Colonization resistance

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Colonization, suprainfection and superinfection: major microbiologic and clinical problems.

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Changes in the oropharyngeal and colon microflora in relation to antimicrobial concentrations in saliva and faeces.

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The gut microbiota of insects – diversity in structure and function

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Necrotizing Enterocolitis

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The population genetics of commensal Escherichia coli

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Microbiota Transfer Therapy Alters Gut Ecosystem and Improves Gastrointestinal and Autism Symptoms: An Open-Label Study

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Microbes in Gastrointestinal Health and Disease

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The oral microbiome in health and disease

Wade, W. G. (2013) · Pharmacological Research · doi:10.1016/j.phrs.2012.11.006 · Cited by 1,347

Variations of Bacterial Populations in Human Feces Measured by Fluorescent In Situ Hybridization with Group-Specific 16S rRNA-Targeted Oligonucleotide Probes

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Intestinal Domination and the Risk of Bacteremia in Patients Undergoing Allogeneic Hematopoietic Stem Cell Transplantation

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Antibiotic-induced shifts in the mouse gut microbiome and metabolome increase susceptibility to Clostridium difficile infection

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

Decreased Diversity of the Fecal Microbiome in Recurrent Clostridium difficile–Associated Diarrhea

Chang, J. Y., Antonopoulos, D. A., Kalra, A., Tonelli, A., Khalife, W. T., Schmidt, T. M., & Young, V. B. (2008) · The Journal of Infectious Diseases · doi:10.1086/525047 · Cited by 1,010

Vancomycin-resistant Enterococcus domination of intestinal microbiota is enabled by antibiotic treatment in mice and precedes bloodstream invasion in humans

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

The effects of intestinal tract bacterial diversity on mortality following allogeneic hematopoietic stem cell transplantation

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Effect of antimicrobial agents on the ecological balance of human microflora

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The oral microbiome: Role of key organisms and complex networks in oral health and disease

Sedghi, L., DiMassa, V., Harrington, A., Lynch, S. V., & Kapila, Y. L. (2021) · Periodontology 2000 · doi:10.1111/prd.12393 · Cited by 755

Multiple-Drug Resistant Enterococci: The Nature of the Problem and an Agenda for the Future

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Effect of dietary components on the gut microbiota of aquatic animals. A never‐ending story?

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Effect of Antibiotic Therapy on the Density of Vancomycin-Resistant Enterococci in the Stool of Colonized Patients

Donskey, C. J., Chowdhry, T. K., Hecker, M. T., Hoyen, C. K., Hanrahan, J., Hujer, A. M., Hutton‐Thomas, R., Whalen, C. C., Bonomo, R. A., & Rice, L. B. (2000) · New England Journal of Medicine · doi:10.1056/nejm200012283432604 · Cited by 691

Profound alterations of intestinal microbiota following a single dose of clindamycin results in sustained susceptibility to Clostridium difficile-induced colitis

Buffie, C. G., Jarchum, I., Equinda, M., Lipuma, L., Gobourne, A., Viale, A., Ubeda, C., Xavier, J., & Pamer, E. G. (2012) · Infection and Immunity · doi:10.1128/iai.05496-11 · Cited by 596

Antimicrobial Properties of Chitosan and Chitosan Derivatives in the Treatment of Enteric Infections

Yan, D., Li, Y., Liu, Y., Li, N., Zhang, X., & Yan, C. (2021) · Molecules · doi:10.3390/molecules26237136 · Cited by 656

Antimicrobial‐Associated Risk Factors for Clostridium difficile Infection

Owens, Jr., Donskey, C. J., Gaynes, R. P., Loo, V. G., & Muto, C. A. (2008) · Clinical Infectious Diseases · doi:10.1086/521859 · Cited by 603

Gut Microbiota and Colonization Resistance against Bacterial Enteric Infection

Ducarmon, Q. R., Zwittink, R. D., Hornung, B. V. H., van Schaik, W., Young, V. B., & Kuijper, E. J. (2019) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00007-19 · Cited by 566

