Cited by 291Gut microbiota and healthClostridium difficile and Clostridium perfringens researchEscherichia coli research studies

Mechanism of the Gut Microbiota Colonization Resistance and Enteric Pathogen Infection

Open access
Khan, Israr, Bai, Yanrui, Zha, Lajia, Ullah, Naeem, Ullah, Habib, Shah, Syed Rafiq Hussain, Sun, Hui, Zhang, Chunjiang·2021·Frontiers in Cellular and Infection Microbiology

Abstract

The mammalian gut microbial community, known as the gut microbiota, comprises trillions of bacteria, which co-evolved with the host and has an important role in a variety of host functions that include nutrient acquisition, metabolism, and immunity development, and more importantly, it plays a critical role in the protection of the host from enteric infections associated with exogenous pathogens or indigenous pathobiont outgrowth that may result from healthy gut microbial community disruption. Microbiota evolves complex mechanisms to restrain pathogen growth, which included nutrient competition, competitive metabolic interactions, niche exclusion, and induction of host immune response, which are collectively termed colonization resistance. On the other hand, pathogens have also developed counterstrategies to expand their population and enhance their virulence to cope with the gut microbiota colonization resistance and cause infection. This review summarizes the available literature on the complex relationship occurring between the intestinal microbiota and enteric pathogens, describing how the gut microbiota can mediate colonization resistance against bacterial enteric infections and how bacterial enteropathogens can overcome this resistance as well as how the understanding of this complex interaction can inform future therapies against infectious diseases.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.3389/fcimb.2021.716299

Cites

29 of 29 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • Klebsiella pneumoniae is naturally present in the respiratory and gastrointestinal tracts of humans and has a lower occurrence in animals, possibly due to diet, competition with other bacteria, or genetic virulence factors.

    “Klebsiella pneumoniae is naturally present in the respiratory and gastrointestinal tracts of humans and has a lower occurrence in animals, possibly due to diet, competition with other bacteria, or genetic virulence factors [70,71,72].”

    From A Systematic Review on Antimicrobial Resistance in Ghana from a One Health Perspective (2024) · cites this paper as [70]

    The Nutrient Competition section (page unavailable) identifies Klebsiella pneumoniae as a pathogen with a mechanism that gives it a growth advantage over gut commensals. The paper also discusses diet and microbial competition generally, but it does not establish that K. pneumoniae naturally inhabits both human respiratory and gastrointestinal tracts, occurs less often in animals, or that the proposed factors explain such a difference. (LLM, conf=0.78)

