Editing Escherichia coli

{{Short description|Enteric, rod-shaped, gram-negative bacterium}}
{{Redirect|E. coli|the protozoan commensal|Entamoeba coli}}
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{{Speciesbox
| image = E coli at 10000x, original.jpg
| taxon = Escherichia coli
| authority = ([[Walter Migula|Migula]] 1895)<br />[[Aldo Castellani|Castellani]] and [[Albert John Chalmers|Chalmers]] 1919 (Approved Lists 1980)
| synonyms = * ''Bacterium coli communis'' <small>[[Theodor Escherich|Escherich]] 1885</small>
* ''Bacillus coli'' <small>Migula 1895</small>
* ''Bacterium coli'' <small>(Migula) Lehmann & Neumann, 1896</small>
}}

'''''Escherichia coli''''' ({{IPAc-en|ˌ|ɛ|ʃ|ə|ˈ|r|ɪ|k|i|ə|_|ˈ|k|oʊ|l|aɪ
}} {{respell|ESH|ə|RIK|ee|ə|_|KOH|lye}})<ref>{{OED|coli}}</ref><ref name="Wells, J. C. 2000">Wells, J. C. (2000) Longman Pronunciation Dictionary. Harlow [England], Pearson Education Ltd.</ref> is a [[Gram-negative bacteria|gram-negative]], [[Facultative anaerobic organism|facultative anaerobic]], [[Bacillus (shape)|rod-shaped]], [[coliform bacteria|coliform bacterium]] of the genus ''[[Escherichia]]'' that is commonly found in the lower [[intestine]] of [[warm-blooded]] organisms.<ref>{{cite journal | vauthors = Tenaillon O, Skurnik D, Picard B, Denamur E | title = The population genetics of commensal Escherichia coli | journal = Nature Reviews. Microbiology | volume = 8 | issue = 3 | pages = 207–17 | date = March 2010 | pmid = 20157339 | doi = 10.1038/nrmicro2298 | s2cid = 5490303 }}</ref><ref name="Singleton">{{cite book | author = Singleton P| title = Bacteria in Biology, Biotechnology and Medicine | edition = 5th | publisher = Wiley | year = 1999 | pages= 444–54| isbn = 978-0-471-98880-9}}</ref> Most ''E. coli'' [[Strain (biology)|strains]] are part of the normal [[Gut microbiota|microbiota of the gut]], where they constitute about 0.1%, along with other  [[facultative anaerobe]]s.<ref name="pmid15831718">{{cite journal | vauthors = Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, Sargent M, Gill SR, Nelson KE, Relman DA | display-authors = 6 | title = Diversity of the human intestinal microbial flora | journal = Science | volume = 308 | issue = 5728 | pages = 1635–38 | date = June 2005 | pmid = 15831718 | pmc = 1395357 | doi = 10.1126/science.1110591 | bibcode = 2005Sci...308.1635E }}</ref> These bacteria are mostly harmless or even beneficial to humans.<ref name="Martinson">{{cite journal | vauthors = ((Martinson JNV)), Walk ST | title = Escherichia coli residency in the gut of healthy human adults | journal = EcoSal Plus | volume = 9 | issue = 1 | year = 2020 | pmid = 32978935 | doi = 10.1177/003335490512000211 | pmc = 7523338 }}</ref> For example, some strains of ''E. coli'' benefit their hosts by producing [[Vitamin K2|vitamin K<sub>2</sub>]]<ref name="Bentley">{{cite journal | vauthors = Bentley R, Meganathan R | title = Biosynthesis of vitamin K (menaquinone) in bacteria | journal = Microbiological Reviews | volume = 46 | issue = 3 | pages = 241–80 | date = September 1982 | pmid = 6127606 | pmc = 281544 | doi = 10.1128/ecosalplus.ESP-0003-2020 }}</ref> or by preventing the colonization of the intestine by harmful [[pathogenic bacteria]]. These mutually beneficial relationships between ''E. coli'' and humans are a type of [[Mutualism (biology)|mutualistic]] biological relationship—where both the humans and the ''E. coli'' are benefitting each other.<ref name="Hudault">{{cite journal | vauthors = Hudault S, Guignot J, Servin AL | title = ''Escherichia coli'' strains colonising the gastrointestinal tract protect germfree mice against ''Salmonella typhimurium'' infection | journal = Gut | volume = 49 | issue = 1 | pages = 47–55 | date = July 2001 | pmid = 11413110 | pmc = 1728375 | doi = 10.1136/gut.49.1.47 }}</ref><ref name="Reid">{{cite journal | vauthors = Reid G, Howard J, Gan BS | title = Can bacterial interference prevent infection? | journal = Trends in Microbiology | volume = 9 | issue = 9 | pages = 424–28 | date = September 2001 | pmid = 11553454 | doi = 10.1016/S0966-842X(01)02132-1 }}</ref> ''E. coli'' is expelled into the environment within fecal matter. The bacterium grows massively in fresh fecal matter under [[Aerobic organism|aerobic conditions]] for three days, but its numbers decline slowly afterwards.<ref name="Russell2001">{{cite journal |vauthors=Russell JB, Jarvis GN |date=April 2001 |title=Practical mechanisms for interrupting the oral-fecal lifecycle of ''Escherichia coli'' |journal=Journal of Molecular Microbiology and Biotechnology |volume=3 |issue=2 |pages=265–72 |pmid=11321582}}</ref>