Role of the Commensal Microbiota in Normal and Pathogenic Host Immune Responses

Littman, D. R., & Pamer, E. G. (2011) · Cell Host & Microbe · doi:10.1016/j.chom.2011.10.004 · Cited by 568

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 564

The role of microbiota in infectious disease

Stecher, B., & Hardt, W. (2008) · Trends in Microbiology · doi:10.1016/j.tim.2007.12.008 · Cited by 547

From Structure to Function: the Ecology of Host-Associated Microbial Communities

Robinson, C. J., Bohannan, B. J. M., & Young, V. B. (2010) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00014-10 · Cited by 473

Like Will to Like: Abundances of Closely Related Species Can Predict Susceptibility to Intestinal Colonization by Pathogenic and Commensal Bacteria

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 427

Probiotics: Considerations for Human Health

Sanders, M. E. (2003) · Nutrition Reviews · doi:10.1301/nr.2003.marr.91-99 · Cited by 426

The Role of the Intestinal Tract as a Reservoir and Source for Transmission of Nosocomial Pathogens

Donskey, C. J. (2004) · Clinical Infectious Diseases · doi:10.1086/422002 · Cited by 425

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 431

Intestinal microflora of Estonian and Swedish infants

Sepp, E., Julge, K., Vasar, M., Naaber, P., Björkstén, B., & Mikelsaar, M. (1997) · Acta Paediatrica · doi:10.1111/j.1651-2227.1997.tb15178.x · Cited by 416

Effect of broad- and narrow-spectrum antimicrobials on Clostridium difficile and microbial diversity in a model of the distal colon

Rea, M. C., Dobson, A., O'Sullivan, O., Crispie, F., Fouhy, F., Cotter, P. D., Shanahan, F., Kiely, B., Hill, C., & Ross, R. P. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1001224107 · Cited by 377

Application of Novel PCR-Based Methods for Detection, Quantitation, and Phylogenetic Characterization of Sutterella Species in Intestinal Biopsy Samples from Children with Autism and Gastrointestinal Disturbances

Williams, B. L., Hornig, M., Parekh, T., & Lipkin, W. I. (2012) · mBio · doi:10.1128/mbio.00261-11 · Cited by 378

Antibiotics, microbiota, and immune defense

Úbeda, C., & Pamer, E. G. (2012) · Trends in Immunology · doi:10.1016/j.it.2012.05.003 · Cited by 369

Antibiotic Treatment of Clostridium difficile Carrier Mice Triggers a Supershedder State, Spore-Mediated Transmission, and Severe Disease in Immunocompromised Hosts

Lawley, T. D., Clare, S., Walker, A. W., Goulding, D., Stabler, R. A., Croucher, N., Mastroeni, P., Scott, P., Raisen, C., Mottram, L., et al. (2009) · Infection and Immunity · doi:10.1128/iai.00558-09 · Cited by 349

The Microbiota Mediates Pathogen Clearance from the Gut Lumen after Non-Typhoidal Salmonella Diarrhea

Endt, K., Stecher, B., Chaffron, S., Slack, E. M. C., Tchitchek, N., Benecke, A., Maele, L. V., Sirard, J., Müller, A. J., Heikenwälder, M. F., et al. (2010) · PLoS Pathogens · doi:10.1371/journal.ppat.1001097 · Cited by 352

Fecal Microbiota Composition and Frailty

van Tongeren, S. P., Slaets, J. P. J., Harmsen, H. J. M., & Welling, G. W. (2005) · Applied and Environmental Microbiology · doi:10.1128/aem.71.10.6438-6442.2005 · Cited by 333

Healthcare-associated infections in adult intensive care unit patients: Changes in epidemiology, diagnosis, prevention and contributions of new technologies

