miller, L., Kim, G. J., Ling, L., & Pamer, E. G. (2017) · Cell Host & Microbe · doi:10.1016/j.chom.2017.04.002 · Cited by 308 · see citing works
Williams, M. R., Costa, S. K., Zaramela, L. S., Khalil, S., Todd, D. A., Winter, H. L., Sanford, J. A., O’Neill, A. M., Liggins, M. C., Nakatsuji, T., et al. (2019) · Science Translational Medicine · doi:10.1126/scitranslmed.aat8329 · Cited by 292 · see citing works
Maltby, R., Leatham-Jensen, M. P., Gibson, T., Cohen, P. S., & Conway, T. (2013) · PLoS ONE · doi:10.1371/journal.pone.0053957 · Cited by 285 · see citing works
Fransen, F., Zagato, E., Mazzini, E., Fosso, B., Manzari, C., Aidy, S. E., Chiavelli, A., D’Erchia, A. M., Sethi, M. K., Pabst, O., et al. (2015) · Immunity · doi:10.1016/j.immuni.2015.08.011 · Cited by 284 · see citing works
Microbiota-derived lantibiotic restores resistance against vancomycin-resistant Enterococcus
Kim, S. G., Becattini, S., Moody, T. U., Shliaha, P. V., Littmann, E. R., Seok, R., Gjonbalaj, M., Eaton, V. P., Fontana, E., Amoretti, L. A., et al. (2019) · Nature · doi:10.1038/s41586-019-1501-z · Cited by 280 · see citing works
The Cytokine IL-22 Promotes Pathogen Colonization by Suppressing Related Commensal Bacteria
Behnsen, J., Jellbauer, S., Wong, C. P., Edwards, R. A., George, M. D., Ouyang, W., & Raffatellu, M. (2014) · Immunity · doi:10.1016/j.immuni.2014.01.003 · Cited by 279 · see citing works
Microbial ecology perturbation in human IgA deficiency
Fadlallah, J., Kafsi, H. E., Sterlin, D., Juste, C., Parizot, C., Dorgham, K., Autaa, G., Gouas, D. A., Almeida, M., Lepage, P., et al. (2018) · Science Translational Medicine · doi:10.1126/scitranslmed.aan1217 · Cited by 274 · see citing works
Neonatal acquisition of Clostridia species protects against colonization by bacterial pathogens
Kim, Y., Sakamoto, K., Seo, S., Pickard, J. M., Gillilland, M. G., Pudlo, N. A., Hoostal, M. J., Li, X., Wang, T. D., Feehley, T., et al. (2017) · Science · doi:10.1126/science.aag2029 · Cited by 272 · see citing works
Self-citationSpatial organization of intestinal microbiota in the mouse ascending colon
Nava, G. M., Friedrichsen, H. J., & Stappenbeck, T. S. (2010) · The ISME Journal · doi:10.1038/ismej.2010.161 · Cited by 270 · see citing works
Commensal Enterobacteriaceae Protect against Salmonella Colonization through Oxygen Competition
Litvak, Y., Mon, K. K. Z., Nguyen, H., Chanthavixay, G., Liou, M. J., Velazquez, E. M., Kutter, L., Alcantara, M. A., Byndloss, M. X., Tiffany, C. R., et al. (2019) · Cell Host & Microbe · doi:10.1016/j.chom.2018.12.003 · Cited by 270 · see citing works
Sorbara, M. T., Dubin, K., Littmann, E. R., Moody, T. U., Fontana, E., Seok, R., Leiner, I. M., Taur, Y., Peled, J. U., van den Brink, M. R. M., et al. (2019) · Journal of Experimental Medicine · doi:10.1084/jem.20181639 · Cited by 259 · see citing works
Innate secretory antibodies protect against natural Salmonella typhimurium infection
Wijburg, O. L. C., Uren, T. K., Simpfendorfer, K. R., Johansen, F., Brandtzæg, P., & Strugnell, R. A. (2006) · The Journal of Experimental Medicine · doi:10.1084/jem.20052093 · Cited by 253 · see citing works
The aetiology of bacterial vaginosis
Turovskiy, Y., Noll, K. S., & Chikindas, M. L. (2011) · Journal of Applied Microbiology · doi:10.1111/j.1365-2672.2011.04977.x · Cited by 250 · see citing works
RESISTANCE OF THE MOUSE'S INTESTINAL TRACT TO EXPERIMENTAL SALMONELLA INFECTION
Bohnhoff, M., Miller, C. P., & Martin, W. R. (1964) · The Journal of Experimental Medicine · doi:10.1084/jem.120.5.805 · Cited by 246 · see citing works
Lopez, C. A., Winter, S., Rivera-Chávez, F., Byndloss, M. X., Poon, V., Nuccio, S., Tsolis, R. M., & Bäumler, A. J. (2012) · mBio · doi:10.1128/mbio.00143-12 · Cited by 242 · see citing works
Sugimoto, S., Iwamoto, T., Takada, K., Okuda, K.-I., Tajima, A., Iwase, T., & Mizunoe, Y. (2013) · Journal of Bacteriology · doi:10.1128/jb.01672-12 · Cited by 242 · see citing works
Paharik, A. E., Parlet, C. P., Chung, N., Todd, D. A., Rodriguez, E. I., Dyke, M. J. V., Cech, N. B., & Horswill, A. R. (2017) · Cell Host & Microbe · doi:10.1016/j.chom.2017.11.001 · Cited by 240 · see citing works
Spees, A. M., Wangdi, T., Lopez, C. A., Kingsbury, D. D., Byndloss, M. X., Winter, S., Tsolis, R. M., & Bäumler, A. J. (2013) · mBio · doi:10.1128/mbio.00430-13 · Cited by 237 · see citing works
Commensal Microbes Induce Serum IgA Responses that Protect against Polymicrobial Sepsis
Wilmore, J. R., Gaudette, B. T., Gómez, D., Hashemi, T., Jones, D. D., Gardner, C. A., Cole, S. D., Misic, A. M., Beiting, D. P., & Allman, D. (2018) · Cell Host & Microbe · doi:10.1016/j.chom.2018.01.005 · Cited by 236 · see citing works
Chatzidaki‐Livanis, M., Geva‐Zatorsky, N., & Comstock, L. E. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1522510113 · Cited by 232 · see citing works
Bacterial killing via a type IV secretion system
Souza, D. P., Oka, G. U., Alvarez-Martinez, C., Bisson-Filho, A. W., Dunger, G., Hobeika, L., Cavalcante, N. S., Alegria, M. C., Barbosa, L. R. S., Salinas, R., et al. (2015) · Nature Communications · doi:10.1038/ncomms7453 · Cited by 228 · see citing works
In vivo IgA coating of anaerobic bacteria in human faeces.
