The DOI matches its Crossref record; 147 of the 147 references it cites were found in a registry or an index.
The intestinal microbiota: Antibiotics, colonization resistance, and enteric pathogens
Open accessAbstract
Summary: The human gastrointestinal tract hosts a diverse network of microorganisms, collectively known as the microbiota that plays an important role in health and disease. For instance, the intestinal microbiota can prevent invading microbes from colonizing the gastrointestinal tract, a phenomenon known as colonization resistance. Perturbations to the microbiota, such as antibiotic administration, can alter microbial composition and result in the loss of colonization resistance. Consequently, the host may be rendered susceptible to colonization by a pathogen. This is a particularly relevant concern in the hospital setting, where antibiotic use and antibiotic‐resistant pathogen exposure are more frequent. Many nosocomial infections arise from gastrointestinal colonization. Due to their resistance to antibiotics, treatment is often very challenging. However, recent studies have demonstrated that manipulating the commensal microbiota can prevent and treat various infections in the intestine. In this review, we discuss the members of the microbiota, as well as the mechanisms, that govern colonization resistance against specific pathogens. We also review the effects of antibiotics on the microbiota, as well as the unique epidemiology of immunocompromised patients that renders them a particularly high‐risk population to intestinal nosocomial infections.
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“Antibiotic treatments, although eliminating both disease- and health-associated bacteria as a side effect, reduce colonization resistance, thereby favoring engraftment. 75,142”
From Key determinants of success in fecal microbiota transplantation: From microbiome to clinic (2023) · cites this paper as [142]
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“Nutrient availability significantly impacts the diversity and abundance of the micro-organisms that colonize the intestine [58–63].”
From Role of the gut microbiota in nutrient competition and protection against intestinal pathogen colonization (2023) · cites this paper as [58]
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Cites
Structure, function and diversity of the healthy human microbiome
The Human Microbiome Project Consortium (2012) · Nature · doi:10.1038/nature11234 · Cited by 11,726
A human gut microbial gene catalogue established by metagenomic sequencing
MetaHIT Consortium, Qin, J., Li, R., Raes, J., Arumugam, M., Burgdorf, K. S., Manichanh, C., Nielsen, T., Pons, N., Levenez, F., et al. (2010) · Nature · doi:10.1038/nature08821 · Cited by 11,624
Diet rapidly and reproducibly alters the human gut microbiome
David, L. A., Maurice, C. F., Carmody, R. N., Gootenberg, D. B., Button, J. E., Wolfe, B. E., Ling, A. V., Devlin, A. S., Varma, Y., Fischbach, M. A., et al. (2014) · Nature · doi:10.1038/nature12820 · Cited by 10,100
Changes of Intestinal Functions in Liver Cirrhosis
Fukui, H., & Wiest, R. (2016) · Inflammatory Intestinal Diseases · doi:10.1159/000444436 · Cited by 6,820
Antimicrobial peptides: pore formers or metabolic inhibitors in bacteria?