Blot, S. I., Ruppé, É., Harbarth, S., Asehnoune, K., Poulakou, G., Luyt, C. E., Rello, J., Klompas, M., Depuydt, P. O., Eckmann, C., et al. (2022) · Intensive and Critical Care Nursing · doi:10.1016/j.iccn.2022.103227 · Cited by 389

Antibiotic Usage in Animals

van den Bogaard, A. E. J. M., & Stobberingh, E. E. (1999) · Drugs · doi:10.2165/00003495-199958040-00002 · Cited by 319

Familial transmission rather than defective innate immunity shapes the distinct intestinal microbiota of TLR-deficient mice

Ubeda, C., Lipuma, L., Gobourne, A., Viale, A., Leiner, I., Equinda, M., Khanin, R., & Pamer, E. G. (2012) · Journal of Experimental Medicine · doi:10.1084/jem.20120504 · Cited by 310

A single-cell nanocoating of probiotics for enhanced amelioration of antibiotic-associated diarrhea

Pan, J., Gong, G., Wang, Q., Shang, J., He, Y., Catania, C., Birnbaum, D., Li, Y., Jia, Z., Zhang, Y., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-29672-z · Cited by 323

Host Transmission of Salmonella enterica Serovar Typhimurium Is Controlled by Virulence Factors and Indigenous Intestinal Microbiota

Lawley, T. D., Bouley, D. M., Hoy-Schulz, Y. E., Gerke, C., Relman, D. A., & Monack, D. M. (2007) · Infection and Immunity · doi:10.1128/iai.01189-07 · Cited by 303

Interactions Between the Gastrointestinal Microbiome and Clostridium difficile

Theriot, C. M., & Young, V. B. (2015) · Annual Review of Microbiology · doi:10.1146/annurev-micro-091014-104115 · Cited by 320

Suppression of Clostridium difficile in the Gastrointestinal Tracts of Germfree Mice Inoculated with a Murine Isolate from the Family Lachnospiraceae

Reeves, A. E., Koenigsknecht, M. J., Bergin, I. L., & Young, V. B. (2012) · Infection and Immunity · doi:10.1128/iai.00647-12 · Cited by 292

Antibiotic-Induced Alterations of the Murine Gut Microbiota and Subsequent Effects on Colonization Resistance against Clostridium difficile

Schubert, A. M., Sinani, H., & Schloss, P. D. (2015) · mBio · doi:10.1128/mbio.00974-15 · Cited by 269

Antimicrobial resistance in the next 30 years, humankind, bugs and drugs: a visionary approach

Bassetti, M., Poulakou, G., Ruppé, É., Bouza, E., van Hal, S. J., & Brink, A. J. (2017) · Intensive Care Medicine · doi:10.1007/s00134-017-4878-x · Cited by 284

Probiotic Bifidobacteria Protect Mice from Lethal Infection with Shiga Toxin-Producing Escherichia coli O157:H7

Asahara, T., Shimizu, K., Nomoto, K., Hamabata, T., Ozawa, A., & Takeda, Y. (2004) · Infection and Immunity · doi:10.1128/iai.72.4.2240-2247.2004 · Cited by 277

Clostridium difficile and the microbiota

Seekatz, A. M., & Young, V. B. (2014) · Journal of Clinical Investigation · doi:10.1172/jci72336 · Cited by 255

Durable Alteration of the Colonic Microbiota by the Administration of Donor Fecal Flora

Grehan, M., Borody, T. J., Leis, S., Campbell, J., Mitchell, H. M., & Wettstein, A. R. (2010) · Journal of Clinical Gastroenterology · doi:10.1097/mcg.0b013e3181e5d06b · Cited by 251

Microbial etiology of periodontitis

Nishihara, T., & Koseki, T. (2004) · Periodontology 2000 · doi:10.1111/j.1600-0757.2004.03671.x · Cited by 248