    Experimental — accuracy not yet measured

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Cites

Flagged first, then by citations

Research works printed but not linked: 172

  1. Abt M. C. McKenney P. T. Pamer E. G. (2016). Clostridium Difficile Colitis: Pathogenesis and Host Defence. Nat. Rev. Microbiol. doi: 10.1038/nrmicro.2016.108 PMC5109054 27573580 · DOI
  2. Alavi S. Mitchell J. D. Cho J. Y. Liu R. Macbeth J. C. Hsiao A. (2020). Interpersonal Gut Microbiome Variation Drives Susceptibility and Resistance to Cholera Infection. Cell. doi: 10.1016/j.cell.2020.05.036 PMC7394201 32631492 · DOI
  3. Alverdy J. Chi H. S. Sheldon G. F. (1985). The Effect of Parenteral Nutrition on Gastrointestinal Immunity. The Importance of Enteral Stimulation. Ann. Surg. doi: 10.1097/00000658-198512000-00003 PMC1250998 3935061 · DOI · Paper page
  4. Anderson C. J. Clark D. E. Adli M. Kendall M. M. (2015). Ethanolamine Signaling Promotes Salmonella Niche Recognition and Adaptation During Infection. PloS Pathog. doi: 10.1371/journal.ppat.1005278 PMC4643982 26565973 · DOI
  5. Autieri S. M. Lins J. J. Leatham M. P. Laux D. C. Conway T. Cohen P. S. (2007). L-Fucose Stimulates Utilization of D-Ribose by Escherichia Coli MG1655 Δfucao and E. Coli Nissle 1917 Δfucao Mutants in the Mouse Intestine and in M9 Minimal Medium. Infect. Immun. doi: 10.1128/IAI.00822-07 PMC2168271 17709419 · DOI
  6. Ayres J. S. Trinidad N. J. Vance R. E. (2012). Lethal Inflammasome Activation by a Multidrug-Resistant Pathobiont Upon Antibiotic Disruption of the Microbiota. Nat. Med. 18 (5), 799– 8065. doi: 10.1038/nm.2729 22522562 PMC3472005 · DOI · Paper page
  7. Baumgart M. Dogan B. Rishniw M. Weitzman G. Bosworth B. Yantiss R.. (2007). Culture Independent Analysis of Ileal Mucosa Reveals a Selective Increase in Invasive Escherichia Coli of Novel Phylogeny Relative to Depletion of Clostridiales in Crohn’s Disease Involving the Ileum. ISME J. doi: 10.1038/ismej.2007.52 18043660 · DOI
  8. Baümler A. J. Sperandio V. (2016). Interactions Between the Microbiota and Pathogenic Bacteria in the Gut. Nature. doi: 10.1038/nature18849 PMC5114849 27383983 · DOI · Paper page
  9. Becattini S. Littmann E. R. Carter R. A. Kim S. G. Morjaria S. M. Ling L.. (2017). Commensal Microbes Provide First Line Defense Against Listeria Monocytogenes Infection. J. Exp. Med. doi: 10.1084/jem.20170495 PMC5502438 28588016 · DOI
  10. Benítez-Páez A. Gómez del Pugar E. M. López-Almela I. Moya-Pérez Á. Codoñer-Franch P. Sanz Y. (2020). Depletion of Blautia Species in the Microbiota of Obese Children Relates to Intestinal Inflammation and Metabolic Phenotype Worsening. MSystems. doi: 10.1128/msystems.00857-19 PMC7093825 32209719 · DOI
  11. Bertin Y. Girardeau J. P. Chaucheyras-Durand F. Lyan B. Pujos-Guillot E. Harel J.. (2011). Enterohaemorrhagic Escherichia Coli Gains a Competitive Advantage by Using Ethanolamine as a Nitrogen Source in the Bovine Intestinal Content. Environ. Microbiol. doi: 10.1111/j.1462-2920.2010.02334.x 20849446 · DOI
  12. Blander J. M. Longman R. S. Iliev I. D. Sonnenberg G. F. Artis D. (2017). Regulation of Inflammation by Microbiota Interactions With the Host. Nat. Immunol. doi: 10.1038/ni.3780 PMC5800875 28722709 · DOI
  13. Bohnhoff M. Drake B. L. Miller C. P. (1954). Effect of Streptomycin on Susceptibility of Intestinal Tract to Experimental Salmonella Infection. Proc. Soc. Exp. Biol. Med. doi: 10.3181/00379727-86-21030 13177610 · DOI
  14. Bouguénec C. L. Schouler C. (2011). Sugar Metabolism, an Additional Virulence Factor in Enterobacteria. Int. J. Med. Microbiol. doi: 10.1016/j.ijmm.2010.04.021 PMC7129668 20705507 · DOI
  15. Bourlioux P. Koletzko B. Guarner F. Braesco V. (2003). The Intestine and Its Microflora Are Partners for the Protection of the Host: Report on the Danone Symposium ‘The Intelligent Intestine,’ Held in Paris, June 14, 2002. Am. J. Clin. Nutr. doi: 10.1093/ajcn/78.4.675 14522724 · DOI
  16. Bouslimani A. Porto C. Rath C. M. Wang M. Guo Y. Gonzalez A.. (2015). Molecular Cartography of the Human Skin Surface in 3D. Proc. Natl. Acad. Sci. U. S. A. doi: 10.1073/pnas.1424409112 PMC4418856 25825778 · DOI
  17. Brinkman B. M. Becker A. Ayiseh R. B. Hildebrand F. Raes J. Huys G.. (2013). Gut Microbiota Affects Sensitivity to Acute DSS-Induced Colitis Independently of Host Genotype. Inflamm. Bowel Dis. doi: 10.1097/MIB.0b013e3182a8759a 24105395 · DOI
  18. Bry L. Falk P. G. Midtvedt T. Gordon J. I. (1996). A Model of Host-Microbial Interactions in an Open Mammalian Ecosystem. Science. doi: 10.1126/science.273.5280.1380 8703071 · DOI
  19. Buffie C. G. Bucci V. Stein R. R. McKenney P. T. Ling L. Gobourne A.. (2015). Precision Microbiome Reconstitution Restores Bile Acid Mediated Resistance to Clostridium Difficile. Nature. doi: 10.1038/nature13828 PMC4354891 25337874 · DOI · Paper page
  20. Burgess S. L. Leslie J. L. Uddin J. Oakland D. N. Gilchrist C. Moreau G. B.. (2020). Gut Microbiome Communication With Bone Marrow Regulates Susceptibility to Amebiasis. J. Clin. Invest. doi: 10.1172/JCI133605 PMC7410058 32369444 · DOI
  21. Cameron E. A. Sperandio V. (2015). Frenemies: Signaling and Nutritional Integration in Pathogen-Microbiota-Host Interactions. Cell Host Microbe. doi: 10.1016/j.chom.2015.08.007 PMC4567707 26355214 · DOI
  22. Carter P. B. Collins F. M. (1974). The Route of Enteric Infection in Normal Mice. J. Exp. Med. doi: 10.1084/jem.139.5.1189 PMC2139651 4596512 · DOI
  23. Ceuppens S. Rajkovic A. Hamelink S. De Wiele T. V. Boon N. Uyttendaele M. (2012). Enterotoxin Production by Bacillus Cereus Under Gastrointestinal Conditions and Their Immunological Detection by Commercially Available Kits. Foodborne Pathog. Dis. doi: 10.1089/fpd.2012.1230 23237409 · DOI
  24. Cherrington C. A. Hinton M. Pearson G. R. Chopra I. (1991). Short-Chain Organic Acids at PH 5.0 Kill Escherichia Coli and Salmonella Spp. Without Causing Membrane Perturbation. J. Appl. Bacteriol. doi: 10.1111/j.1365-2672.1991.tb04442.x 1902205 · DOI · Paper page
  25. Chiodini R. J. Dowd S. E. Chamberlin W. M. Galandiuk S. Davis B. Glassing A. (2015). Microbial Population Differentials Between Mucosal and Submucosal Intestinal Tissues in Advanced Crohn’s Disease of the Ileum. PloS One. doi: 10.1371/journal.pone.0134382 PMC4519195 26222621 · DOI
  26. Chow W. L. Lee Y. K. (2008). Free Fucose Is a Danger Signal to Human Intestinal Epithelial Cells. Br. J. Nutr. doi: 10.1017/S0007114507812062 17697405 · DOI
  27. Crosa J. H. Walsh C. T. (2002). Genetics and Assembly Line Enzymology of Siderophore Biosynthesis in Bacteria. Microbiol. Mol. Biol. Rev. doi: 10.1128/mmbr.66.2.223-249.2002 PMC120789 12040125 · DOI · Paper page
  28. Curtis M. M. Hu Z. Klimko C. Narayanan S. Deberardinis R. Sperandio V. (2014). The Gut Commensal Bacteroides Thetaiotaomicron Exacerbates Enteric Infection Through Modification of the Metabolic Landscape. Cell Host Microbe. doi: 10.1016/j.chom.2014.11.005 PMC4269104 25498343 · DOI