van der Waaij, L. A., Limburg, P. C., Mesander, G., & van der Waaij, D. (1996) · Gut · doi:10.1136/gut.38.3.348 · Cited by 220 · see citing works
Nagao‐Kitamoto, H., Leslie, J. L., Kitamoto, S., Jin, C., Thomsson, K. A., Gillilland, M. G., Kuffa, P., Goto, Y., Jenq, R. R., Ishii, C., et al. (2020) · Nature Medicine · doi:10.1038/s41591-020-0764-0 · Cited by 220 · see citing works
Human symbionts inject and neutralize antibacterial toxins to persist in the gut
Wexler, A. G., Bao, Y., Whitney, J. C. C., Bobay, L., Xavier, J. B., Schofield, W. B., Barry, N. A., Russell, A. B., Tran, B. Q., Goo, Y. A., et al. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1525637113 · Cited by 216 · see citing works
The nasal cavity microbiota of healthy adults
Bassis, C. M., Tang, A. L., Young, V. B., & Pynnonen, M. A. (2014) · Microbiome · doi:10.1186/2049-2618-2-27 · Cited by 209 · see citing works
Zarepour, M., Bhullar, K., Montero, M., Ma, C., Huang, T., Velcich, A., Xia, L., & Vallance, B. A. (2013) · Infection and Immunity · doi:10.1128/iai.00854-13 · Cited by 206 · see citing works
Adaptive immunity induces mutualism between commensal eukaryotes
Ost, K. S., O’Meara, T. R., Stephens, W. Z., Chiaro, T. R., Zhou, H., Penman, J., Bell, R. S., Catanzaro, J., Song, D., Singh, S., et al. (2021) · Nature · doi:10.1038/s41586-021-03722-w · Cited by 205 · see citing works
Virulence factors enhance <i>Citrobacter rodentium</i> expansion through aerobic respiration
Lopez, C. A., Miller, B. M., Rivera-Chávez, F., Velazquez, E. M., Byndloss, M. X., Chávez-Arroyo, A., Lokken, K. L., Tsolis, R. M., Winter, S. E., & Bäumler, A. J. (2016) · Science · doi:10.1126/science.aag3042 · Cited by 201 · see citing works
Endogenous Enterobacteriaceae underlie variation in susceptibility to Salmonella infection
Velazquez, E. M., Nguyen, H., Heasley, K. T., Saechao, C. H., Gil, L. M., Rogers, A. W. L., Miller, B. M., Rolston, M. R., Lopez, C. A., Litvak, Y., et al. (2019) · Nature Microbiology · doi:10.1038/s41564-019-0407-8 · Cited by 201 · see citing works
Studer, N., Desharnais, L., Beutler, M., Brugiroux, S., Miani, M. A. T., Menin, L., Schürch, C. M., McCoy, K. D., Kuehne, S. A., Minton, N. P., et al. (2016) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2016.00191 · Cited by 198 · see citing works
Freter, R. (1955) · The Journal of Infectious Diseases · doi:10.1093/infdis/97.1.57 · Cited by 194 · see citing works
Antagonism toward the intestinal microbiota and its effect on Vibrio cholerae virulence
Zhao, W., Caro, F., Robins, W. P., & Mekalanos, J. J. (2018) · Science · doi:10.1126/science.aap8775 · Cited by 190 · see citing works
Transition Metal Sequestration by the Host-Defense Protein Calprotectin
Zygiel, E. M., & Nolan, E. M. (2018) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-062917-012312 · Cited by 187 · see citing works
Coyne, M. J., Roelofs, K., & Comstock, L. E. (2016) · BMC Genomics · doi:10.1186/s12864-016-2377-z · Cited by 184 · see citing works
Respiration of Microbiota-Derived 1,2-propanediol Drives Salmonella Expansion during Colitis
Faber, F., Thiennimitr, P., Spiga, L., Byndloss, M. X., Litvak, Y., Lawhon, S. D., Andrews‐Polymenis, H. L., Winter, S., & Bäumler, A. J. (2017) · PLoS Pathogens · doi:10.1371/journal.ppat.1006129 · Cited by 184 · see citing works
In Vitro Antibacterial Activity of Unconjugated and Conjugated Bile Salts on Staphylococcus aureus
Sannasiddappa, T. H., Lund, P. A., & Clarke, S. R. (2017) · Frontiers in Microbiology · doi:10.3389/fmicb.2017.01581 · Cited by 183 · see citing works
Strain competition restricts colonization of an enteric pathogen and prevents colitis
Hecht, A. L., Casterline, B. W., Earley, Z. M., Goo, Y. A., Goodlett, D. R., & Wardenburg, J. B. (2016) · EMBO Reports · doi:10.15252/embr.201642282 · Cited by 182 · see citing works
Host Selection of Microbiota via Differential Adhesion
McLoughlin, K. G., Schlüter, J., Rakoff-Nahoum, S., Smith, A. L., & Foster, K. R. (2016) · Cell Host & Microbe · doi:10.1016/j.chom.2016.02.021 · Cited by 180 · see citing works
Host-mediated sugar oxidation promotes post-antibiotic pathogen expansion
Faber, F., Tran, L., Byndloss, M. X., Lopez, C. A., Velazquez, E. M., Kerrinnes, T., Nuccio, S., Wangdi, T., Fiehn, O., Tsolis, R. M., et al. (2016) · Nature · doi:10.1038/nature18597 · Cited by 180 · see citing works
Whitney, J. C. C., Peterson, S. B., Kim, J., Pazos, M., Verster, A. J., Radey, M. C., Kulasekara, H. D., Ching, M. Q., Bullen, N. P., Bryant, D., et al. (2017) · eLife · doi:10.7554/elife.26938 · Cited by 179 · see citing works
Microbiota-Derived Hydrogen Fuels Salmonella Typhimurium Invasion of the Gut Ecosystem
Maier, L., Vyas, R., Cordova, C. D., Lindsay, H. A., Schmidt, T., Brugiroux, S., Periaswamy, B., Bauer, R., Sturm, A., Schreiber, F., et al. (2013) · Cell Host & Microbe · doi:10.1016/j.chom.2013.11.002 · Cited by 173 · see citing works
Shigella sonnei Encodes a Functional T6SS Used for Interbacterial Competition and Niche Occupancy
Anderson, M. C., Vonaesch, P., Saffarian, A., Marteyn, B., & Sansonetti, P. J. (2017) · Cell Host & Microbe · doi:10.1016/j.chom.2017.05.004 · Cited by 169 · see citing works
Diaz-Ochoa, V. E., Lam, D., Lee, C. S., Klaus, S., Behnsen, J., Liu, J. Z., Chim, N., Nuccio, S.-P., Rathi, S. G., Mastroianni, J. R., et al. (2016) · Cell Host & Microbe · doi:10.1016/j.chom.2016.05.005 · Cited by 164 · see citing works
O'Sullivan, J. N., Rea, M. C., O’Connor, P. M., Hill, C., & Ross, R. P. (2018) · FEMS Microbiology Ecology · doi:10.1093/femsec/fiy241 · Cited by 164 · see citing works
Hung, C., Garner, C. D., Slauch, J. M., Dwyer, Z. W., Lawhon, S. D., Frye, J. G., McClelland, M., Ahmer, B. M. M., & Altier, C. (2013) · Molecular Microbiology · doi:10.1111/mmi.12149 · Cited by 163 · see citing works
Probiotics for prevention of Clostridium difficile infection
Mills, J., Rao, K. K., & Young, V. B. (2017) · Current Opinion in Gastroenterology · doi:10.1097/mog.0000000000000410 · Cited by 162 · see citing works
Human gut bacteria contain acquired interbacterial defence systems
Ross, B. D., Verster, A. J., Radey, M. C., Schmidtke, D. T., Pope, C. E., Hoffman, L. R., Hajjar, A. M., Peterson, S. B., Borenstein, E., & Mougous, J. D. (2019) · Nature · doi:10.1038/s41586-019-1708-z · Cited by 162 · see citing works
Segmented Filamentous Bacteria Prevent and Cure Rotavirus Infection
Shi, Z., Zou, J., Zhang, Z., Zhao, X., Noriega, J., Zhang, B., Zhao, C., Ingle, H., Bittinger, K. L., Mattei, L. M., et al. (2019) · Cell · doi:10.1016/j.cell.2019.09.028 · Cited by 158 · see citing works
Microbiota-targeted maternal antibodies protect neonates from enteric infection
Zheng, W., Zhao, W., Wu, M., Song, X., Caro, F., Sun, X., Gazzaniga, F., Stefanetti, G., Oh, S., Mekalanos, J. J., et al. (2020) · Nature · doi:10.1038/s41586-019-1898-4 · Cited by 158 · see citing works
The role of iron in host–microbiota crosstalk and its effects on systemic glucose metabolism