Brogden, K. A. (2005) · Nature Reviews Microbiology · doi:10.1038/nrmicro1098 · Cited by 5,829
Diversity, stability and resilience of the human gut microbiota
Lozupone, C. A., Stombaugh, J. I., Gordon, J. I., Jansson, J. K., & Knight, R. (2012) · Nature · doi:10.1038/nature11550 · Cited by 5,533
The Microbial Metabolites, Short-Chain Fatty Acids, Regulate Colonic T reg Cell Homeostasis
Smith, P. M., Howitt, M. R., Panikov, N., Michaud, M., Gallini, C. A., Bohlooly-Y, M., Glickman, J. N., & Garrett, W. S. (2013) · Science · doi:10.1126/science.1241165 · Cited by 5,413
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
Recognition of Commensal Microflora by Toll-Like Receptors Is Required for Intestinal Homeostasis
Rakoff-Nahoum, S., Paglino, J., Eslami-Varzaneh, F., Edberg, S., & Medzhitov, R. (2004) · Cell · doi:10.1016/j.cell.2004.07.002 · Cited by 4,251
Gut microbiota in health and disease
Sekirov, I., Russell, S. L., Antunes, L. C. M., & Finlay, B. B. (2010) · Physiological Reviews · doi:10.1152/physrev.00045.2009 · Cited by 4,182
Flagged first, then by citations
Research works printed but not linked: 2
- Gilbert DN, 2013, The Sanford Guide to Antimicrobial Therapy 2013: 43rd edition, 71
- Mandell GL, 2009, Mandell, Douglas, and Bennett's Principles and Practice of Infectious Diseases: Seventh edition, 309
Cited by
Sorted by citations
Items 701–761 of 761
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Zhou, A., Tang, B., Xie, Y., Li, S., Xiao, X., Wu, L., Tu, D., Wang, S., Feng, Y., Feng, X., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26647395
Ma, L., Song, Y., Lyu, W., Chen, Q., Xiao, X., Jin, Y., Yang, H., Wang, W., & Xiao, Y. (2024) · Figshare · doi:10.6084/m9.figshare.26637600
Kim, J.-A., Jang, B.-R., Kim, Y.-R., Jung, Y.-C., Kim, K.-S., & Lee, K.-H. (2021) · Figshare · doi:10.6084/m9.figshare.15026565
Li, X., Song, J., Shi, X., Huang, M., Liu, L., Yi, G., Yang, N., Xu, G., & Zheng, J. (2022) · Figshare · doi:10.6084/m9.figshare.21564306
Zhou, A., Tang, B., Xie, Y., Li, S., Xiao, X., Wu, L., Tu, D., Wang, S., Feng, Y., Feng, X., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26647410
Wang, J., Teng, M., Feng, R., Su, X., Xu, K., Wang, J., Wang, G., Zhang, Y., & Xu, P. (2024) · Figshare · doi:10.6084/m9.figshare.26692777
Zhou, A., Tang, B., Xie, Y., Li, S., Xiao, X., Wu, L., Tu, D., Wang, S., Feng, Y., Feng, X., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26647392
Bonillo-Lopez, L., Obregón-Gutierrez, P., Huerta, E., Correa‐Fiz, F., Sibila, M., & Aragón, V. (2024) · Figshare · doi:10.6084/m9.figshare.26645065
Zhou, A., Tang, B., Xie, Y., Li, S., Xiao, X., Wu, L., Tu, D., Wang, S., Feng, Y., Feng, X., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26647416
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Wang, J., Teng, M., Feng, R., Su, X., Xu, K., Wang, J., Wang, G., Zhang, Y., & Xu, P. (2024) · Figshare · doi:10.6084/m9.figshare.26692780
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BindingDB Entry 50011353: Ultrapotent Inhibitor of
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Metadata
- Authors
- Kim, S., Covington, A., & Pamer, E. G.
- Affiliations
- Memorial Sloan Kettering Cancer Center (US)
- Corresponding author
- Pamer, Eric G.
- Venue
- Immunological Reviews
- Publisher
- Wiley
- Published
- 2017-08-30
- Volume
- 279
- Issue
- 1
- Pages
- 90-105
- ISSN
- 0105-2896 (ISSN-L)
- 1600-065X
- PMC
- PMC6026851
- OpenAlex
- W2753747201
- Cited by
- 741
- References
- 147
- Citations by year
- 2026: 49 · 2025: 67 · 2024: 112 · 2023: 95 · 2022: 136 · 2021: 117 · 2020: 69 · 2019: 68 · 2018: 27 · 2017: 1
- FWCI
- 4.22
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Immunological Reviews (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Cancer Institute (P01CA023766, P30CA008748)
- National Institute of General Medical Sciences (T32GM007739)
- National Institute of Allergy and Infectious Diseases (R01AI095706, U01AI124275, R01AI042135)
- 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
- Health Sciences › Medicine › Microbiology (medical) › Antibiotic Resistance in Bacteria
- Keywords
- gut microbiota, colonization resistance, antibiotics, enteric pathogens, nosocomial infections, antibiotic resistance, immunocompromised patients, commensal microbiota, intestinal colonization
- MeSH terms
- Gastrointestinal Microbiome, Animals, Anti-Bacterial Agents, Bacterial Infections, Cross Infection, Drug Resistance, Humans, Immunocompromised Host, Host-Pathogen Interactions, Dysbiosis
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