  29. Dridi B. Raoult D. Drancourt M. (2011). Archaea as Emerging Organisms in Complex Human Microbiomes. Anaerobe. doi: 10.1016/j.anaerobe.2011.03.001 21420503 · DOI · Paper page
  30. Earle K. A. Billings G. Sigal M. Lichtman J. S. Hansson G. C. Elias J. E.. (2015). Quantitative Imaging of Gut Microbiota Spatial Organization. Cell Host Microbe. doi: 10.1016/j.chom.2015.09.002 PMC4628835 26439864 · DOI · Paper page
  31. Endt K. Stecher B. Chaffron S. Slack E. Tchitchek N. Benecke A.. (2010). The Microbiota Mediates Pathogen Clearance From the Gut Lumen After Non-Typhoidal Salmonella Diarrhea. PloS Pathog. doi: 10.1371/journal.ppat.1001097 PMC2936549 20844578 · DOI
  32. Enocksson A. Lundberg J. Weitzberg E. Norrby-Teglund A. Svenungsson B. (2004). Rectal Nitric Oxide Gas and Stool Cytokine Levels During the Course of Infectious Gastroenteritis. Clin. Diagn. Lab. Immunol. doi: 10.1128/CDLI.11.2.250-254.2004 PMC371199 15013971 · DOI
  33. Fabich A. J. Jones S. A. Chowdhury F. Z. Cernosek A. Anderson A. Smalley D.. (2008). Comparison of Carbon Nutrition for Pathogenic and Commensal Escherichia Coli Strains in the Mouse Intestine. Infect. Immun. doi: 10.1128/IAI.01386-07 PMC2258830 18180286 · DOI · Paper page
  34. Fagarasan S. Kawamoto S. Kanagawa O. Suzuki K. (2010). Adaptive Immune Regulation in the Gut: T Cell-Dependent and T Cell-Independent IgA Synthesis. Annu. Rev. Immunol. doi: 10.1146/annurev-immunol-030409-101314 20192805 · DOI
  35. Fan Y. Pedersen O. (2021). Gut Microbiota in Human Metabolic Health and Disease. Nat. Rev. Microbiol. doi: 10.1038/s41579-020-0433-9 32887946 · DOI · Paper page
  36. Feng Q. Chen W. D. Wang Y. D. (2018). Gut Microbiota: An Integral Moderator in Health and Disease. Front. Microbiol. doi: 10.3389/fmicb.2018.00151 PMC5826318 29515527 · DOI · Paper page
  37. Ferreira R. B. R. Gill N. Willing B. P. Antunes L.C. M. Russell S. L. Croxen M. A.. (2011). The Intestinal Microbiota Plays a Role in Salmonella-Induced Colitis Independent of Pathogen Colonization. PloS One. doi: 10.1371/journal.pone.0020338 PMC3102097 21633507 · DOI
  38. Ferreyra J. A. Ng K. M. Sonnenburg J. L. (2014a). The Enteric Two-Step: Nutritional Strategies of Bacterial Pathogens Within the Gut. Cell. Microbiol. doi: 10.1111/cmi.12300 PMC4866598 24720567 · DOI
  39. Ferreyra J. A. Wu K. J. Hryckowian A. J. Bouley D. M. Weimer B. C. Sonnenburg J. L. (2014b). Gut Microbiota-Produced Succinate Promotes C. Difficile Infection After Antibiotic Treatment or Motility Disturbance. Cell Host Microbe. doi: 10.1016/j.chom.2014.11.003 PMC4859344 25498344 · DOI
  40. Fischbach M. A. Lin H. Liu D. R. Walsh C. T. (2006). How Pathogenic Bacteria Evade Mammalian Sabotage in the Battle for Iron. Nat. Chem. Biol. doi: 10.1038/nchembio771 16485005 · DOI · Paper page
  41. Fischbach M. A. Sonnenburg J. L. (2011). Eating for Two: How Metabolism Establishes Interspecies Interactions in the Gut. Cell Host Microbe. doi: 10.1016/j.chom.2011.10.002 PMC3225337 22018234 · DOI
  42. Franchi L. Kamada N. Nakamura Y. Burberry A. Kuffa P. Suzuki S.. (2012). NLRC4-Driven Production of IL-1β Discriminates Between Pathogenic and Commensal Bacteria and Promotes Host Intestinal Defense. Nat. Immunol. doi: 10.1038/ni.2263 PMC3361590 22484733 · DOI
  43. Fukuda S. Toh H. Taylor T. D. Ohno H. Hattori M. (2012). Acetate-Producing Bifidobacteria Protect the Host From Enteropathogenic Infection via Carbohydrate Transporters. Gut Microbes. doi: 10.4161/gmic.21214 22825494 · DOI
  44. Furne J. Springfield J. Koenig T. DeMaster E. Levitt M. D. (2001). Oxidation of Hydrogen Sulfide and Methanethiol to Thiosulfate by Rat Tissues: A Specialized Function of the Colonic Mucosa. Biochem. Pharmacol. doi: 10.1016/S0006-2952(01)00657-8 11389886 · DOI
  45. Gagliardi A. Totino V. Cacciotti F. Iebba V. Neroni B. Bonfiglio G.. (2018). Rebuilding the Gut Microbiota Ecosystem. Int. J. Environ. Res. Public Health. doi: 10.3390/ijerph15081679 PMC6121872 30087270 · DOI · Paper page
  46. Gantois I. Ducatelle R. Pasmans F. Haesebrouck F. Hautefort I. Thompson A.. (2006). Butyrate Specifically Down-Regulates Salmonella Pathogenicity Island 1 Gene Expression. Appl. Environ. Microbiol. doi: 10.1128/AEM.72.1.946-949.2006 PMC1352287 16391141 · DOI
  47. Garrett W. S. Gallini C. A. Yatsunenko T. Michaud M. Dubois A. Delaney M. L.. (2010). Enterobacteriaceae Act in Concert With the Gut Microbiota to Induce Spontaneous and Maternally Transmitted Colitis. Cell Host Microbe. doi: 10.1016/j.chom.2010.08.004 PMC2952357 20833380 · DOI · Paper page
  48. Garsin D. A. (2010). Ethanolamine Utilization in Bacterial Pathogens: Roles and Regulation. Nat. Rev. Microbiol. doi: 10.1038/nrmicro2334 PMC2950637 20234377 · DOI
  49. Gevers D. Kugathasan S. Denson L. A. Vázquez-Baeza Y. Van Treuren W. Ren B.. (2014). The Treatment-Naive Microbiome in New-Onset Crohn’s Disease. Cell Host Microbe. doi: 10.1016/j.chom.2014.02.005 PMC4059512 24629344 · DOI · Paper page
  50. Ghosh S. Dai C. Brown K. Rajendiran E. Makarenko S. Baker J.. (2011). Colonic Microbiota Alters Host Susceptibility to Infectious Colitis by Modulating Inflammation, Redox Status, and Ion Transporter Gene Expression. Am. J. Physiol. Gastrointest. Liver Physiol. doi: 10.1152/ajpgi.00509.2010 21454446 · DOI
  51. Godinez I. Haneda T. Raffatellu M. George M. D. Paixão T. A. Rolán H. G.. (2008). T Cells Help to Amplify Inflammatory Responses Induced by Salmonella Enterica Serotype Typhimurium in the Intestinal Mucosa. Infect. Immun. doi: 10.1128/IAI.01691-07 PMC2346712 18347048 · DOI
  52. Gophna U. Sommerfeld K. Gophna S. Ford Doolittle W. Veldhuyzen Van Zanten S. J. O. (2006). Differences Between Tissue-Associated Intestinal Microfloras of Patients With Crohn’s Disease and Ulcerative Colitis. J. Clin. Microbiol. doi: 10.1128/JCM.01004-06 PMC1698347 16988016 · DOI
  53. Grünewald T. Ruf B. R. (2016). Clostridium Difficile Infections. Gynakol. Prax. doi: 10.7748/nop.22.4.13.s19 · DOI
  54. Haberman Y. Tickle T. L. Dexheimer P. J. Kim M. O. Tang D. Karns R.. (2014). Pediatric Crohn Disease Patients Exhibit Specific Ileal Transcriptome and Microbiome Signature. J. Clin. Invest. doi: 10.1172/JCI75436 PMC4109533 25003194 · DOI
  55. Hammami R. Fernandez B. Lacroix C. Fliss I. (2013). Anti-Infective Properties of Bacteriocins: An Update. Cell. Mol. Life Sci. doi: 10.1007/s00018-012-1202-3 PMC11113238 23109101 · DOI
  56. Harper R. W. Xu C. Eiserich J. P. Chen Y. Kao C. Y. Thai P.. (2005). Differential Regulation of Dual NADPH Oxidases/Peroxidases, Duox1 and Duox2, by Th1 and Th2 Cytokines in Respiratory Tract Epithelium. FEBS Lett. doi: 10.1016/j.febslet.2005.08.002 16111680 · DOI
  57. Hasegawa M. Kamada N. Jiao Y. Liu M. Z. Núñez G. Inohara N. (2012). Protective Role of Commensals Against Clostridium Difficile Infection via an IL-1β–Mediated Positive-Feedback Loop. J. Immunol. doi: 10.4049/jimmunol.1200821 PMC3752782 22888139 · DOI