Some [[serotype]]s, such as [[Enteropathogenic Escherichia coli|EPEC]] and [[Enterotoxigenic Escherichia coli|ETEC]], are pathogenic, causing serious [[Foodborne illness|food poisoning]] in their hosts.<ref name="CDC">{{cite web |title=Escherichia coli |url=https://www.cdc.gov/ecoli/index.html/ |access-date=2 October 2012 |work=CDC National Center for Emerging and Zoonotic Infectious Diseases}}</ref>  [[fecal–oral route|Fecal–oral transmission]] is the major route through which pathogenic strains of the bacterium cause disease. This transmission method is occasionally responsible for [[food contamination]] incidents that prompt product recalls.<ref name="Vogt">{{cite journal |vauthors=Vogt RL, Dippold L |year=2005 |title=''Escherichia coli'' O157:H7 outbreak associated with consumption of ground beef, June–July 2002 |journal=Public Health Reports |volume=120 |issue=2 |pages=174–78 |doi=10.1177/003335490512000211 |pmc=1497708 |pmid=15842119}}</ref> Cells are able to survive outside the body for a limited amount of time, which makes them potential [[indicator organism]]s to test environmental samples for [[Feces|fecal contamination]].<ref name="Feng_2002">{{cite web | vauthors = Feng P, Weagant S, Grant M |title=Enumeration of ''Escherichia coli'' and the Coliform Bacteria |work=Bacteriological Analytical Manual (8th ed.) |publisher=FDA/Center for Food Safety & Applied Nutrition |date=1 September 2002 |url=http://www.cfsan.fda.gov/~ebam/bam-4.html |access-date=25 January 2007 |url-status=dead |archive-url= https://web.archive.org/web/20090519200935/http://www.cfsan.fda.gov/~ebam/bam-4.html |archive-date=19 May 2009 }}</ref><ref name="Thompson">{{cite news | vauthors = Thompson A |title=E. coli Thrives in Beach Sands |url=http://www.livescience.com/health/070604_beach_ecoli.html |publisher=Live Science |date=4 June 2007 |access-date=3 December 2007 }}</ref> A growing body of research, though, has examined environmentally persistent ''E. coli'' which can survive for many days and grow outside a host.<ref>{{cite journal | vauthors = Montealegre MC, Roy S, Böni F, Hossain MI, Navab-Daneshmand T, Caduff L, Faruque AS, Islam MA, Julian TR | display-authors = 6 | title = Risk Factors for Detection, Survival, and Growth of Antibiotic-Resistant and Pathogenic Escherichia coli in Household Soils in Rural Bangladesh | journal = Applied and Environmental Microbiology | volume = 84 | issue = 24 | pages = e01978–18 | date = December 2018 | pmid = 30315075 | pmc = 6275341 | doi = 10.1128/AEM.01978-18 | bibcode = 2018ApEnM..84E1978M }}</ref>