Mayneris‐Perxachs, J., Moreno‐Navarrete, J. M., & Fernández‐Real, J. M. (2022) · Nature Reviews Endocrinology · doi:10.1038/s41574-022-00721-3 · Cited by 158 · see citing works
Janek, D., Zipperer, A., Kulik, A., Krismer, B., & Peschel, A. (2016) · PLoS Pathogens · doi:10.1371/journal.ppat.1005812 · Cited by 157 · see citing works
Regulation of virulence by butyrate sensing in enterohaemorrhagic Escherichia coli
Nakanishi, N., Tashiro, K., Kuhara, S., Hayashi, T., Sugimoto, N., & Tobe, T. (2009) · Microbiology · doi:10.1099/mic.0.023499-0 · Cited by 156 · see citing works
Xu, Z., Takizawa, F., Casadei, E., Shibasaki, Y., Ding, Y., Sauters, T. J. C., Yu, Y., Salinas, I., & Sunyer, J. O. (2020) · Science Immunology · doi:10.1126/sciimmunol.aay3254 · Cited by 151 · see citing works
Osbelt, L., Wende, M., Almási, É. D. H., Derksen, E., Muthukumarasamy, U., Lesker, T. R., Gálvez, E. J. C., Pils, M. C., Schalk, E., Chhatwal, P., et al. (2021) · Cell Host & Microbe · doi:10.1016/j.chom.2021.09.003 · Cited by 147 · see citing works
Liu, Q., Liu, Q., Meng, H., Lv, H., Liu, Y., Liu, J., Wang, H., He, L., Qin, J., Wang, Y., et al. (2019) · Cell Host & Microbe · doi:10.1016/j.chom.2019.11.003 · Cited by 146 · see citing works
Bitschar, K., Sauer, B., Focken, J., Dehmer, H., Moos, S., Konnerth, M. C., Schilling, N. A., Grond, S., Kalbacher, H., Kurschus, F. C., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-10646-7 · Cited by 143 · see citing works
Role of volatile fatty acids in colonization resistance to Clostridium difficile
Rolfe, R. D. (1984) · Infection and Immunity · doi:10.1128/iai.45.1.185-191.1984 · Cited by 142 · see citing works
Preventing dysbiosis of the neonatal mouse intestinal microbiome protects against late-onset sepsis
Singer, J. R., Blosser, E. G., Zindl, C. L., Silberger, D. J., Conlan, S., Laufer, V. A., Ditoro, D. F., Deming, C., Kumar, R., Morrow, C. D., et al. (2019) · Nature Medicine · doi:10.1038/s41591-019-0640-y · Cited by 142 · see citing works
Guo, X., Liang, Y., Zhang, Y., Lasorella, A., Kee, B. L., & Fu, Y.-X. (2015) · Immunity · doi:10.1016/j.immuni.2015.03.012 · Cited by 138 · see citing works
Watanabe, M., Fukiya, S., & Yokota, A. (2017) · Journal of Lipid Research · doi:10.1194/jlr.m075143 · Cited by 137 · see citing works
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 · see citing works
Sequeira, R. P., McDonald, J. A. K., Marchesi, J. R., & Clarke, T. B. (2020) · Nature Microbiology · doi:10.1038/s41564-019-0640-1 · Cited by 132 · see citing works
Vancomycin-Resistant Enterococci
Reyes, K., Bardossy, A. C., & Zervos, M. (2016) · Infectious Disease Clinics of North America · doi:10.1016/j.idc.2016.07.009 · Cited by 128 · see citing works
Durant, J. A., Corrier, D. E., & Ricke, S. C. (2000) · Journal of Food Protection · doi:10.4315/0362-028x-63.5.573 · Cited by 118 · see citing works
Singh, V., Yeoh, B. S., Chassaing, B., Zhang, B., Saha, P., Xiao, X., Awasthi, D., Shashidharamurthy, R., Dikshit, M., Gewirtz, A., et al. (2016) · Cellular and Molecular Gastroenterology and Hepatology · doi:10.1016/j.jcmgh.2016.03.007 · Cited by 117 · see citing works
Intestinally Secreted C-Type Lectin Reg3b Attenuates Salmonellosis but Not Listeriosis in Mice
van Ampting, M. T. J., Loonen, L., Schonewille, A., Konings, I. B. M., Vink, C., Iovanna, J., Chamaillard, M., Dekker, J., van der Meer, R. V. D., Wells, J., et al. (2012) · Infection and Immunity · doi:10.1128/iai.06165-11 · Cited by 108 · see citing works
Ryouichi, S. H. I. N., Suzuki, M., & Morishita, Y. (2002) · Journal of Medical Microbiology · doi:10.1099/0022-1317-51-3-201 · Cited by 106 · see citing works
Antagonistic activity against pathogenic bacteria by human vaginal lactobacilli
Voravuthikunchai, S. P., Bilasoi, S., & Supamala, O. (2006) · Anaerobe · doi:10.1016/j.anaerobe.2006.06.003 · Cited by 104 · see citing works
Mechanisms and Biological Roles of Contact-Dependent Growth Inhibition SystemsPreprint
Hayes, C. S., Koskiniemi, S., Ruhe, Z. C., Poole, S. J., & Low, D. A. (2014) · Cold Spring Harbor Perspectives in Medicine · doi:10.1101/cshperspect.a010025 · Cited by 102 · see citing works
Chen, J., Waddell, A., Lin, Y.-D., & Cantorna, M. T. (2014) · Mucosal Immunology · doi:10.1038/mi.2014.94 · Cited by 101 · see citing works
Siderophore-mediated zinc acquisition enhances enterobacterial colonization of the inflamed gut
Behnsen, J., Zhi, H., Aron, A. T., Subramanian, V., Santus, W., Lee, M. H., Gerner, R. R., Petras, D., Liu, J. Z., Green, K. D., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-27297-2 · Cited by 101 · see citing works
Murphy, K., & Mitchell, C. M. (2016) · The Journal of Infectious Diseases · doi:10.1093/infdis/jiw140 · Cited by 100 · see citing works
Osbelt, L., Thiemann, S., Smit, N., Lesker, T. R., Schröter, M., Gálvez, E. J. C., Schmidt‐Hohagen, K., Pils, M. C., Mühlen, S., Dersch, P., et al. (2020) · PLoS Pathogens · doi:10.1371/journal.ppat.1008448 · Cited by 100 · see citing works
Zhou, P., Zhou, Y., Liu, B., Jin, Z., Zhuang, X., Dai, W., Yang, Z., Feng, X., Zhou, Q., Liu, Y., et al. (2020) · mSphere · doi:10.1128/msphere.00984-19 · Cited by 95 · see citing works
Abt, M. C., Buffie, C. G., Sušac, B., Becattini, S., Carter, R. A., Leiner, I., Keith, J. W., Artis, D., Osborne, L. C., & Pamer, E. G. (2016) · Science Translational Medicine · doi:10.1126/scitranslmed.aad6663 · Cited by 94 · see citing works
IFN-I and IL-22 mediate protective effects of intestinal viral infection
Neil, J. A., Matsuzawa, Y., Kernbauer, E., Schuster, S. L., Sota, S., Venzon, M., Dallari, S., Neto, A. G., Hine, A. M., Hudesman, D. P., et al. (2019) · Nature Microbiology · doi:10.1038/s41564-019-0470-1 · Cited by 94 · see citing works
Roelofs, K., Coyne, M. J., Gentyala, R. R., Chatzidaki‐Livanis, M., & Comstock, L. E. (2016) · mBio · doi:10.1128/mbio.01055-16 · Cited by 92 · see citing works
Bile acid-independent protection against Clostridioides difficile infection
Aguirre, A. M., Yalçınkaya, N., Wu, Q., Swennes, A. G., Tessier, M. E. M., Roberts, P., Miyajima, F., Savidge, T., & Sorg, J. A. (2021) · PLoS Pathogens · doi:10.1371/journal.ppat.1010015 · Cited by 91 · see citing works
A family of anti-Bacteroidales peptide toxins wide-spread in the human gut microbiota
Coyne, M. J., Béchon, N., Matano, L. M., McEneany, V. L., Chatzidaki‐Livanis, M., & Comstock, L. E. (2019) · Nature Communications · doi:10.1038/s41467-019-11494-1 · Cited by 88 · see citing works
Persistence of colicinogenic Escherichia coli in the mouse gastrointestinal tract
Gillor, O., Giladi, I., & Riley, M. A. (2009) · BMC Microbiology · doi:10.1186/1471-2180-9-165 · Cited by 87 · see citing works
Microbiota-Derived Metabolic Factors Reduce Campylobacteriosis in Mice
Sun, X., Winglee, K., Gharaibeh, R. Z., Gauthier, J., He, Z., Tripathi, P., Avram, D., Bruner, S. D., Fodor, A. A., & Jobin, C. (2018) · Gastroenterology · doi:10.1053/j.gastro.2018.01.042 · Cited by 85 · see citing works