  58. Hasegawa M. Osaka T. Tawaratsumida K. Yamazaki T. Tada H. Chen G. Y.. (2010). Transitions in Oral and Intestinal Microflora Composition and Innate Immune Receptor-Dependent Stimulation During Mouse Development Infect. Immun. doi: 10.1128/IAI.01043-09 PMC2812188 19933833 · DOI
  59. Hooper L. V. Xu J. Falk P. G. Midtvedt T. Gordon J. I. (1999). A Molecular Sensor That Allows a Gut Commensal to Control Its Nutrient Foundation in a Competitive Ecosystem. Proc. Natl. Acad. Sci. U. S. A. doi: 10.1073/pnas.96.17.9833 PMC22296 10449780 · DOI
  60. Hsiao A. Ahmed A.M.S. Subramanian S. Griffin N. W. Drewry L. L. Petri W. A.. (2014). Members of the Human Gut Microbiota Involved in Recovery From Vibrio Cholerae Infection. Nature. doi: 10.1038/nature13738 PMC4353411 25231861 · DOI · Paper page
  61. Huttenhower C. Gevers D. Knight R. Abubucker S. Badger J. H. Chinwalla A. T.. (2012). Structure, Function and Diversity of the Healthy Human Microbiome. Nature. doi: 10.1038/nature11234 PMC3564958 22699609 · DOI · Paper page
  62. Ivanov I. I. Atarashi K. Manel N. Brodie E. L. Shima T. Karaoz U.. (2009). Induction of Intestinal Th17 Cells by Segmented Filamentous Bacteria. Cell 139 (3), 485– 498. doi: 10.1016/j.cell.2009.09.033 19836068 PMC2796826 · DOI · Paper page
  63. Jacobson A. Lam L. Rajendram M. Tamburini F. Honeycutt J. Pham T.. (2018). A Gut Commensal-Produced Metabolite Mediates Colonization Resistance to Salmonella Infection. Cell Host Microbe. doi: 10.1016/j.chom.2018.07.002 PMC6223613 30057174 · DOI · Paper page
  64. Jenior M. L. Leslie J. L. Young V. B. Schloss P. D. (2018). Clostridium Difficile Alters the Structure and Metabolism of Distinct Cecal Microbiomes During Initial Infection To Promote Sustained Colonization. MSphere. doi: 10.1128/msphere.00261-18 PMC6021602 29950381 · DOI
  65. Joseph B. Przybilla K. Stühler C. Schauer K. Slaghuis J. Fuchs T. M.. (2006). Identification of Listeria Monocytogenes Genes Contributing to Intracellular Replication by Expression Profiling and Mutant Screening. J. Bacteriol. doi: 10.1128/JB.188.2.556-568.2006 PMC1347271 16385046 · DOI
  66. Kamada N. Chen G. Y. Inohara N. Núñez G. (2013). Control of Pathogens and Pathobionts by the Gut Microbiota. Nat. Immunol. doi: 10.1038/ni.2608 PMC4083503 23778796 · DOI · Paper page
  67. Kamada N. Kim Y. G. Sham H. P. Vallance B. A. Puente J. L. Martens E. C.. (2012). Regulated Virulence Controls the Ability of a Pathogen to Compete With the Gut Microbiota. Science. doi: 10.1126/science.1222195 PMC3439148 22582016 · DOI · Paper page
  68. Karmali M. A. Petric M. Lim C. Fleming P. C. Steele B. T. (1983). Escherichia Coli Cytotoxin, Haemolytic-Uraemic Syndrome, And Haemorrhagic Colitis. Lancet. doi: 10.1016/S0140-6736(83)91167-4 6139632 · DOI
  69. Kendall M. M. Gruber C. C. Parker C. T. Sperandio V. (2012). Ethanolamine Controls Expression of Genes Encoding Components Involved in Interkingdom Signaling and Virulence in Enterohemorrhagic Escherichia Coli O157:H7. MBio. doi: 10.1128/mBio.00050-12 PMC3372972 22589288 · DOI
  70. Khan I. Ullah N. Zha L. Bai Y. Khan A. Zhao T.. (2019). Alteration of Gut Microbiota in Inflammatory Bowel Disease (IBD): Cause or Consequence? IBD Treatment Targeting the Gut Microbiome. Pathogens. doi: 10.3390/pathogens8030126 PMC6789542 31412603 · DOI · Paper page
  71. Kim S. M. DeFazio J. R. Hyoju S. K. Sangani K. Keskey R. Krezalek M. A.. (2020). Fecal Microbiota Transplant Rescues Mice From Human Pathogen Mediated Sepsis by Restoring Systemic Immunity. Nat. Commun. doi: 10.1038/s41467-020-15545-w PMC7214422 32393794 · DOI
  72. Kiss E. A. Vonarbourg C. Kopfmann S. Hobeika E. Finke D. Esser C.. (2011). Natural Aryl Hydrocarbon Receptor Ligands Control Organogenesis of Intestinal Lymphoid Follicles. Science. doi: 10.1126/science.1214914 22033518 · DOI · Paper page
  73. Kobayashi K. S. Chamaillard M. Ogura Y. Henegariu O. Inohara N. Nuñez G.. (2005). Nod2-Dependent Regulation of Innate and Adaptive Immunity in the Intestinal Tract. Science. doi: 10.1126/science.1104911 15692051 · DOI
  74. Koh A. Bäckhed F. (2020). From Association to Causality: The Role of the Gut Microbiota and Its Functional Products on Host Metabolism. Mol. Cell. doi: 10.1016/j.molcel.2020.03.005 32234490 · DOI
  75. Koh A. Vadder F. D. Kovatcheva-Datchary P. Bäckhed F. (2016). From Dietary Fiber to Host Physiology: Short-Chain Fatty Acids as Key Bacterial Metabolites. Cell. doi: 10.1016/j.cell.2016.05.041 27259147 · DOI · Paper page
  76. Kolios G. Valatas V. Ward S. G. (2004). Nitric Oxide in Inflammatory Bowel Disease: A Universal Messenger in an Unsolved Puzzle. Immunology. doi: 10.1111/j.1365-2567.2004.01984.x PMC1782592 15554920 · DOI
  77. Korbel J. O. Doerks T. Jensen L. J. Perez-Iratxeta C. Kaczanowski S. Hooper S. D.. (2005). Systematic Association of Genes to Phenotypes by Genome and Literature Mining. PloS Biol. doi: 10.1371/journal.pbio.0030134 PMC1073694 15799710 · DOI
  78. Koropatkin N. M. Cameron E. A. Martens E. C. (2012). How Glycan Metabolism Shapes the Human Gut Microbiota. Nat. Rev. Microbiol. doi: 10.1038/nrmicro2746 PMC4005082 22491358 · DOI · Paper page
  79. Lapidot Y. Amir A. Nosenko R. Uzan-Yulzari A. Veitsman E. Cohen-Ezra O.. (2020). Alterations in the Gut Microbiome in the Progression of Cirrhosis to Hepatocellular Carcinoma. MSystems. doi: 10.1128/msystems.00153-20 PMC7300357 32546668 · DOI
  80. Law R. J. Gur-Arie L. Rosenshine I. Finlay B. B. (2013). In Vitro and In Vivo Model Systems for Studying Enteropathogenic Escherichia Coli Infections. Cold Spring Harbor Perspect. Med. 3 (3). doi: 10.1101/cshperspect.a009977 PMC3579205 23457294 · DOI
  81. Lawhon S. D. Maurer R. Suyemoto M. Altier C. (2002). Intestinal Short-Chain Fatty Acids Alter Salmonella Typhimurium Invasion Gene Expression and Virulence Through BarA/SirA. Mol. Microbiol. doi: 10.1046/j.1365-2958.2002.03268.x 12453229 · DOI
  82. Lawley T. D. Walker A. W. (2013). Intestinal Colonization Resistance. Immunology. doi: 10.1111/j.1365-2567.2012.03616.x PMC3533696 23240815 · DOI · Paper page
  83. Leatham M. P. Banerjee S. Autieri S. M. Mercado-Lubo R. Conway T. Cohen P. S. (2009). Precolonized Human Commensal Escherichia Coli Strains Serve as a Barrier to E. Coli O157:H7 Growth in the Streptomycin-Treated Mouse Intestine. Infect. Immun. doi: 10.1128/IAI.00059-09 PMC2708557 19364832 · DOI
  84. Leger A. J. St. Desai J. V. Drummond R. A. Kugadas A. Almaghrabi F. Silver P.. (2017). An Ocular Commensal Protects Against Corneal Infection by Driving an Interleukin-17 Response From Mucosal Γδ T Cells. Immunity. doi: 10.1016/j.immuni.2017.06.014 PMC5553552 28709803 · DOI
  85. Levitt M. D. Furne J. Springfield J. Suarez F. DeMaster E. (1999). Detoxification of Hydrogen Sulfide and Methanethiol in the Cecal Mucosa. J. Clin. Invest. doi: 10.1172/JCI7712 PMC408582 10525049 · DOI
  86. Ley R. E. Peterson D. A. Gordon J. I. (2006). Ecological and Evolutionary Forces Shaping Microbial Diversity in the Human Intestine. Cell. doi: 10.1016/j.cell.2006.02.017 16497592 · DOI · Paper page