Oral Bacteria and Intestinal Dysbiosis in Colorectal Cancer

Koliarakis, I., Messaritakis, I., Νikolouzakis, Τ. Κ., Hamilos, G., Souglakos, J., & Tsiaoussis, J. (2019) · International Journal of Molecular Sciences · doi:10.3390/ijms20174146 · Cited by 255

Enterococci and Their Interactions with the Intestinal Microbiome

Dubin, K. A., & Pamer, E. G. (2017) · Microbiology Spectrum · doi:10.1128/microbiolspec.bad-0014-2016 · Cited by 259

The Roles of Inflammation, Nutrient Availability and the Commensal Microbiota in Enteric Pathogen Infection

Stecher, B. (2015) · Microbiology Spectrum · doi:10.1128/microbiolspec.mbp-0008-2014 · Cited by 250

Probiotics and prebiotics: A brief overview

Chow, J. (2002) · Journal of Renal Nutrition · doi:10.1053/jren.2002.31759 · Cited by 236

The Early Settlers: Intestinal Microbiology in Early Life

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Selective decontamination of the digestive tract: 13 years on, what it is and what it is not

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Friend Turned Foe: Evolution of Enterococcal Virulence and Antibiotic Resistance

Tyne, D. V., & Gilmore, M. S. (2014) · Annual Review of Microbiology · doi:10.1146/annurev-micro-091213-113003 · Cited by 223

Altered gut flora are associated with septic complications and death in critically ill patients with systemic inflammatory response syndrome

Shimizu, K., Ogura, H., Hamasaki, T., Goto, M., Tasaki, O., Asahara, T., Nomoto, K., Morotomi, M., Matsushima, A., Kuwagata, Y., et al. (2011) · Digestive Diseases and Sciences · doi:10.1007/s10620-010-1418-8 · Cited by 213

Effect of Fermented Feed on the Microbial Population of the Gastrointestinal Tracts of Pigs

van Winsen, R. L., Urlings, H. A. P., Lipman, L. J. A., Snijders, J. M. A., Keuzenkamp, D., Verheijden, J. H. M., & Knapen, F. V. (2001) · Applied and Environmental Microbiology · doi:10.1128/aem.67.7.3071-3076.2001 · Cited by 212

The intestinal microbiota in allogeneic hematopoietic cell transplant and graft-versus-host disease

Staffas, A., da Silva, M. B., & van den Brink, M. R. M. (2016) · Blood · doi:10.1182/blood-2016-09-691394 · Cited by 215

Antibiotic-resistant enterococci: the mechanisms and dynamics of drug introduction and resistance

Shepard, B. D., & Gilmore, M. S. (2002) · Microbes and Infection · doi:10.1016/s1286-4579(01)01530-1 · Cited by 202

Probiotics and gastrointestinal diseases

Sullivan, Å., & Nord, C. E. (2004) · Journal of Internal Medicine · doi:10.1111/j.1365-2796.2004.01410.x · Cited by 202

Effectiveness and Cost of Selective Decontamination of the Digestive Tract in Critically Ill Intubated Patients: A Randomized, Double-blind, Placebo-controlled, Multicenter Trial

García, M. S., Galache, J. A. C., DIAZ, J. L., Cerdá, E., BLASCO, J. R., AGUINAGA, M. A. G., Reiz, A. N., MARÍN, S. R., Cañaveral, J. J. O., & del CASTILLO, J. A. S. (1998) · American Journal of Respiratory and Critical Care Medicine · doi:10.1164/ajrccm.158.3.9712079 · Cited by 199

Antimicrobials: a global alliance for optimizing their rational use in intra-abdominal infections (AGORA)

Sartelli, M., Weber, D., Ruppé, É., Bassetti, M., Wright, B. J., Ansaloni, L., Catena, F., Coccolini, F., Abu‐Zidan, F. M., Coimbra, R. S. M., et al. (2016) · World Journal of Emergency Surgery · doi:10.1186/s13017-016-0089-y · Cited by 203

Metabolism of Bile Salts in Mice Influences Spore Germination in Clostridium difficile