Salmonella effector driven invasion of the gut epithelium: breaking in and setting the house on fire
Fattinger, S. A., Sellin, M. E., & Hardt, W. (2021) · Current Opinion in Microbiology · doi:10.1016/j.mib.2021.08.007 · Cited by 84 · see citing works
Genetic Ablation of Butyrate Utilization Attenuates Gastrointestinal Salmonella Disease
Bronner, D. N., Faber, F., Olsan, E. E., Byndloss, M. X., Sayed, N. A., Xu, G., Yoo, W., Kim, D., Ryu, S., Lebrilla, C. B., et al. (2018) · Cell Host & Microbe · doi:10.1016/j.chom.2018.01.004 · Cited by 77 · see citing works
Neumann, M., Steimle, A., Grant, E. T., Wolter, M., Parrish, A., Willième, S., Brenner, D., Martens, E. C., & Desai, M. S. (2021) · Gut Microbes · doi:10.1080/19490976.2021.1966263 · Cited by 77 · see citing works
Caballero-Flores, G., Pickard, J. M., Fukuda, S., Inohara, N., & Núñez, G. (2020) · Cell Host and Microbe · doi:10.1016/j.chom.2020.06.018 · Cited by 76 · see citing works
Self-citationJimenez, A. G., Ellermann, M., Abbott, D. W., & Sperandio, V. (2019) · Nature Microbiology · doi:10.1038/s41564-019-0641-0 · Cited by 75 · see citing works
Kohli, N., Crisp, Z., Riordan, R., Li, M., Alaniz, R. C., & Jayaraman, A. (2018) · PLoS ONE · doi:10.1371/journal.pone.0190613 · Cited by 73 · see citing works
Sweeney, N. J., Klemm, P., McCormick, B. A., Nielsen, E. M., Utley, M., Schembri, M. A., Laux, D. C., & Cohen, P. S. (1996) · Infection and Immunity · doi:10.1128/iai.64.9.3497-3503.1996 · Cited by 72 · see citing works
Pathogenic E. coli Extracts Nutrients from Infected Host Cells Utilizing Injectisome Components
Pal, R. R., Baidya, A. K., Mamou, G., Bhattacharya, S., Socol, Y., Kobi, S., Katsowich, N., Ben-Yehuda, S., & Rosenshine, I. (2019) · Cell · doi:10.1016/j.cell.2019.02.022 · Cited by 72 · see citing works
Miller, B. M., Liou, M. J., Zhang, L. F., Nguyen, H., Litvak, Y., Schorr, E., Jang, K. K., Tiffany, C. R., Butler, B. P., & Bäumler, A. J. (2020) · Cell Host & Microbe · doi:10.1016/j.chom.2020.10.009 · Cited by 71 · see citing works
Shelton, C. D., Yoo, W., Shealy, N. G., Torres, T. P., Zieba, J. K., Calcutt, M. W., Foegeding, N. J., Kim, D., Kim, J., Ryu, S., et al. (2022) · Cell Reports · doi:10.1016/j.celrep.2021.110180 · Cited by 69 · see citing works
Flaugnatti, N., Isaac, S., Rocha, L. F. L., Stutzmann, S., Rendueles, O., Stoudmann, C., Vesel, N., Garcia‐Garcerà, M., Nucci, A., Sana, T. G., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-26041-0 · Cited by 68 · see citing works
Type VI secretion systems of pathogenic and commensal bacteria mediate niche occupancy in the gut
Serapio-Palacios, A., Woodward, S. E., Vogt, S. L., Deng, W., Creus-Cuadros, A., Huus, K. E., Cirstea, M. S., Gerrie, M., Barcik, W., Yu, H., et al. (2022) · Cell Reports · doi:10.1016/j.celrep.2022.110731 · Cited by 65 · see citing works
Connolly, J. P. R., Slater, S. L., O’Boyle, N., Goldstone, R. J., Crepin, V. F., Ruano‐Gallego, D., Herzyk, P., Smith, D. G., Douce, G. R., Frankel, G. M., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-06701-4 · Cited by 63 · see citing works
Centenary of the death of Elie Metchnikoff: a visionary and an outstanding team leader
Cavaillon, J., & Legout, S. (2016) · Microbes and Infection · doi:10.1016/j.micinf.2016.05.008 · Cited by 62 · see citing works
Lewis, B. B., Carter, R. A., Ling, L., Leiner, I. M., Taur, Y., Kamboj, M., Dubberke, E. R., Xavier, J. B., & Pamer, E. G. (2017) · mBio · doi:10.1128/mbio.00885-17 · Cited by 61 · see citing works
Leatham-Jensen, M. P., Frimodt-Møller, J., Adediran, J., Mokszycki, M. E., Banner, M., Caughron, J. E., Krogfelt, K. A., Conway, T., & Cohen, P. S. (2012) · Infection and Immunity · doi:10.1128/iai.06193-11 · Cited by 60 · see citing works
Host cells subdivide nutrient niches into discrete biogeographical microhabitats for gut microbes
Liou, M. J., Miller, B. M., Litvak, Y., Nguyen, H., Natwick, D. E., Savage, H. P., Rixon, J. A., Mahan, S. P., Hiyoshi, H., Rogers, A. W. L., et al. (2022) · Cell Host & Microbe · doi:10.1016/j.chom.2022.04.012 · Cited by 59 · see citing works
Pheromone killing of multidrug-resistant Enterococcus faecalis V583 by native commensal strains
Gilmore, M. S., Rauch, M., Ramsey, M. M., Himes, P., Varahan, S., Manson, J. M., Lebreton, F., & Hancock, L. E. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1500553112 · Cited by 56 · see citing works
Antimicrobial Peptides in Gut Health: A Review
Gong, T., Fu, J., Shi, L., Chen, X., & Zong, X. (2021) · Frontiers in Nutrition · doi:10.3389/fnut.2021.751010 · Cited by 52 · see citing works
Antimicrobial Peptides—or How Our Ancestors Learned to Control the Microbiome
Bosch, T. C. G., & ZASLOFF, M. A. (2021) · mBio · doi:10.1128/mbio.01847-21 · Cited by 43 · see citing works
Stecher, B. (2021) · International Journal of Medical Microbiology · doi:10.1016/j.ijmm.2021.151484 · Cited by 37 · see citing works
Leslie, J. L., Jenior, M. L., Vendrov, K. C., Standke, A. K., Barron, M. R., O’Brien, T. J., Unverdorben, L. V., Thaprawat, P., Bergin, I. L., Schloss, P. D., et al. (2021) · mBio · doi:10.1128/mbio.00522-21 · Cited by 35 · see citing works
Zhang, T., Sasabe, J., Hullahalli, K., Sit, B., & Waldor, M. K. (2021) · Infection and Immunity · doi:10.1128/iai.00667-20 · Cited by 32 · see citing works
Kafkova, L. R., Brokešová, D., Křupka, M., Stehlíková, Z., Dvořák, J., Coufal, Š., Fajstová, A., Šrůtková, D., Štěpánová, K., Hermanová, P. P., et al. (2020) · Mucosal Immunology · doi:10.1038/s41385-020-00345-8 · Cited by 31 · see citing works
Klüber, P., Meurer, S. K., Lambertz, J., Schwarz, R., Zechel-Gran, S., Braunschweig, T. A., Hurka, S., Domann, E., & Weiskirchen, R. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms222313156 · Cited by 31 · see citing works
Waldschmitt, N., Kitamoto, S., Sécher, T., Zacharioudaki, V., Boulard, O., Floquet, E., Delacre, M., Lamas, B., Pham, H., Six, A., et al. (2018) · Gut · doi:10.1136/gutjnl-2018-316757 · Cited by 22 · see citing works
Bile acid sensitivity and in vivo virulence of clinical Clostridium difficile isolates
Lewis, B. B., Carter, R. A., & Pamer, E. G. (2016) · Anaerobe · doi:10.1016/j.anaerobe.2016.05.010 · Cited by 21 · see citing works
Citrobacter amalonaticus Inhibits the Growth of Citrobacter rodentium in the Gut Lumen
Mullineaux-Sanders, C., Carson, D., Hopkins, E. G. D., Glegola-Madejska, I., Escobar‐Zepeda, A., Browne, H. P., Lawley, T. D., & Frankel, G. M. (2021) · mBio · doi:10.1128/mbio.02410-21 · Cited by 20 · see citing works
Betz, K. J., Maier, E. A., Amarachintha, S. P., Wu, D. X.-Y., Karmele, E. P., Kinder, J. M., Steinbrecher, K. A., McNeal, M., Luzader, D., Hogan, S. P., et al. (2018) · PLoS ONE · doi:10.1371/journal.pone.0198434 · Cited by 12 · see citing works
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- [13]Hutchinson GE An Introduction to Population Ecology (Yale Univ. Press, 1978).