  87. Li E. Hamm C. M. Gulati A. S. Sartor R. B. Chen H. Wu X.. (2012). Inflammatory Bowel Diseases Phenotype, C. Difficile and NOD2 Genotype Are Associated With Shifts in Human Ileum Associated Microbial Composition. PloS One. doi: 10.1371/journal.pone.0026284 PMC3374607 22719818 · DOI
  88. Lim M. Y. You H. J. Yoon H. S. Kwon B. Lee J. Y. Lee S.. (2017). The Effect of Heritability and Host Genetics on the Gut Microbiota and Metabolic Syndrome. Gut. doi: 10.1136/gutjnl-2015-311326 27053630 · DOI
  89. Li J. Wang J. Jia H. Cai X. Zhong H. Feng Q.. (2014). An Integrated Catalog of Reference Genes in the Human Gut Microbiome. Nat. Biotechnol. doi: 10.1038/nbt.2942 24997786 · DOI · Paper page
  90. Lopez C. A. Rivera-Chávez F. Byndloss M. X. Bäumler A. J. (2015). The Periplasmic Nitrate Reductase NapABC Supports Luminal Growth of Salmonella Enterica Serovar Typhimurium During Colitis. Infect. Immun. doi: 10.1128/IAI.00351-15 PMC4534643 26099579 · DOI
  91. Lopez C. A. Winter S. E. Rivera-Chávez F. Xavier M. N. Poon V. Nuccio S. P.. (2012). Phage-Mediated Acquisition of a Type III Secreted Effector Protein Boosts Growth of Salmonella by Nitrate Respiration. MBio. doi: 10.1128/mBio.00143-12 PMC3374392 22691391 · DOI
  92. Lundberg J. O. N. Weitzberg E. Lundberg J. M. Alving K. (1994). Intragastric Nitric Oxide Production in Humans: Measurements in Expelled Air. Gut. doi: 10.1136/gut.35.11.1543 PMC1375608 7828969 · DOI · Paper page
  93. Lv L.-X. Jiang H.-Y. Yan R. Li L. (2019). Interactions Between Gut Microbiota and Hosts and Their Role in Infectious Diseases. Infect. Microbes Dis. doi: 10.1097/im9.0000000000000001 · DOI
  94. Macpherson A. J. Geuking M. B. McCoy K. D. (2012). Homeland Security: IgA Immunity at the Frontiers of the Body. Trends Immunol. doi: 10.1016/j.it.2012.02.002 22410243 · DOI
  95. Macy J. M. Ljungdahl L. G. Gottschalk G. (1978). Pathway of Succinate and Propionate Formation in Bacteroides Fragilis. J. Bacteriol. doi: 10.1128/jb.134.1.84-91.1978 PMC222221 148460 · DOI
  96. Maier L. Vyas R. Cordova C. D. Lindsay H. Schmidt T. S. B. Brugiroux S.. (2013). Microbiota-Derived Hydrogen Fuels Salmonella Typhimurium Invasion of the Gut Ecosystem. Cell Host Microbe. doi: 10.1016/j.chom.2013.11.002 24331462 · DOI
  97. Marcobal A. Kashyap P. C. Nelson T. A. Aronov P. A. Donia M. S. Spormann A.. (2013). A Metabolomic View of How the Human Gut Microbiota Impacts the Host Metabolome Using Humanized and Gnotobiotic Mice. ISME J. doi: 10.1038/ismej.2013.89 PMC3965317 23739052 · DOI
  98. Marteyn B. West N. P. Browning D. F. Cole J. A. Shaw J. G. Palm F.. (2010). Modulation of Shigella Virulence in Response to Available Oxygen In Vivo. Nature. doi: 10.1038/nature08970 PMC3750455 20436458 · DOI
  99. Matamoros S. Gras-Leguen C. Le Vacon F. Potel G. de la Cochetiere M. F. (2013). Development of Intestinal Microbiota in Infants and Its Impact on Health. Trends Microbiol. doi: 10.1016/j.tim.2012.12.001 23332725 · DOI
  100. McKenney P. T. Pamer E. G. (2015). From Hype to Hope: The Gut Microbiota in Enteric Infectious Disease. Cell. doi: 10.1016/j.cell.2015.11.032 PMC4672394 26638069 · DOI
  101. Momose Y. (2008b). Effect of Organic Acids on Inhibition of Escherichia Coli O157:H7 Colonization in Gnotobiotic Mice Associated With Infant Intestinal Microbiota. Antonie Van Leeuwenhoek Int. J. Gen. Mol. Microbiol. doi: 10.1007/s10482-007-9188-9 17674138 · DOI
  102. Momose Y. Hirayama K. Itoh K. (2008a). Competition for Proline Between Indigenous Escherichia Coli and E. Coli O157:H7 in Gnotobiotic Mice Associated With Infant Intestinal Microbiota and Its Contribution to the Colonization Resistance Against E. Coli O157:H7. Antonie Van Leeuwenhoek Int. J. Gen. Mol. Microbiol. doi: 10.1007/s10482-008-9222-6 18247153 · DOI
  103. Mullineaux-Sanders C. Suez J. Elinav E. Frankel G. (2018). Sieving Through Gut Models of Colonization Resistance. Nat. Microbiol. 3 (2), 132– 405. doi: 10.1038/s41564-017-0095-1 29358683 · DOI
  104. Ng K. M. Ferreyra J. A. Higginbottom S. K. Lynch J. B. Kashyap P. C. Gopinath S.. (2013). Microbiota-Liberated Host Sugars Facilitate Post-Antibiotic Expansion of Enteric Pathogens. Nature. doi: 10.1038/nature12503 PMC3825626 23995682 · DOI · Paper page
  105. Ng J. Hirota S. A. Gross O. Li Y. Ulke-Lemee A. Potentier M. S.. (2010). Clostridium Difficile Toxin-Induced Inflammation and Intestinal Injury Are Mediated by the Inflammasome. Gastroenterology. doi: 10.1053/j.gastro.2010.04.005 20398664 · DOI
  106. Nood E. V. Vrieze A. Nieuwdorp M. Fuentes S. Zoetendal E. G. de Vos W. M.. (2013). Duodenal Infusion of Donor Feces for Recurrent Clostridium Difficile. N Engl. J. Med. doi: 10.1056/nejmoa1205037 23323867 · DOI · Paper page
  107. Oh P. L. Martínez I. Sun Y. Walter J. Peterson D. A. Mercer D. F. (2012). Characterization of the Ileal Microbiota in Rejecting and Nonrejecting Recipients of Small Bowel Transplants. Am. J. Transplant. doi: 10.1111/j.1600-6143.2011.03860.x 22152019 · DOI
  108. Pacheco A. R. Munera D. Waldor M. K. Sperandio V. Ritchie J. M. (2012). Fucose Sensing Regulates Bacterial Intestinal Colonization. Nature. doi: 10.1038/nature11623 PMC3518558 23160491 · DOI · Paper page
  109. Pacheco A. R. Sperandio V. (2015). “ Enteric Pathogens Exploit the Microbiota-Generated Nutritional Environment of the Gut,” in Metabolism and Bacterial Pathogenesis. doi: 10.1128/microbiolspec.mbp-0001-2014 PMC5070792 26185079 · DOI
  110. Palmer R. M. J. Rees D. D. Ashton D. S. Moncada S. (1988). L-Arginine Is the Physiological Precursor for the Formation of Nitric Oxide in Endothelium-Dependent Relaxation. Biochem. Biophys. Res. Commun. doi: 10.1016/S0006-291X(88)81362-7 3390182 · DOI
  111. Parhi L. Alon-Maimon T. Sol A. Nejman D. Shhadeh A. Fainsod-Levi T.. (2020). Breast Cancer Colonization by Fusobacterium Nucleatum Accelerates Tumor Growth and Metastatic Progression. Nat. Commun. doi: 10.1038/s41467-020-16967-2 PMC7320135 32591509 · DOI · Paper page
  112. Pavia A. T. Shipman L. D. Wells J. G. Puhr N. D. Smith J. D. McKinley T. W.. (1990). Epidemiologic Evidence That Prior Antimicrobial Exposure Decreases Resistance to Infection by Antimicrobial-Sensitive Salmonella. J. Infect. Dis. doi: 10.1093/infdis/161.2.255 2299207 · DOI
  113. Pedicord V. A. Lockhart A. A. K. Rangan K. J. Craig J. W. Loschko J. Rogoz A.. (2016). Exploiting a Host-Commensal Interaction to Promote Intestinal Barrier Function and Enteric Pathogen Tolerance. Sci. Immunol. doi: 10.1126/sciimmunol.aai7732 PMC5453653 28580440 · DOI
  114. Perna N. T. Plunkett G. Burland V. Mau B. Glasner J. D. Rose D. J.. (2001). Genome Sequence of Enterohaemorrhagic Escherichia Coli O157:H7. Nature. doi: 10.1038/35054089 11206551 · DOI
  115. Petrof E. O. Gloor G. B. Vanner S. J. Weese S. J. Carter D. Daigneault M. C.. (2013). Stool Substitute Transplant Therapy for the Eradication of Clostridium Difficile Infection: ‘Repoopulating’ the Gut. Microbiome. doi: 10.1186/2049-2618-1-3 PMC3869191 24467987 · DOI · Paper page