The bacterium can be [[Microbiological culture|grown and cultured]] easily and inexpensively in a laboratory setting, and has been intensively investigated for over 60 years. ''E. coli'' is a [[Chemotroph#Chemoheterotroph|chemoheterotroph]] whose chemically defined medium must include a source of [[carbon]] and [[energy]].<ref name="Tortora" /> ''E. coli'' is the most widely studied [[prokaryote|prokaryotic]] [[model organism]], and an important species in the fields of [[biotechnology]] and [[microbiology]], where it has served as the [[host organism]] for the majority of work with [[recombinant DNA]]. Under favourable conditions, it takes as little as 20 minutes to reproduce.<ref>{{cite web|title=Bacteria|url=http://www.microbiologyonline.org.uk/about-microbiology/introducing-microbes/bacteria|publisher=Microbiologyonline|access-date=27 February 2014|archive-url=https://web.archive.org/web/20140227212658/http://www.microbiologyonline.org.uk/about-microbiology/introducing-microbes/bacteria|archive-date=27 February 2014|url-status=live}}</ref>

==Biology and biochemistry==
[[File:Life cycle of Escherichia coli.png|thumb|350px|Model of successive binary [[Fission (biology)|fission]] in ''E. coli'']]

===Type and morphology===
''E. coli'' is a gram-negative, [[facultative anaerobic organism|facultative anaerobe]], [[Endospore|nonsporulating]] [[coliform bacteria|coliform bacterium]].<ref>{{cite web |title=Escherichia coli |date=15 April 2011 |url=http://www.redorbit.com/education/reference_library/health_1/bacteria/2584144/escherichia_coli/ |publisher=Redorbit |access-date=27 November 2013}}</ref> Cells are typically rod-shaped, and are about 2.0 [[micrometers|μm]] long and 0.25–1.0&nbsp;[[μm]] in diameter, with a cell volume of 0.6–0.7&nbsp;μm<sup>3</sup>.<ref>{{cite encyclopedia |url=https://www.britannica.com/science/bacteria/Diversity-of-structure-of-bacteria  |title=Facts about ''E. coli'': dimensions, as discussed in bacteria: Diversity of structure of bacteria |encyclopedia=Encyclopaedia Britannica|access-date=25 June 2015}}</ref><ref name="pmid24287933">{{cite journal |vauthors = Yu AC, Loo JF, Yu S, Kong SK, Chan TF |s2cid = 2956197 |title = Monitoring bacterial growth using tunable resistive pulse sensing with a pore-based technique |journal = Applied Microbiology and Biotechnology |volume = 98 |issue = 2 | pages = 855–62 | date = January 2014 | pmid = 24287933 | doi = 10.1007/s00253-013-5377-9 }}</ref><ref>{{cite journal | vauthors = Kubitschek HE | title = Cell volume increase in ''Escherichia coli'' after shifts to richer media | journal = Journal of Bacteriology | volume = 172 | issue = 1 | pages = 94–101 | date = January 1990 | pmid = 2403552 | pmc = 208405 | doi = 10.1128/jb.172.1.94-101.1990 }}</ref>

''E. coli'' stains gram-negative because its [[cell wall]] is composed of a thin [[peptidoglycan layer]] and an [[Bacterial outer membrane|outer membrane]]. During the staining process, ''E. coli'' picks up the color of the counterstain [[safranin]] and stains pink. The outer membrane surrounding the cell wall provides a barrier to certain [[antibiotics]], such that ''E. coli'' is not damaged by [[penicillin]].<ref name="Tortora"/>