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Microbiota–gut–brain axis and its therapeutic applications in neurodegenerative diseases
Loh, J. S., Mak, W. Q., Tan, L. K. S., Ng, C. X., Chan, H. H., Yeow, S. H., Foo, J. B., Ong, Y. S., How, C. W., & Khaw, K. Y. (2024) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-024-01743-1 · Cited by 1,193 · see citing works
Faecalibacterium : a bacterial genus with promising human health applications
Martín, R., Ríos-Covián, D., Huillet, E., Auger, S., Khazaal, S., Bermúdez‐Humarán, L. G., Sokol, H., Chatel, J., & Langella, P. (2023) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuad039 · Cited by 583 · see citing works
Microbiome diversity protects against pathogens by nutrient blocking
Spragge, F., Bakkeren, E., Jahn, M. T., Araujo, E. B. N., Pearson, C. F., Wang, X., Pankhurst, L. J., Cunrath, O., & Foster, K. R. (2023) · Science · doi:10.1126/science.adj3502 · Cited by 434 · see citing works
Drug-microbiota interactions: an emerging priority for precision medicine
Zhao, Q. C., Chen, Y., Huang, W., Zhou, H., & Zhang, W. (2023) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-023-01619-w · Cited by 296 · see citing works
Ma, Z., Zuo, T., Frey, N., & Rangrez, A. Y. (2024) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-024-01946-6 · Cited by 297 · see citing works
Benedé-Ubieto, R., Cubero, F. J., & Nevzorova, Y. A. (2024) · Gut Microbes · doi:10.1080/19490976.2024.2331460 · Cited by 242 · see citing works
The conceptual foundations of innate immunity: Taking stock 30 years later.
Pradeu, T., Thomma, B. P., Girardin, S., & Lemaître, B. (2024) · Immunity · doi:10.1016/j.immuni.2024.03.007 · Cited by 149 · see citing works
Li, L., Peng, P., Ding, N., Jia, W., Huang, C., & Tang, Y. (2023) · Antioxidants · doi:10.3390/antiox12040967 · Cited by 140 · see citing works
Antibiotic-induced collateral damage to the microbiota and associated infections
de Nies, L., Kobras, C. M., & Stracy, M. (2023) · Nature Reviews Microbiology · doi:10.1038/s41579-023-00936-9 · Cited by 145 · see citing works
Kopczyńska, J., & Kowalczyk, M. (2024) · Frontiers in Immunology · doi:10.3389/fimmu.2024.1380476 · Cited by 142 · see citing works
Microbial transmission in the social microbiome and host health and disease
Sarkar, A., McInroy, C. J. A., Harty, S., Raulo, A., Ibata, N. G. O., Valles‐Colomer, M., Johnson, K. V. ‐., Brito, I., Henrich, J., Archie, E. A., et al. (2024) · Cell · doi:10.1016/j.cell.2023.12.014 · Cited by 130 · see citing works
Horrocks, V., King, O. G., Yip, A. Y. G., Marques, I. M., & McDonald, J. A. K. (2023) · Microbiology · doi:10.1099/mic.0.001377 · Cited by 104 · see citing works
A cross-systems primer for synthetic microbial communities
Mehlferber, E. C., Arnault, G., Joshi, B., Partida‐Martínez, L. P., Patras, K. A., Simonin, M., & Koskella, B. (2024) · Nature Microbiology · doi:10.1038/s41564-024-01827-2 · Cited by 92 · see citing works
How plants manage pathogen infection
Jian, Y., Gong, D., Wang, Z., Liu, L., He, J., Han, X., & Tsuda, K. (2023) · EMBO Reports · doi:10.1038/s44319-023-00023-3 · Cited by 88 · see citing works
Intrahost evolution of the gut microbiota
Barreto, H. C., & Gordo, I. (2023) · Nature Reviews Microbiology · doi:10.1038/s41579-023-00890-6 · Cited by 81 · see citing works
Čaušević, S., Dubey, M., Morales, M., Salazar, G., Sentchilo, V., Carraro, N., Ruscheweyh, H., Sunagawa, S., & van der Meer, J. R. (2024) · Nature Communications · doi:10.1038/s41467-024-46933-1 · Cited by 87 · see citing works
Antibiotic-perturbed microbiota and the role of probiotics
Szajewska, H., Scott, K. P., de Meij, T. G. J., Forslund, S. K., Knight, R. D., Koren, O., Little, P. S., Johnston, B. C., Łukasik, J., Suez, J., et al. (2024) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/s41575-024-01023-x · Cited by 76 · see citing works
Commensalism and pathogenesis of Candida albicans at the mucosal interface
Schille, T. B., Sprague, J. L., Naglik, J. R., Brunke, S., & Hube, B. (2025) · Nature Reviews Microbiology · doi:10.1038/s41579-025-01174-x · Cited by 77 · see citing works
Entila, F. D., Han, X., Mine, A., Schulze‐Lefert, P., & Tsuda, K. (2024) · Nature Communications · doi:10.1038/s41467-024-44724-2 · Cited by 68 · see citing works
Soil microbiome interventions for carbon sequestration and climate mitigation
Beattie, G. A., Edlund, A., Esiobu, N., Gilbert, J. A., Nicolaisen, M. H., Jansson, J. K., Jensen, P. R., Keiluweit, M., Lennon, J. T., Martiny, J. B. H., et al. (2024) · mSystems · doi:10.1128/msystems.01129-24 · Cited by 74 · see citing works
Colonization resistance: the role of gut microbiota in preventing Salmonella invasion and infection
Deng, L., & Wang, S. (2024) · Gut Microbes · doi:10.1080/19490976.2024.2424914 · Cited by 71 · see citing works
The microbiota: a crucial mediator in gut homeostasis and colonization resistance
Chen, Y., Xiao, L., Zhou, M., & Zhang, H. (2024) · Frontiers in Microbiology · doi:10.3389/fmicb.2024.1417864 · Cited by 69 · see citing works
Wang, Z., Kang, S., Wu, Z., Liu, X., Zhang, X., Wu, Y., Wen, Y., Zhou, X., Zhang, G., Wang, J., et al. (2025) · The ISME Journal · doi:10.1093/ismejo/wraf069 · Cited by 55 · see citing works
Non-antibiotics disrupt colonization resistance against enteropathogens
Grießhammer, A., de la Cuesta‐Zuluaga, J., Müller, P., Gekeler, C., Homolak, J., Chang, H., Schmitt, K., Planker, C., Schmidtchen, V., Gallage, S., et al. (2025) · Nature · doi:10.1038/s41586-025-09217-2 · Cited by 61 · see citing works
Angiogenesis, a key point in the association of gut microbiota and its metabolites with disease
Wang, Y., Bai, M., Peng, Q., Li, L., Tian, F., Guo, Y., & Jing, C. (2024) · European journal of medical research · doi:10.1186/s40001-024-02224-5 · Cited by 49 · see citing works
Deciphering the gastrointestinal carriage of Klebsiella pneumoniae
Bray, A. S., & Zafar, M. A. (2024) · Infection and Immunity · doi:10.1128/iai.00482-23 · Cited by 48 · see citing works