  116. Pham T. A. N. Clare S. Goulding D. Arasteh J. M. Stares M. D. Browne H. P.. (2014). Epithelial IL-22ra1-Mediated Fucosylation Promotes Intestinal Colonization Resistance to an Opportunistic Pathogen. Cell Host Microbe. doi: 10.1016/j.chom.2014.08.017 PMC4190086 25263220 · DOI
  117. Pickard J. M. Maurice C. F. Kinnebrew M. A. Abt M. C. Schenten D. Golovkina T. V.. (2014). Rapid Fucosylation of Intestinal Epithelium Sustains Host-Commensal Symbiosis in Sickness. Nature. doi: 10.1038/nature13823 PMC4214913 25274297 · DOI
  118. Pickard J. M. Núñez G. (2019). Pathogen Colonization Resistance in the Gut and Its Manipulation for Improved Health. Am. J. Pathol. doi: 10.1016/j.ajpath.2019.03.003 PMC6617533 31100210 · DOI
  119. Piewngam P. Zheng Y. Nguyen T. H. Dickey S. W. Joo H. S. Villaruz A. E.. (2018). Pathogen Elimination by Probiotic Bacillus via Signalling Interference. Nature. doi: 10.1038/s41586-018-0616-y PMC6202238 30305736 · DOI
  120. Pridmore R. D. Berger B. Desiere F. Vilanova D. Barretto C. Pittet A. C.. (2004). The Genome Sequence of the Probiotic Intestinal Bacterium Lactobacillus Johnsionii NCC 533. Proc. Natl. Acad. Sci. U. S. A. doi: 10.1073/pnas.0307327101 PMC356981 14983040 · DOI
  121. Qiu J. Heller J. J. Guo X. Chen Z. M. E. Fish K. Fu Y. X.. (2012). The Aryl Hydrocarbon Receptor Regulates Gut Immunity Through Modulation of Innate Lymphoid Cells. Immunity. doi: 10.1016/j.immuni.2011.11.011 PMC3268875 22177117 · DOI
  122. Rakoff-Nahoum S. Coyne M. J. Comstock L. E. (2014). An Ecological Network of Polysaccharide Utilization Among Human Intestinal Symbionts. Curr. Biol doi: 10.1016/j.cub.2013.10.077 PMC3924574 24332541 · DOI
  123. Rath C. M. Alexandrov T. Higginbottom S. K. Song J. Milla M. E. Fischbach M. A.. (2012). Molecular Analysis of Model Gut Microbiotas by Imaging Mass Spectrometry and Nanodesorption Electrospray Ionization Reveals Dietary Metabolite Transformations. Anal. Chem. doi: 10.1021/ac302039u PMC3711173 23009651 · DOI
  124. Reinders C. I. Jonkers D. Jansson E. Å. Stockbrügger R. W. Stobberingh E. E. Hellström P. M.. (2007). Rectal Nitric Oxide and Fecal Calprotectin in Inflammatory Bowel Disease. Scand. J. Gastroenterol. doi: 10.1080/00365520701320505 17852876 · DOI
  125. Rivera-Chávez F. Bäumler A. J. (2015). The Pyromaniac Inside You: Salmonella Metabolism in the Host Gut. Annu. Rev. Microbiol. doi: 10.1146/annurev-micro-091014-104108 26002180 · DOI
  126. Rolhion N. Chassaing B. (2016). When Pathogenic Bacteria Meet the Intestinal Microbiota. Philos. Trans. R. Soc. B Biol. Sci. doi: 10.1098/rstb.2015.0504 PMC5052746 27672153 · DOI
  127. Ryan F. J. Ahern A. M. Fitzgerald R. S. Laserna-Mendieta E. J. Power E. M. Clooney A. G.. (2020). Colonic Microbiota Is Associated With Inflammation and Host Epigenomic Alterations in Inflammatory Bowel Disease. Nat. Commun. doi: 10.1038/s41467-020-15342-5 PMC7089947 32251296 · DOI
  128. Salzman A. L. Denenberg A. G. Ueta I. O’Connor M. Linn S. C. Szabó C. (1996). Induction and Activity of Nitric Oxide Synthase in Cultured Human Intestinal Epithelial Monolayers. Am. J. Physiol. Gastrointest. Liver Physiol. doi: 10.1152/ajpgi.1996.270.4.g565 8928785 · DOI
  129. Salzman N. H. Hung K. Haribhai D. Chu H. Karlsson-Sjöberg J. Amir E.. (2010). Enteric Defensins Are Essential Regulators of Intestinal Microbial Ecology. Nat. Immunol. doi: 10.1038/ni.1825 PMC2795796 19855381 · DOI · Paper page
  130. Sanos S. L. Bui V. L. Mortha A. Oberle K. Heners C. Johner C.. (2009). RORγt and Commensal Microflora Are Required for the Differentiation of Mucosal Interleukin 22-Producing NKp46+ Cells. Nat. Immunol. doi: 10.1038/ni.1684 PMC4217274 19029903 · DOI
  131. Sassone-Corsi M. Raffatellu M. (2015). No Vacancy: How Beneficial Microbes Cooperate With Immunity To Provide Colonization Resistance to Pathogens. J. Immunol. doi: 10.4049/jimmunol.1403169 PMC4402713 25888704 · DOI
  132. Satoh-Takayama N. Vosshenrich C. A. J. Lesjean-Pottier S. Sawa S. Lochner M. Rattis F.. (2008). Microbial Flora Drives Interleukin 22 Production in Intestinal NKp46+ Cells That Provide Innate Mucosal Immune Defense. Immunity. doi: 10.1016/j.immuni.2008.11.001 19084435 · DOI
  133. Schamberger G. P. Diez-Gonzalez F. (2002). Selection of Recently Isolated Colicinogenic Escherichia Coli Strains Inhibitory to Escherichia Coli O157:H7. J. Food Prot. doi: 10.4315/0362-028X-65.9.1381 12233846 · DOI
  134. Schauer D. B. Falkow S. (1993). Attaching and Effacing Locus of a Citrobacter Freundii Biotype That Causes Transmissible Murine Colonic Hyperplasia. Infect. Immun. 61 (6), 2486– 2492. doi: 10.1128/iai.61.6.2486-2492.1993 8500884 PMC280873 · DOI
  135. Schroeder B. O. Bäckhed F. (2016). Signals From the Gut Microbiota to Distant Organs in Physiology and Disease. Nat. Med. doi: 10.1038/nm.4185 27711063 · DOI · Paper page
  136. Scott S. A. Fu J. Chang P. V. (2020). Microbial Tryptophan Metabolites Regulate Gut Barrier Function via the Aryl Hydrocarbon Receptor. Proc. Natl. Acad. Sci. U. S. A. doi: 10.1073/pnas.2000047117 PMC7431026 32719140 · DOI · Paper page
  137. Sekirov I. Russell S. L. Antunes L.C. M. Finlay B. B. (2010). Gut Microbiota in Health and Disease. Physiol. Rev. doi: 10.1152/physrev.00045.2009 20664075 · DOI · Paper page
  138. Sekirov I. Tam N. M. Jogova M. Robertson M. L. Li Y. Lupp C.. (2008). Antibiotic-Induced Perturbations of the Intestinal Microbiota Alter Host Susceptibility to Enteric Infection. Infect. Immun. doi: 10.1128/IAI.00319-08 PMC2546810 18678663 · DOI
  139. Seksik P. Rigottier-Gois L. Gramet G. Sutren M. Pochart P. Marteau P.. (2003). Alterations of the Dominant Faecal Bacterial Groups in Patients With Crohn’s Disease of the Colon. Gut 52 (2), 237– 242. doi: 10.1136/gut.52.2.237 12524406 PMC1774977 · DOI
  140. Sender R. Fuchs S. Milo R. (2016). Are We Really Vastly Outnumbered? Revisiting the Ratio of Bacterial to Host Cells in Humans. Cell. doi: 10.1016/j.cell.2016.01.013 26824647 · DOI · Paper page
  141. Shin R. Suzuki M. Morishita Y. (2002). Influence of Intestinal Anaerobes and Organic Acids on the Growth of Enterohaemorrhagic Escherichia Coli O157:H7. J. Med. Microbiol. doi: 10.1099/0022-1317-51-3-201 11871614 · DOI
  142. Singer I. I. Kawka D. W. Scott S. Weidner J. R. Mumford R. A. Riehl T. E.. (1996). Expression of Inducible Nitric Oxide Synthase and Nitrotyrosine in Colonic Epithelium in Inflammatory Bowel Disease. Gastroenterology. doi: 10.1016/S0016-5085(96)70055-0 8831582 · DOI
  143. Sorbara M. T. Pamer E. G. (2019). Correction: Interbacterial Mechanisms of Colonization Resistance and the Strategies Pathogens Use to Overcome Them (Mucosal Immunology, (2019), 12, 1, (1-9), 10.1038/S41385-018-0053-0). Mucosal Immunol. doi: 10.1038/s41385-019-0151-7 30796335 · DOI