Giel, J. L., Sorg, J. A., Sonenshein, A. L., & Zhu, J. (2010) · PLoS ONE · doi:10.1371/journal.pone.0008740 · Cited by 202

Gut microbiota and probiotics in chronic liver diseases

Cesaro, C., Tiso, A., Del Prete, A., Cariello, R., Tuccillo, C., Cotticelli, G., del Vecchio Blanco, C., & Loguercio, C. (2011) · Digestive and Liver Disease · doi:10.1016/j.dld.2010.10.015 · Cited by 182

High Rate of False‐Negative Results of the Rectal Swab Culture Method in Detection of Gastrointestinal Colonization with Vancomycin‐Resistant Enterococci

D’Agata, E. M. C., Gautam, S., Green, W. K., & Tang, Y. (2002) · Clinical Infectious Diseases · doi:10.1086/338234 · Cited by 179

Intestinal microbiology in early life: specific prebiotics can have similar functionalities as human-milk oligosaccharides

Oozeer, R., van Limpt, K., Ludwig, T., Amor, K. B., Martín, R., Wind, R. D., Boehm, G., & Knol, J. (2013) · American Journal of Clinical Nutrition · doi:10.3945/ajcn.112.038893 · Cited by 183

A human stool-derived Bilophila wadsworthia strain caused systemic inflammation in specific-pathogen-free mice

Zhou, F., Long, W., Hao, B., Ding, D., Ma, X., Zhao, L., & Pang, X. (2017) · Gut Pathogens · doi:10.1186/s13099-017-0208-7 · Cited by 178

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 181

Characteristics of Polyclonal Endemicity of Pseudomonas aeruginosa Colonization in Intensive Care Units: Implications for Infection Control

Bonten, M. J. M., Bergmans, D. C. J. J., Speijer, H., & Stobberingh, E. E. (1999) · American Journal of Respiratory and Critical Care Medicine · doi:10.1164/ajrccm.160.4.9809031 · Cited by 173

The Gut Microbiome as a Reservoir for Antimicrobial Resistance

Anthony, W., Burnham, C. D., Dantas, G. A., & Kwon, J. H. (2020) · The Journal of Infectious Diseases · doi:10.1093/infdis/jiaa497 · Cited by 177

Oxytetracycline Treatment Reduces Bacterial Diversity of Intestinal Microbiota of Atlantic Salmon

Navarrete, P., Mardones, P., Opazo, R., Espejo, R. T., & Romero, J. (2008) · Journal of Aquatic Animal Health · doi:10.1577/h07-043.1 · Cited by 169

Veterinary drug residues in meat: Concerns and rapid methods for detection

Reig, M., & Toldrá, F. (2007) · Meat Science · doi:10.1016/j.meatsci.2007.07.029 · Cited by 169

Clostridioides difficile infection: history, epidemiology, risk factors, prevention, clinical manifestations, treatment, and future options

Bella, S. D., Sanson, G., Monticelli, J., Zerbato, V., Principe, L., Giuffrè, M., Pipitone, G., & Luzzati, R. (2024) · Clinical Microbiology Reviews · doi:10.1128/cmr.00135-23 · Cited by 202

Antibiotic Regimens and Intestinal Colonization with Antibiotic-Resistant Gram-Negative Bacilli

Donskey, C. J. (2006) · Clinical Infectious Diseases · doi:10.1086/504481 · Cited by 152

Impact of microbial derived secondary bile acids on colonization resistance against Clostridium difficile in the gastrointestinal tract

Winston, J. A., & Theriot, C. M. (2016) · Anaerobe · doi:10.1016/j.anaerobe.2016.05.003 · Cited by 155

Dietary fructo-oligosaccharides and lactulose inhibit intestinal colonisation but stimulate translocation of salmonella in rats

Bovee-Oudenhoven, I. M. J. (2003) · Gut · doi:10.1136/gut.52.11.1572 · Cited by 148