Loveikyte, R., Bourgonje, A. R., van Goor, H., Dijkstra, G. D. H., & Jong, A. E. V. D. M. (2023) · Redox Biology · doi:10.1016/j.redox.2023.102950 · Cited by 49 · see citing works
Pet cats may shape the antibiotic resistome of their owner’s gut and living environment
Yang, Y., Hu, X., Cai, S., Hu, N., Yuan, Y., Wu, Y., Wang, Y., Mi, J., & Liao, X. (2023) · Microbiome · doi:10.1186/s40168-023-01679-8 · Cited by 46 · see citing works
Fungicide-tolerant persister formation during cryptococcal pulmonary infection
Ke, W., Xie, Y., Chen, Y., Ding, H., Ye, L., Qiu, H., Li, H., Zhang, L., Chen, L., Tian, X., et al. (2024) · Cell Host & Microbe · doi:10.1016/j.chom.2023.12.012 · Cited by 45 · see citing works
Chang, K. C., Nagarajan, N., & Gan, Y. (2024) · mSphere · doi:10.1128/msphere.00781-23 · Cited by 48 · see citing works
Core Species Derived from Multispecies Interactions Facilitate the Immobilization of Cadmium
Xing, Y., Liu, S., Tan, S., Jiang, Y. W., Luo, X., Hao, X., Huang, Q., & Chen, W. (2023) · Environmental Science & Technology · doi:10.1021/acs.est.3c00486 · Cited by 43 · see citing works
Role of the gut microbiota in tumorigenesis and treatment
Liu, Q., Yang, Y., Pan, M., Yang, F., Yu, Y., & Qian, Z. (2024) · Theranostics · doi:10.7150/thno.91700 · Cited by 43 · see citing works
Human microbiome acquisition and transmission
Heidrich, V., Valles‐Colomer, M., & Segata, N. (2025) · Nature Reviews Microbiology · doi:10.1038/s41579-025-01166-x · Cited by 44 · see citing works
Lawal, H., Gaddafi, M. S., Jamiu, A. M., Edo, G. S., Fremah, O. G., El-yakub, A. U., Mahunu, G. K., Wang, K., Zhang, H., & Yang, Q. (2025) · Foods · doi:10.3390/foods14162782 · Cited by 43 · see citing works
Design of probiotic delivery systems for targeted release
Xu, C., Gantumur, M., Sun, J., Guo, J., Ma, J., Jiang, Z., Wang, W., Zhang, J., Ma, Y., Hou, J., et al. (2023) · Food Hydrocolloids · doi:10.1016/j.foodhyd.2023.109588 · Cited by 41 · see citing works
From trash to treasure: the role of bacterial extracellular vesicles in gut health and disease
Sun, D., Chen, P., Xi, Y., & Sheng, J. (2023) · Frontiers in Immunology · doi:10.3389/fimmu.2023.1274295 · Cited by 39 · see citing works
Macroencapsulated bacteria for in vivo sensing and therapeutics
Lyu, Y., Huang, H., Su, Y., Ying, B., Liu, W.-C., Dong, K., Du, N., Langer, R., Gu, Z., & Nan, K. (2024) · Matter · doi:10.1016/j.matt.2024.01.031 · Cited by 38 · see citing works
The soil-plant-human gut microbiome axis into perspective
Ma, H., Cornadó, D., & Raaijmakers, J. M. (2025) · Nature Communications · doi:10.1038/s41467-025-62989-z · Cited by 38 · see citing works
Metagenomic editing of commensal bacteria in vivo using CRISPR-associated transposases
Gelsinger, D. R., Ronda, C., Ma, J., Kar, O. B., Edwards, M., Huang, Y., Mavros, C. F., Sun, Y., Perdue, T., Vo, P. L. H., et al. (2025) · Science · doi:10.1126/science.adx7604 · Cited by 36 · see citing works
Kim, D. M., Liu, J., Whitmore, M. A., Tobin, I., Zhao, Z., & Zhang, G. (2024) · Journal of Animal Science and Biotechnology/Journal of animal science and biotechnology · doi:10.1186/s40104-024-00995-9 · Cited by 37 · see citing works
Host–pathobiont interactions in Crohn’s disease
Caruso, R., Lo, B. C., Chen, G., & Núñez, G. (2024) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/s41575-024-00997-y · Cited by 35 · see citing works
Self-citationBioinspired approaches to encapsulate and deliver bacterial live biotherapeutic products
Brittain, N. Y., & Finbloom, J. A. (2025) · Advanced Drug Delivery Reviews · doi:10.1016/j.addr.2025.115663 · Cited by 32 · see citing works
The Microbiota and Evolution of Obesity
Saad, M. J. A., & Santos, A. (2024) · Endocrine Reviews · doi:10.1210/endrev/bnae033 · Cited by 31 · see citing works
The gut microbiota links disease to human genome evolution
Quan, Y., Zhang, K., & Zhang, H. (2023) · Trends in Genetics · doi:10.1016/j.tig.2023.02.006 · Cited by 32 · see citing works
Merrick, B., Sergaki, C., Edwards, L. A., Moyes, D. L., Kertanegara, M., Prossomariti, D., Shawcross, D. L., & Goldenberg, S. D. (2023) · Infectious Disease Reports · doi:10.3390/idr15030025 · Cited by 30 · see citing works
Pötgens, S. A., Lecop, S., Havelange, V., Li, F., Neyrinck, A. M., Neveux, N., Maertens, J. A., Walter, J., Schoemans, H. M., Delzenne, N. M., et al. (2023) · Clinical Nutrition · doi:10.1016/j.clnu.2023.09.021 · Cited by 31 · see citing works
Applying ecological principles to microbiome engineering
Henry, L. P., & Bergelson, J. M. (2025) · Nature Microbiology · doi:10.1038/s41564-025-02076-7 · Cited by 31 · see citing works
A multicellular self-organized probiotic platform for oral delivery enhances intestinal colonization
Liu, H., Chen, Z., Lin, Q., Chen, Y., Hong, L., Zhong, J., Cai, Z., Wang, Z., & Cui, W. (2025) · Nature Communications · doi:10.1038/s41467-025-62349-x · Cited by 32 · see citing works
Cherrak, Y., Salazar, M. A., Yilmaz, K., Kreuzer, M., & Hardt, W. (2024) · PLoS Biology · doi:10.1371/journal.pbio.3002616 · Cited by 27 · see citing works
RETRACTED: Beyond correlation: Understanding the causal link between microbiome and plant health
Olanrewaju, O. S., Glick, B. R., & Babalola, O. O. (2024) · Heliyon · doi:10.1016/j.heliyon.2024.e40517 · Cited by 27 · see citing works
RetractedZong, E., Yang, J., Zhang, J., Wang, X., Zhang, S., Peng, Y., Lai, J., Sun, X., Zeng, S., Ao, L., et al. (2025) · Food Research International · doi:10.1016/j.foodres.2025.118097 · Cited by 29 · see citing works
Monosaccharides drive Salmonella gut colonization in a context-dependent or -independent manner
Schubert, C., Nguyen, B. D., Sichert, A., Näpflin, N. C., Sintsova, A., Feer, L., Näf, J., Daniel, B. B. J., Steiger, Y., von Mering, C., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-56890-y · Cited by 29 · see citing works
Mkilima, T. (2025) · Annals of the New York Academy of Sciences · doi:10.1111/nyas.15352 · Cited by 26 · see citing works
CRISPR–Cas therapies targeting bacteria