  144. Sprinz H. Kundel D. W. Dammin G. J. Horowitz R. E. Schneider H. Formal S. B. (1961). The Response of the Germfree Guinea Pig to Oral Bacterial Challenge With Escherichia Coli and Shigella Flexneri. Am. J. Pathol. PMC1942415 13915950
  145. Steed A. L. Christophi G. P. Kaiko G. E. Sun L. Goodwin V. M. Jain U.. (2017). The Microbial Metabolite Desaminotyrosine Protects From Influenza Through Type I Interferon. Science. doi: 10.1126/science.aam5336 PMC5753406 28774928 · DOI · Paper page
  146. Strugnell R. A. Wijburg O. L. C. (2010). The Role of Secretory Antibodies in Infection Immunity. Nat. Rev. Microbiol. doi: 10.1038/nrmicro2384 20694027 · DOI
  147. Suzuki K. Maruya M. Kawamoto S. Sitnik K. Kitamura H. Agace W. W.. (2010). The Sensing of Environmental Stimuli by Follicular Dendritic Cells Promotes Immunoglobulin A Generation in the Gut. Immunity. doi: 10.1016/j.immuni.2010.07.003 20643338 · DOI
  148. Szabady R. L. Lokuta M. A. Walters K. B. Huttenlocher A. Welch R. A. (2009). Modulation of Neutrophil Function by a Secreted Mucinase of Escherichia Coli O157:H7. PloS Pathog. doi: 10.1371/journal.ppat.1000320 PMC2642718 19247439 · DOI
  149. Takao M. Yen H. Tobe T. (2014). LeuO Enhances Butyrate-Induced Virulence Expression Through a Positive Regulatory Loop in Enterohaemorrhagic Escherichia Coli. Mol. Microbiol. doi: 10.1111/mmi.12737 25069663 · DOI
  150. The Human Microbiome Project Consortium (2012). Structure, Function and Diversity of the Healthy Human Microbiome The Human Microbiome Project Consortium*. Nature. PMC3564958 22699609
  151. Theriot C. M. Young V. B. (2015). Interactions Between the Gastrointestinal Microbiome and Clostridium Difficile. Annu. Rev. Microbiol. doi: 10.1146/annurev-micro-091014-104115 PMC4892173 26488281 · DOI
  152. Thiennimitr P. Winter S. E. Winter M. G. Xavier M. N. Tolstikov V. Huseby D. L.. (2011). Intestinal Inflammation Allows Salmonella to Use Ethanolamine to Compete With the Microbiota. Proc. Natl. Acad. Sci. U. S. A. doi: 10.1073/pnas.1107857108 PMC3198331 21969563 · DOI
  153. Tierney B. T. Yang Z. Luber J. M. Beaudin M. Wibowo M. C. Baek C.. (2019). The Landscape of Genetic Content in the Gut and Oral Human Microbiome. Cell Host Microbe. doi: 10.1016/j.chom.2019.07.008 PMC6716383 31415755 · DOI
  154. Turnbaugh P. J. Bäckhed F. Fulton L. Gordon J. I. (2008). Diet-Induced Obesity Is Linked to Marked But Reversible Alterations in the Mouse Distal Gut Microbiome. Cell Host Microbe. doi: 10.1016/j.chom.2008.02.015 PMC3687783 18407065 · DOI · Paper page
  155. Turovskiy Y. Sutyak Noll K. Chikindas M. L. (2011). The Aetiology of Bacterial Vaginosis. J. Appl. Microbiol. doi: 10.1111/j.1365-2672.2011.04977.x PMC3072448 21332897 · DOI
  156. Ubeda C. Lipuma L. Gobourne A. Viale A. Leiner I. Equinda M.. (2012). Familial Transmission Rather Than Defective Innate Immunity Shapes the Distinct Intestinal Microbiota of TLR-Deficient Mice. J. Exp. Med. doi: 10.1084/jem.20120504 PMC3409501 22826298 · DOI · Paper page
  157. Vaishnava S. Yamamoto M. Severson K. M. Ruhn K. A. Yu X. Koren O.. (2011). The Antibacterial Lectin RegIIIγ Promotes the Spatial Segregation of Microbiota and Host in the Intestine. Science. doi: 10.1126/science.1209791 PMC3321924 21998396 · DOI · Paper page
  158. Waaij D.V. D. Berghuis-de Vries J. M. Lekkerkerk-Van Der Wees J. E. C. (1971). Colonization Resistance of the Digestive Tract in Conventional and Antibiotic-Treated Mice. J. Hyg. doi: 10.1017/S0022172400021653 PMC2130899 4999450 · DOI
  159. Walker A. W. Sanderson J. D. Churcher C. Parkes G. C. Hudspith B. N. Rayment N.. (2011). High-Throughput Clone Library Analysis of the Mucosa-Associated Microbiota Reveals Dysbiosis and Differences Between Inflamed and Non-Inflamed Regions of the Intestine in Inflammatory Bowel Disease. BMC Microbiol. doi: 10.1186/1471-2180-11-7 PMC3032643 21219646 · DOI
  160. Willing B. Halfvarson J. Dicksved J. Rosenquist M. Järnerot G. Engstrand L.. (2009). Twin Studies Reveal Specific Imbalances in the Mucosa-Associated Microbiota of Patients With Ileal Crohn’s Disease. Inflamm. Bowel Dis. doi: 10.1002/ibd.20783 19023901 · DOI · Paper page
  161. Willing B. P. Vacharaksa A. Croxen M. Thanachayanont T. Brett Finlay B. (2011). Altering Host Resistance to Infections Through Microbial Transplantation. PloS One. doi: 10.1371/journal.pone.0026988 PMC3203939 22046427 · DOI
  162. Winkler E. S. Shrihari S. Hykes B. L. Handley S. A. Andhey P. S. Huang Y. J. S.. (2020). The Intestinal Microbiome Restricts Alphavirus Infection and Dissemination Through a Bile Acid-Type I IFN Signaling Axis. Cell. doi: 10.1016/j.cell.2020.06.029 PMC7483520 32668198 · DOI
  163. Winter S. E. Thiennimitr P. Winter M. G. Butler B. P. Huseby D. L. Crawford R. W.. (2010). Gut Inflammation Provides a Respiratory Electron Acceptor for Salmonella. Nature. doi: 10.1038/nature09415 PMC2946174 20864996 · DOI
  164. Winter S. E. Winter M. G. Xavier M. N. Thiennimitr P. Poon V. Keestra A. M.. (2013). Host-Derived Nitrate Boosts Growth of E. Coli in the Inflamed Gut. Science. doi: 10.1126/science.1232467 PMC4004111 23393266 · DOI · Paper page
  165. Wlodarska M. Willing B. P. Bravo D. M. Finlay B. B. (2015). Phytonutrient Diet Supplementation Promotes Beneficial Clostridia Species and Intestinal Mucus Secretion Resulting in Protection Against Enteric Infection. Sci. Rep. doi: 10.1038/srep09253 PMC4365398 25787310 · DOI
  166. Wu L. Estrada O. Zaborina O. Bains M. Shen L. Kohler J. E.. (2005). Microbiology: Recognition of Host Immune Activation by Pseudomonas Aeruginosa. Science. doi: 10.1126/science.1112422 16051797 · DOI
  167. Yilmaz B. Portugal S. Tran T. M. Gozzelino R. Ramos S. Gomes J.. (2014). Gut Microbiota Elicits a Protective Immune Response Against Malaria Transmission. Cell. doi: 10.1016/j.cell.2014.10.053 PMC4261137 25480293 · DOI
  168. Zachar Z. Savage D. C. (1979). Microbial Interference and Colonization of the Murine Gastrointestinal Tract by Listeria Monocytogenes. Infect. Immun. doi: 10.1128/iai.23.1.168-174.1979 PMC550704 106003 · DOI
  169. Zeng M. Y. Cisalpino D. Varadarajan S. Hellman J. Warren H. S. Cascalho M.. (2016). Gut Microbiota-Induced Immunoglobulin G Controls Systemic Infection by Symbiotic Bacteria and Pathogens. Immunity. doi: 10.1016/j.immuni.2016.02.006 PMC4794373 26944199 · DOI · Paper page
  170. Zheng D. Liwinski T. Elinav E. (2020). Interaction Between Microbiota and Immunity in Health and Disease. Cell Res. doi: 10.1038/s41422-020-0332-7 PMC7264227 32433595 · DOI · Paper page
  171. Zheng Y. Valdez P. A. Danilenko D. M. Hu Y. Sa S. M. Gong Q.. (2008). Interleukin-22 Mediates Early Host Defense Against Attaching and Effacing Bacterial Pathogens. Nat. Med. doi: 10.1038/nm1720 18264109 · DOI
  172. Zumbrun S. D. Melton-Celsa A. R. Smith M. A. Gilbreath J. J. Merrell D. S. O’Brien A. D. (2013). Dietary Choice Affects Shiga Toxin-Producing Escherichia Coli (STEC) O157:H7 Colonization and Disease. Proc. Natl. Acad. Sci. U. S. A. doi: 10.1073/pnas.1222014110 PMC3677460 23690602 · DOI