The [[flagellum|flagella]] which allow the bacteria to swim have a [[Flagellum#Flagellar arrangement schemes|peritrichous arrangement]].<ref name="pmid17189361">{{cite journal | vauthors = Darnton NC, Turner L, Rojevsky S, Berg HC | title = On torque and tumbling in swimming Escherichia coli | journal = Journal of Bacteriology | volume = 189 | issue = 5 | pages = 1756–64 | date = March 2007 | pmid = 17189361 | pmc = 1855780 | doi = 10.1128/JB.01501-06 }}</ref> It also attaches and effaces to the [[Microvillus|microvilli]] of the intestines via an [[Bacterial adhesin|adhesion molecule]] known as [[intimin]].<ref name="microbewiki.kenyon.edu">{{cite web | url=https://microbewiki.kenyon.edu/index.php/E._coli_O157_in_North_America | title=''E. coli'' O157 in North America – microbewiki}}</ref>

=== Metabolism ===
''E. coli'' can live on a wide variety of substrates and uses [[mixed acid fermentation]] in anaerobic conditions, producing [[lactic acid|lactate]], [[succinate]], [[ethanol]], [[acetate]], and [[carbon dioxide]]. Since many pathways in [[Mixed acid fermentation|mixed-acid fermentation]] produce [[hydrogen]] gas, these pathways require the levels of hydrogen to be low, as is the case when ''E. coli'' lives together with hydrogen-consuming organisms, such as [[methanogen]]s or [[sulphate-reducing bacteria]].<ref>{{cite book | title=Brock Biology of microorganisms|vauthors=Madigan MT, Martinko JM | year=2006| publisher=Pearson| isbn=978-0-13-196893-6| edition=11th}}</ref>

In addition, ''E. coli''{{'}}s metabolism can be rewired to solely use [[Carbon dioxide|CO<sub>2</sub>]] as the source of [[carbon]] for biomass production. In other words, this obligate heterotroph's metabolism can be altered to display autotrophic capabilities by heterologously expressing [[carbon fixation]] genes as well as [[formate dehydrogenase]] and conducting laboratory evolution experiments. This may be done by using [[formate]] to reduce [[electron carrier]]s and supply the [[Adenosine triphosphate|ATP]] required in anabolic pathways inside of these synthetic autotrophs.<ref>{{cite journal | vauthors = Gleizer S, Ben-Nissan R, Bar-On YM, Antonovsky N, Noor E, Zohar Y, Jona G, Krieger E, Shamshoum M, Bar-Even A, Milo R | display-authors = 6 | title = 2 | journal = Cell | volume = 179 | issue = 6 | pages = 1255–1263.e12 | date = November 2019 | pmid = 31778652 | pmc = 6904909 | doi = 10.1016/j.cell.2019.11.009 }}</ref>[[File:Ecoli_Metabolism.webp|thumb|''Redistribution of fluxes between the three primary glucose catabolic pathways: EMPP (red), EDP (blue), and OPPP (orange) via the knockout of pfkA and overexpression of EDP genes (edd and eda).'']]

''E. coli'' has three native glycolytic pathways: [[Embden–Meyerhof–Parnas pathway|EMPP]], [[Entner–Doudoroff pathway|EDP]], and [[Pentose phosphate pathway|OPPP]]. The EMPP employs ten enzymatic steps to yield two [[pyruvates]], two [[Adenosine triphosphate|ATP]], and two [[NADH]] per [[glucose]] molecule  while OPPP serves as an oxidation route for [[NADPH]] synthesis. Although the EDP is the more thermodynamically favourable of the three pathways, ''E. coli'' do not use the EDP for [[glucose metabolism]], relying mainly on the EMPP and the OPPP. The EDP mainly remains inactive except for during growth with [[gluconate]].<ref>{{cite journal | vauthors = Hollinshead WD, Rodriguez S, Martin HG, Wang G, Baidoo EE, Sale KL, Keasling JD, Mukhopadhyay A, Tang YJ | display-authors = 6 | title = pfk mutants | journal = Biotechnology for Biofuels | volume = 9 | issue = 1 | pages = 212 | date = 2016-10-10 | pmid = 27766116 | pmc = 5057261 | doi = 10.1186/s13068-016-0630-y | doi-access = free }}</ref>

