What is the function of the bacterium, E. coli, in the human gut?

I have tried to find the answer by searching the Internet (e.g. here), but have been unsuccesful.


3 Answers 3


Nonpathogenic E. coli strains are a component of the gut microbiome of humans and many other organisms.

They are commensals, meaning that when they remain in the areas they have evolved to live in, and when they do not acquire virulence factors, they are benign. They live in our digestive tract and basically do nothing to harm us.

In fact, commensal microorganisms like E. coli can be considered part of the innate immune systems of their multicellular hosts. They take up space on the surfaces of the intestines and prevent colonization by pathogens.

Along with the endothelial cells and mucous, commensals form the barrier defenses that are the first line of protection against pathogenic organisms. Basically they are the good neighbors that don't cause problems and they don't leave space for bad neighbors to move in.

Problems can occur if they gain access to areas that are normally sterile. If the intestine is perforated and E. coli gain access to the thoracic cavity, they can become an opportunistic pathogen, as they will not be interacting with the host in a way that can control their proliferation. They can also come in contact with cells that are not expressing the necessary proteins to protect them from E. coli.

You can also end up with the situation where a pathogenic bacteria or a bacteriophage carrying a virulence factor can transfer that virulence factor to the commensal E. coli, turning them pathogenic.

But, for the most part, E. coli are there to take up space that could otherwise be colonized by harmful bacteria.

  • $\begingroup$ Commensal bacteria can produce usable metabolites, but I was unclear as to whether or not E.coli specifically provided any symbiotic benefit to the host or if they were simple commensal, space filling organisms. $\endgroup$
    – AMR
    Commented Sep 24, 2015 at 17:27

Some relevant research has been published in the time since this question was asked and initially answered.

The label "commensal E. coli" encompasses a diverse group of strains. Different strains of E. coli, each isolated from the microbiota of healthy mice, have been shown to elicit different immunopathological responses after gnotobiotic colonization.1 Generally, strain-level differences in pathogenic potential are attributed to the carriage and expression of virulence factors 2,3, many of which are mobilizable.4,5 However, I find classifications that rely on the presence/absence of genes to be oversimplified and anthropocentric, and I favor a presentation of E. coli as a genetically and metabolically versatile organism whose activity in the gut is a function of the evolutionary balancing of inter-species interactions with fitness in the intestinal niche.6,7,8


  1. Kittana H, Gomes-Neto JC, Heck K, Geis AL, Segura Muñoz RR, Cody LA, Schmaltz RJ, Bindels LB, Sinha R, Hostetter JM, Benson AK, Ramer-Tait AE. Commensal Escherichia coli Strains Can Promote Intestinal Inflammation via Differential Interleukin-6 Production. Front Immunol. 2018 Oct 9;9:2318.
  2. Stromberg ZR, Van Goor A, Redweik GAJ, Wymore Brand MJ, Wannemuehler MJ, Mellata M. Pathogenic and non-pathogenic Escherichia coli colonization and host inflammatory response in a defined microbiota mouse model. Dis Model Mech. 2018 Nov 16;11(11):dmm035063.
  3. Sarowska J, Futoma-Koloch B, Jama-Kmiecik A, Frej-Madrzak M, Ksiazczyk M, Bugla-Ploskonska G, Choroszy-Krol I. Virulence factors, prevalence and potential transmission of extraintestinal pathogenic Escherichia coli isolated from different sources: recent reports. Gut Pathog. 2019 Feb 21;11:10.
  4. Proença JT, Barral DC, Gordo I. Commensal-to-pathogen transition: One-single transposon insertion results in two pathoadaptive traits in Escherichia coli -macrophage interaction. Sci Rep. 2017 Jul 3;7(1):4504.
  5. Desvaux M, Dalmasso G, Beyrouthy R, Barnich N, Delmas J, Bonnet R. Pathogenicity Factors of Genomic Islands in Intestinal and Extraintestinal Escherichia coli. Front Microbiol. 2020 Sep 25;11:2065.
  6. Le Gall T, Clermont O, Gouriou S, Picard B, Nassif X, Denamur E, Tenaillon O. Extraintestinal virulence is a coincidental by-product of commensalism in B2 phylogenetic group Escherichia coli strains. Mol Biol Evol. 2007 Nov;24(11):2373-84.
  7. Barroso-Batista J, Pedro MF, Sales-Dias J, Pinto CJG, Thompson JA, Pereira H, Demengeot J, Gordo I, Xavier KB. Specific Eco-evolutionary Contexts in the Mouse Gut Reveal Escherichia coli Metabolic Versatility. Curr Biol. 2020 Mar 23;30(6):1049-1062.e7.
  8. Braz VS, Melchior K, Moreira CG. Escherichia coli as a Multifaceted Pathogenic and Versatile Bacterium. Front Cell Infect Microbiol. 2020 Dec 21;10:548492.

E. coli do not serve a human function but live inside our digestive system because our bodies can't prevent bacteria like them from living there. They live there because they can prosper and reproduce there. Most strains of E. coli do not cause problems for us, and by being part of the normal bacterial population in our gut they out-compete other, potentially more harmful bacteria and keep them suppressed. E. coli mainly live in the large intestine, not the stomach.

  • 2
    $\begingroup$ This is partially incorrect. In addition to regulating the intestinal flora (out competing more harmful bacteria), E. coli play a symbiotic role in the metabolism of carbohydrates and vitamin K $\endgroup$
    – De Novo
    Commented Mar 25, 2019 at 18:34

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