Benz, F., Beamud, B., Laurenceau, R., Maire, A., Duportet, X., Decrulle, A. L., & Bikard, D. (2025) · Nature Reviews Bioengineering · doi:10.1038/s44222-025-00311-8 · Cited by 26 · see citing works
Present and future of microbiome-targeting therapeutics
Lynch, L. E., Lahowetz, R., Maresso, C., Terwilliger, A. L., Pizzini, J. D., Hebib, V. M., Britton, R. A., Maresso, A. W., & Preidis, G. A. (2025) · Journal of Clinical Investigation · doi:10.1172/jci184323 · Cited by 27 · see citing works
Xu, Z., Wu, X. M., Luo, Y., Li, H., Zhou, Y. Q., Liu, Z. Q., & Li, Z. Y. (2024) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2024.137436 · Cited by 23 · see citing works
Zhang, J., Yang, J., Luo, J., Wu, W., Luo, H., Wei, W., Lyu, H., Wang, Y., Yi, H., Zhang, Y., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-58407-z · Cited by 23 · see citing works
Ling, Z., Ding, W., Liu, X., Zhang, J., Cheng, Y., Zhu, Z., Wu, L., Xu, X., Gao, Y., & Jiang, R. (2025) · Journal of Translational Medicine · doi:10.1186/s12967-025-07049-2 · Cited by 25 · see citing works
Clostridioides difficile pathogenesis and control
Chilton, C. H., Viprey, V. F., Normington, C., Moura, I. B., Buckley, A. M., Freeman, J., Davies, K., & Wilcox, M. H. (2025) · Nature Reviews Microbiology · doi:10.1038/s41579-025-01242-2 · Cited by 26 · see citing works
The gut microbiota and host immunity synergistically orchestrate colonization resistance
Li, N., & Guo, X. (2026) · Gut Microbes · doi:10.1080/19490976.2025.2611545 · Cited by 23 · see citing works
Jiang, C., Chen, Z., Liao, W., Zhang, R., Chen, G., Ma, L., & Yu, H. (2024) · Plants · doi:10.3390/plants13111531 · Cited by 22 · see citing works
Harnessing the human gut microbiota: an emerging frontier in combatting multidrug-resistant bacteria
Ding, W., Cheng, Y., Liu, X., Zhu, Z., Wu, L., Gao, J., Lei, W., Li, Y., Zhou, X., Wu, J., et al. (2025) · Frontiers in Immunology · doi:10.3389/fimmu.2025.1563450 · Cited by 25 · see citing works
Amino acid competition shapes Acinetobacter baumannii gut carriage
Ren, X., Clark, R. C., Bansah, D. A., Varner, E. N., Tiffany, C. R., Jaswal, K., Geary, J. H., Todd, O. A., Winkelman, J. D., Friedman, E. S., et al. (2025) · Cell Host & Microbe · doi:10.1016/j.chom.2025.07.003 · Cited by 21 · see citing works
Beyond Digestion: The Gut Microbiota as an Immune–Metabolic Interface in Disease Modulation
Mohammad, I., Ansari, M. R., Khan, M. S., Bari, M. N., Kamal, M. A., & Poyil, M. M. (2025) · Gastrointestinal Disorders · doi:10.3390/gidisord7040077 · Cited by 24 · see citing works
Wang, X., Cheng, Y., Huang, J., Xu, F., Jiang, J., Nalinratana, N., Jin, L., & Xue, Y. (2026) · Frontiers in Microbiology · doi:10.3389/fmicb.2025.1696524 · Cited by 21 · see citing works
Meng, J., Li, M., Wang, X., Li, S., Zhang, Y., Ni, H., Ma, H., Liu, R., Yan, J.-C., Li, X., et al. (2025) · Ecotoxicology and Environmental Safety · doi:10.1016/j.ecoenv.2025.117976 · Cited by 20 · see citing works
Recent advances in the application of microbiota transplantation in chickens
Zhao, H., Comer, L., Akram, M. Z., Corion, M., Li, Y., & Everaert, N. (2025) · Journal of Animal Science and Biotechnology/Journal of animal science and biotechnology · doi:10.1186/s40104-025-01233-6 · Cited by 20 · see citing works
Liu, S., Zhang, X., Wang, H., Kuzyakov, Y. V., Pan, J., Chen, F., Wang, F., Li, D., Tang, Y., & Ma, Z. (2025) · Soil Biology and Biochemistry · doi:10.1016/j.soilbio.2025.109915 · Cited by 21 · see citing works
Soil microbial diversity: A key factor in pathogen suppression and inoculant performance
Nishisaka, C. S., Quevedo, H. D., Ventura, J. P., Andreote, F. D., Mauchline, T. H., & Mendes, R. (2025) · Geoderma · doi:10.1016/j.geoderma.2025.117444 · Cited by 20 · see citing works
Lee, I., Jo, J.-W., Woo, H., Suk, K. T., Lee, S. S., & Kim, B. S. (2024) · Gut Microbes · doi:10.1080/19490976.2024.2341635 · Cited by 20 · see citing works
Microbes Saving Lives and Reducing Suffering
Timmis, K. N., Karahan, Z. C., Ramos, J. L., Koren, O., Pérez‐Cobas, A. E., Steward, K. F., de Lorenzo, V., Caselli, E., Douglas, M., Schwab, C., et al. (2025) · Microbial Biotechnology · doi:10.1111/1751-7915.70068 · Cited by 23 · see citing works
Deza, D. C., Alcedo, J., Lafuente, M., López, F. J., Pérez‐Aísa, Á., Pavoni, M., Tepeš, B., Jonaitis, L. V., Castro‐Fernández, M., Pabón‐Carrasco, M., et al. (2025) · The American Journal of Gastroenterology · doi:10.14309/ajg.0000000000003351 · Cited by 19 · see citing works
Idowu, P. A., Mbambalala, L., Akinmoladun, O. F., & Idowu, A. P. (2025) · Applied Microbiology · doi:10.3390/applmicrobiol5040149 · Cited by 19 · see citing works
Cherrak, Y., Salazar, M. A., Näpflin, N. C., Malfertheiner, L., Herzog, M. K.-M., Schubert, C., von Mering, C., & Hardt, W. (2024) · Nature Microbiology · doi:10.1038/s41564-024-01775-x · Cited by 18 · see citing works
Bacterial warfare is associated with virulence and antimicrobial resistance
Sharp, C., & Foster, K. R. (2025) · Nature Communications · doi:10.1038/s41467-025-64363-5 · Cited by 19 · see citing works
Sugimoto, T., Atobe, S., Kado, Y., Takahashi, A., Motoori, M., Sugimura, K., Miyata, H., Yano, M., Tanaka, K., Doki, Y., et al. (2023) · Journal of Medical Microbiology · doi:10.1099/jmm.0.001723 · Cited by 18 · see citing works
SUMOylation at the crossroads of gut health: insights into physiology and pathology
Ma, X., Li, M., Qi, G.-Q., Wei, L., & Zhang, D. (2024) · Cell Communication and Signaling · doi:10.1186/s12964-024-01786-5 · Cited by 18 · see citing works
Zhou, X., Xu, Q., Zhang, X., Wang, H., Bai, Y., Wu, Y., Liu, X., Wang, Z., Hu, J., Huang, M., et al. (2024) · mSystems · doi:10.1128/msystems.00246-24 · Cited by 18 · see citing works
Yuan, J., Yu, Y., Li, S., Zhang, X., Zhang, C., Li, R., Hu, J., Si, S., Zhang, C., Xiang, J., et al. (2024) · PLoS Pathogens · doi:10.1371/journal.ppat.1012321 · Cited by 17 · see citing works
Activating Biocake Communities Retards Jumps of Transmembrane Pressure in Membrane Bioreactors