==== Catabolite repression ====
When growing in the presence of a mixture of sugars, bacteria will often consume the sugars sequentially through a process known as [[Catabolism|catabolite]] repression. By repressing the expression of the genes involved in metabolizing the less preferred sugars, cells will usually first consume the sugar yielding the highest growth rate, followed by the sugar yielding the next highest growth rate, and so on. In doing so the cells ensure that their limited metabolic resources are being used to maximize the rate of growth. The well-used example of this with ''E. coli'' involves the growth of the bacterium on [[glucose]] and [[lactose]], where ''E. coli'' will consume [[glucose]] before [[lactose]]. Catabolite repression has also been observed in ''E. coli'' in the presence of other non-glucose sugars, such as [[arabinose]] and [[xylose]], [[sorbitol]], [[rhamnose]], and [[ribose]]. In ''E. coli'', glucose catabolite repression is regulated by the [[phosphotransferase system]], a multi-protein [[phosphorylation]] cascade that couples [[glucose uptake]] and [[metabolism]].<ref>{{cite journal | vauthors = Ammar EM, Wang X, Rao CV | title = Regulation of metabolism in ''Escherichia coli'' during growth on mixtures of the non-glucose sugars: arabinose, lactose, and xylose | journal = Scientific Reports | volume = 8 | issue = 1 | pages = 609 | date = January 2018 | pmid = 29330542 | pmc = 5766520 | doi = 10.1038/s41598-017-18704-0 | bibcode = 2018NatSR...8..609A }}</ref>

===Culture growth===
[[Image:e.coli-colony-growth.gif|thumb|200px|A colony of ''E. coli'' growing]]Optimum growth of ''E. coli'' occurs at {{convert|37|C}}, but some laboratory strains can multiply at temperatures up to {{convert|49|C}}.<ref>{{cite journal | vauthors = Fotadar U, Zaveloff P, Terracio L | title = Growth of ''Escherichia coli'' at elevated temperatures | journal = Journal of Basic Microbiology | volume = 45 | issue = 5 | pages = 403–04 | year = 2005 | pmid = 16187264 | doi = 10.1002/jobm.200410542 | s2cid = 44876092 }}</ref> ''E. coli'' grows in a variety of defined laboratory media, such as [[lysogeny broth]], or any medium that contains [[glucose]], [[Monoammonium phosphate|ammonium phosphate monobasic]], [[sodium chloride]], [[magnesium sulfate]], [[Dipotassium phosphate|potassium phosphate dibasic]], and [[water]]. Growth can be driven by [[aerobic respiration|aerobic]] or [[anaerobic respiration]], using a large variety of [[redox|redox pairs]], including the oxidation of [[pyruvic acid]], [[formic acid]], [[hydrogen]], and [[amino acid]]s, and the reduction of substrates such as [[oxygen]], [[nitrate]], [[fumarate]], [[dimethyl sulfoxide]], and [[trimethylamine N-oxide]].<ref name="Ingledew">{{cite journal | vauthors = Ingledew WJ, Poole RK | title = The respiratory chains of ''Escherichia coli'' | journal = Microbiological Reviews | volume = 48 | issue = 3 | pages = 222–71 | date = September 1984 | pmid = 6387427 | pmc = 373010 | doi = 10.1128/MMBR.48.3.222-271.1984 }}</ref> ''E. coli'' is classified as a [[facultative anaerobe]]. It uses [[oxygen]] when it is present and available. It can, however, continue to grow in the absence of [[oxygen]] using [[fermentation]] or [[anaerobic respiration]]. Respiration type is managed in part by the [[arc system]].  The ability to continue growing in the absence of [[oxygen]] is an advantage to bacteria because their survival is increased in environments where [[water]] predominates.<ref name="Tortora">{{Cite book|title = Microbiology: An Introduction| vauthors = Tortora G |publisher = Benjamin Cummings|year = 2010|isbn = 978-0-321-55007-1|location = San Francisco, CA|pages = 85–87, 161, 165}}</ref>