Gut bacteria in health and disease: a survey on the interface between intestinal microbiology and colorectal cancer

Boleij, A., & Tjalsma, H. (2012) · Biological reviews/Biological reviews of the Cambridge Philosophical Society · doi:10.1111/j.1469-185x.2012.00218.x · Cited by 153

Increased resistance of mice to Salmonella enterica serovar Typhimurium infection by synbiotic administration of Bifidobacteria and transgalactosylated oligosaccharides

Asahara, T., Nomoto, K., Shimizu, K., Watanuki, M., & Tanaka, R. (2001) · Journal of Applied Microbiology · doi:10.1046/j.1365-2672.2001.01461.x · Cited by 147

Synbiotic consumption changes the metabolism and composition of the gut microbiota in older people and modifies inflammatory processes: a randomised, double-blind, placebo-controlled crossover study

Macfarlane, S., Cleary, S., Bahrami, B., Reynolds, N., & Macfarlane, G. T. (2013) · Alimentary Pharmacology & Therapeutics · doi:10.1111/apt.12453 · Cited by 148

Results from a randomized placebo-controlled clinical trial of a RBX2660-a microbiota-based drug for the prevention of recurrent Clostridium difficile infection

Dubberke, E. R., Lee, C. H., Orenstein, R., Khanna, S., Hecht, G., & Gerding, D. N. (2018) · Clinical Infectious Diseases · doi:10.1093/cid/ciy259 · Cited by 140

Robustness of the Bacterial Community in the Cabbage White Butterfly Larval Midgut

Robinson, C. J., Schloss, P. D., Ramos, Y., Raffa, K. F., & Handelsman, J. (2009) · Microbial Ecology · doi:10.1007/s00248-009-9595-8 · Cited by 143

Collateral damage from oral ciprofloxacin versus nitrofurantoin in outpatients with urinary tract infections: a culture-free analysis of gut microbiota

Stewardson, A. J., Gaïa, N., François, P., Malhotra-Kumar, S., Delémont, C., de Tejada, B. M., Schrenzel, J., Harbarth, S., & Lazarević, V. (2014) · Clinical Microbiology and Infection · doi:10.1016/j.cmi.2014.11.016 · Cited by 147

The intestinal microbiota and susceptibility to infection in immunocompromised patients

Taur, Y., & Pamer, E. G. (2013) · Current Opinion in Infectious Diseases · doi:10.1097/qco.0b013e3283630dd3 · Cited by 144

Effect of Parenteral Antibiotic Administration on Persistence of Vancomycin‐ResistantEnterococcus faeciumin the Mouse Gastrointestinal Tract

Donskey, C. J., Hanrahan, J., Hutton, R. A., & Rice, L. B. (1999) · The Journal of Infectious Diseases · doi:10.1086/314874 · Cited by 139

Protective Effect ofLactobacillus caseiStrain Shirota on Shiga Toxin-ProducingEscherichia coliO157:H7 Infection in Infant Rabbits

Ogawa, M., Shimizu, K., Nomoto, K., Takahashi, M., Watanuki, M., Tanaka, R., Tanaka, T., Hamabata, T., Yamasaki, S., & Takeda, Y. (2001) · Infection and Immunity · doi:10.1128/iai.69.2.1101-1108.2001 · Cited by 139

Adjustment of dosing of antimicrobial agents for bodyweight in adults

Falagas, M. E., & Karageorgopoulos, D. E. (2009) · The Lancet · doi:10.1016/s0140-6736(09)60743-1 · Cited by 136

Guidance for substantiating the evidence for beneficial effects of probiotics: prevention and management of infections by probiotics

Wolvers, D., Antoine, J.-M., Myllyluoma, E., Schrezenmeir, J., Szajewska, H., & Rijkers, G. T. (2010) · The Journal of Nutrition · doi:10.3945/jn.109.113753 · Cited by 268

Risk factors for multidrug-resistant Pseudomonas aeruginosa nosocomial infection

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