Qi, J., Gao, T., Zhou, Q., Huang, S., Lin, J., Xu, R., Tang, C. Y., & Meng, F. (2024) · Environmental Science & Technology · doi:10.1021/acs.est.4c03038 · Cited by 17 · see citing works
Huang, Y., Tang, S., Liu, R., Yu, P., Liu, J., Xiao, T., Zhang, Y., Fan, M., Zhang, F. S., & Ni, B. (2025) · Cell Host & Microbe · doi:10.1016/j.chom.2025.10.002 · Cited by 18 · see citing works
Applying evolutionary theory to understand host–microbiome evolution
Week, B., Russell, S. L., Hinrich Schulenburg, Y., Bohannan, B. J. M., & Bruijning, M. (2025) · Nature Ecology & Evolution · doi:10.1038/s41559-025-02846-w · Cited by 16 · see citing works
Moreira-Souza, A. C. A., Nanini, H. F., Rangel, T. P., da Silva, S. R. B., Pêgo, B., Ribeiro, B. E., Cascabulho, C. M., Thompson, F. L., Leal, C. V., Santana, P. T., et al. (2023) · Biomedicines · doi:10.3390/biomedicines11020555 · Cited by 16 · see citing works
Winter, M. G., Hughes, E. R., Muramatsu, M. K., Jimenez, A. G., Chanin, R. B., Spiga, L., Gillis, C. C., McClelland, M., Andrews‐Polymenis, H. L., & Winter, S. (2023) · mBio · doi:10.1128/mbio.00921-23 · Cited by 15 · see citing works
Valiei, A., Dickson, A. M., Aminian-Dehkordi, J., & Mofrad, M. R. K. (2024) · BMC Microbiology · doi:10.1186/s12866-024-03566-0 · Cited by 14 · see citing works
Adaptation to skin mycobiota promotes antibiotic tolerance in Staphylococcus aureus
Kowalski, C. H., Nguyen, U. T., Lawhorn, S., Smith, T. J., Corrigan, R. M., Suh, W. S., Kalan, L., & Barber, M. F. (2024) · Current Biology · doi:10.1016/j.cub.2025.03.055 · Cited by 15 · see citing works
Takada, K. (2025) · Frontiers in Immunology · doi:10.3389/fimmu.2025.1547303 · Cited by 16 · see citing works
Gene-level analysis of core carbohydrate metabolism across the Enterobacteriaceae pan-genome
Näpflin, N. C., Schubert, C., Malfertheiner, L., Hardt, W., & von Mering, C. (2025) · Communications Biology · doi:10.1038/s42003-025-08640-5 · Cited by 15 · see citing works
Interkingdom sensing of fungal tyrosol promotes bacterial antifungal T6SS activity in the murine gut
Zhu, L., Zuo, Y., Cui, R., Fu, P., Liu, Y., Wang, Z., He, X., Yu, D., Wei, Z., Li, S., et al. (2025) · Nature Microbiology · doi:10.1038/s41564-025-02208-z · Cited by 16 · see citing works
Next-generation probiotics: an outlook into current applications and future developments
Kern, L., Tofield, A., Frame, J., & Elinav, E. (2026) · Nature Reviews Microbiology · doi:10.1038/s41579-026-01311-0 · Cited by 20 · see citing works
Vogt, S. L., Serapio-Palacios, A., Woodward, S. E., Santos, A. S., de Vries, S. P. W., Daigneault, M. C., Brandmeier, L. V., Grant, A. J., Maskell, D. J., Allen‐Vercoe, E., et al. (2023) · Gut Microbes · doi:10.1080/19490976.2023.2190303 · Cited by 15 · see citing works
Metabolism of l-arabinose converges with virulence regulation to promote enteric pathogen fitness
Cottam, C., White, R. T., Beck, L. C., Stewart, C. J., Beatson, S., Lowe, E. C., Grinter, R., & Connolly, J. P. R. (2024) · Nature Communications · doi:10.1038/s41467-024-48933-7 · Cited by 16 · see citing works
Zhou, Z., Lv, Y., Zuo, A., Zhu, X., Xu, Y., Zuo, L., Xu, H., Liu, S., Zhang, Y., Weng, S., et al. (2025) · hLife · doi:10.1016/j.hlife.2025.05.008 · Cited by 15 · see citing works
Targeting Intratumoral Bacteria for Cancer Treatment
Shi, J., Liang, J., Li, Y., Zhang, Z., Sun, J. X., He, Z., Luo, C., Qu, X., Che, X., & Zhang, S. (2025) · Small · doi:10.1002/smll.202505651 · Cited by 14 · see citing works
Synthetic microbial consortia based on quorum-sensing for disease therapy
Guo, Y., Gao, M., Jiang, L., Huang, H., Kang, G., & Yu, H. (2025) · Bioresources and Bioprocessing · doi:10.1186/s40643-025-00962-w · Cited by 14 · see citing works
Cheung, M. K., Ng, R. W. Y., Lai, C. K. C., Zhu, C., Au, E. T. K., Yau, J. W., Li, C., Wong, H. C., Wong, B. C. K., Kwok, K. O., et al. (2023) · Journal of Travel Medicine · doi:10.1093/jtm/taad027 · Cited by 14 · see citing works
Hou, J., Yang, M., Wu, X., Chen, Q., Lu, Y., Zhang, J., & Lin, D. (2023) · Eco-Environment & Health · doi:10.1016/j.eehl.2023.11.001 · Cited by 14 · see citing works
Xu, L., Wu, Y., Yang, X., Pang, X., Wu, Y., Li, X., Liu, X., Zhao, Y., Yu, L., Wang, P., et al. (2024) · Gut Microbes · doi:10.1080/19490976.2024.2359665 · Cited by 14 · see citing works
Chemical genetic approaches to dissect microbiota mechanisms in health and disease
Yang, X., & Hang, H. C. (2024) · Science · doi:10.1126/science.ado8548 · Cited by 15 · see citing works
Luo, Y., Lan, C., Ren, W., Wu, A., Yu, B., He, J., & Chen, D. (2025) · Journal of Advanced Research · doi:10.1016/j.jare.2025.04.016 · Cited by 14 · see citing works
- Authors
- Caballero-Flores, G., Pickard, J. M., & Núñez, G.
- Affiliations
- University of Michigan (US)
- Corresponding author
- Caballero-Flores, Gustavo
- Núñez, Gabriel
- Venue
- Nature Reviews Microbiology
- Published
- 2022-12-20
- Volume
- 21
- Issue
- 6
- Pages
- 347-360
- ISSN
- 1740-1526 (ISSN-L)
- 1740-1534
- PMC
- PMC10249723
- OpenAlex
- W4312065785
- Cited by
- 474
- References
- 196
- Citations by year
- 2026: 160 · 2025: 182 · 2024: 100 · 2023: 32
- FWCI
- 8.16
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- Locations
- Nature Reviews Microbiology (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Institutes of Health (K99-R00)
- National Institute of Allergy and Infectious Diseases (K99AI159620, R00AI159620)
- National Institute of Diabetes and Digestive and Kidney Diseases (R01DK095782)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Health Sciences › Medicine › Infectious Diseases › Clostridium difficile and Clostridium perfringens research
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Plant-Microbe Interactions and Immunity
- Keywords
- gut microbiota, colonization resistance, pathogen colonization, dysbiosis, pathobionts, microbial competition, host immune response, host-microbe interactions, microbiota-based therapy
- MeSH terms
- Immunity, Microbiota
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