===Cell cycle===
{{main|Cell cycle}}

The bacterial cell cycle is divided into three stages.  The B period occurs between the completion of cell division and the beginning of [[DNA replication]].  The C period encompasses the time it takes to replicate the [[Cytogenetics|chromosomal DNA.]]  The D period refers to the stage between the conclusion of [[DNA replication]] and the end of cell division.<ref name="Wang2009">{{cite journal | vauthors = Wang JD, Levin PA | title = Metabolism, cell growth and the bacterial cell cycle | journal = Nature Reviews. Microbiology | volume = 7 | issue = 11 | pages = 822–27 | date = November 2009 | pmid = 19806155 | pmc = 2887316 | doi = 10.1038/nrmicro2202 }}</ref>  The doubling rate of ''E. coli'' is higher when more nutrients are available.  However, the length of the C and D periods do not change, even when the doubling time becomes less than the sum of the C and D periods.  At the fastest growth rates, replication begins before the previous round of replication has completed, resulting in multiple replication forks along the [[DNA]] and overlapping cell cycles.<ref name="Cooper1968">{{cite journal | vauthors = Cooper S, Helmstetter CE | title = Chromosome replication and the division cycle of ''Escherichia coli'' B/r | journal = Journal of Molecular Biology | volume = 31 | issue = 3 | pages = 519–40 | date = February 1968 | pmid = 4866337 | doi = 10.1016/0022-2836(68)90425-7 }}</ref>

The number of replication forks in fast growing ''E. coli'' typically follows 2n (n = 1, 2 or 3). This only happens if [[DNA replication|replication]] is initiated simultaneously from all [[Origin of replication|origins of replications]], and is referred to as synchronous [[DNA replication|replication]]. However, not all cells in a culture replicate synchronously. In this case cells do not have multiples of two [[replication fork]]s. Replication initiation is then referred to being asynchronous.<ref name=":2">{{cite journal | vauthors = Skarstad K, Boye E, Steen HB | title = Timing of initiation of chromosome replication in individual Escherichia coli cells | journal = The EMBO Journal | volume = 5 | issue = 7 | pages = 1711–7 | date = July 1986 | pmid = 3527695 | pmc = 1166998 | doi = 10.1002/j.1460-2075.1986.tb04415.x }}</ref> However, asynchrony can be caused by mutations to for instance [[DnaA]]<ref name=":2" /> or [[DnaA]] initiator-associating protein [[DiaA]].<ref>{{cite journal | vauthors = Ishida T, Akimitsu N, Kashioka T, Hatano M, Kubota T, Ogata Y, Sekimizu K, Katayama T | display-authors = 6 | title = DiaA, a novel DnaA-binding protein, ensures the timely initiation of ''Escherichia coli'' chromosome replication | journal = The Journal of Biological Chemistry | volume = 279 | issue = 44 | pages = 45546–55 | date = October 2004 | pmid = 15326179 | doi = 10.1074/jbc.M402762200 | doi-access = free }}</ref>

Although ''E. coli'' reproduces by [[fission (biology)|binary fission]] the two supposedly identical cells produced by cell division are functionally asymmetric with the old pole cell acting as an aging parent that repeatedly produces rejuvenated offspring.<ref name="Stewart_2005">{{cite journal | vauthors = Stewart EJ, Madden R, Paul G, Taddei F | title = Aging and death in an organism that reproduces by morphologically symmetric division | journal = PLOS Biology | volume = 3 | issue = 2 | pages = e45 | date = February 2005 | pmid = 15685293 | pmc = 546039 | doi = 10.1371/journal.pbio.0030045 | doi-access = free }}</ref> When exposed to an elevated stress level, damage accumulation in an old ''E. coli'' lineage may surpass its immortality threshold so that it arrests division and becomes mortal.<ref name="Proenca_2019">{{cite journal | vauthors = Proenca AM, Rang CU, Qiu A, Shi C, Chao L | title = Cell aging preserves cellular immortality in the presence of lethal levels of damage | journal = PLOS Biology | volume = 17 | issue = 5 | pages = e3000266 | date = May 2019 | pmid = 31120870 | pmc = 6532838 | doi = 10.1371/journal.pbio.3000266 | doi-access = free }}</ref> [[cellular senescence|Cellular aging]] is a general process, affecting [[prokaryote]]s and [[eukaryote]]s alike.<ref name="Proenca_2019" />