Cited by

Sorted by citations

Authors
Khan, I., Bai, Y., Zha, L., Ullah, N., Ullah, H., Shah, S. R. H., Sun, H., & Zhang, C.
Affiliations
  • Lanzhou University Second Hospital (CN)
  • Lanzhou University (CN)
  • Dalian Medical University (CN)
Corresponding author
  • Sun, Hui
  • Zhang, Chunjiang
Venue
Frontiers in Cellular and Infection Microbiology
Published
2021-12-23
Volume
11
Pages
716299-716299
ISSN
2235-2988 (ISSN-L)
OpenAlex
W4200078072
Cited by
291
References
29
Citations by year
2026: 60 · 2025: 79 · 2024: 79 · 2023: 54 · 2022: 19
FWCI
3.99
Type
journal article
Language
en
Open access
Locations
  • Frontiers in Cellular and Infection Microbiology (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Lanzhou University Institutional Repository (submittedVersion, cc-by-nc-sa)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
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 › Biochemistry, Genetics and Molecular Biology › Endocrinology › Escherichia coli research studies
Keywords
gut microbiota, colonization resistance, enteric pathogens, nutrient competition, host immune response, pathogen virulence, dysbiosis, host defense against infection
MeSH terms
Gastrointestinal Microbiome, Animals, Bacteria, Bacterial Infections, Virulence

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review