===Genetic adaptation===

''E. coli'' and related bacteria possess the ability to transfer [[DNA]] via [[bacterial conjugation]] or [[transduction (genetics)|transduction]], which allows genetic material to [[Horizontal gene transfer|spread horizontally]] through an existing population. The process of transduction, which uses the bacterial virus called a [[bacteriophage]],<ref>{{cite journal | vauthors = Brüssow H, Canchaya C, Hardt WD | title = Phages and the evolution of bacterial pathogens: from genomic rearrangements to lysogenic conversion | journal = Microbiology and Molecular Biology Reviews | volume = 68 | issue = 3 | pages = 560–602, table of contents | date = September 2004 | pmid = 15353570 | pmc = 515249 | doi = 10.1128/MMBR.68.3.560-602.2004 }}</ref> is where the spread of the gene encoding for the [[Shiga toxin]] from the ''[[Shigella]]'' bacteria to ''E. coli'' helped produce [[Escherichia coli O157:H7|''E. coli'' O157:H7]], the Shiga toxin-producing strain of ''E. coli.''

==Diversity==
[[File:E.coli on growing on various agar media.jpg|alt=E. coli colonies|thumb|''E. coli growing on basic cultivation media'']]
''E. coli'' encompasses an enormous population of bacteria that exhibit a very high degree of both genetic and phenotypic diversity. [[Whole genome sequencing|Genome sequencing]] of many isolates of ''E. coli'' and related bacteria shows that a taxonomic reclassification would be desirable. However, this has not been done, largely due to its medical importance,<ref>{{cite book | veditors = Krieg NR, Holt JG |title=Bergey's Manual of Systematic Bacteriology |edition=First |volume=1 |publisher=The Williams & Wilkins Co |location=Baltimore |year=1984 |pages=408–20 |isbn=978-0-683-04108-8 }}</ref> and ''E. coli'' remains one of the most diverse bacterial species: only 20% of the genes in a typical ''E. coli'' genome is shared among all strains.<ref name="comparison">{{cite journal | vauthors = Lukjancenko O, Wassenaar TM, Ussery DW | title = Comparison of 61 sequenced Escherichia coli genomes | journal = Microbial Ecology | volume = 60 | issue = 4 | pages = 708–20 | date = November 2010 | pmid = 20623278 | pmc = 2974192 | doi = 10.1007/s00248-010-9717-3 | bibcode = 2010MicEc..60..708L }}</ref>

In fact, from the more constructive point of view, the members of genus ''Shigella'' (''S. dysenteriae'', ''S. flexneri'', ''S. boydii'', and ''S. sonnei'') should be classified as ''E. coli'' strains, a phenomenon termed [[taxa in disguise]].<ref name="pmid12361912">{{cite journal | vauthors = Lan R, Reeves PR | title = Escherichia coli in disguise: molecular origins of ''Shigella'' | journal = Microbes and Infection | volume = 4 | issue = 11 | pages = 1125–32 | date = September 2002 | pmid = 12361912 | doi = 10.1016/S1286-4579(02)01637-4 }}</ref> Similarly, other strains of ''E. coli'' (e.g. the [[E. coli K-12|K-12]] strain commonly used in [[recombinant DNA]] work) are sufficiently different that they would merit reclassification.

A [[strain (biology)|strain]] is a [[subgroup]] within the species that has unique characteristics that distinguish it from other [[Strain (biology)|strains]]. These differences are often detectable only at the molecular level; however, they may result in changes to the physiology or lifecycle of the bacterium. For example, a strain may gain [[pathogenicity|pathogenic capacity]], the ability to use a unique [[carbon source (biology)|carbon source]], the ability to take upon a particular [[ecological niche]], or the ability to resist [[antimicrobial agents]]. Different strains of ''E. coli'' are often host-specific, making it possible to determine the source of fecal contamination in environmental samples.<ref name="Feng_2002" /><ref name="Thompson" /> For example, knowing which ''E. coli'' strains are present in a water sample allows researchers to make assumptions about whether the contamination originated from a human, another [[mammal]], or a [[bird]].

===Serotypes===
{{main|Pathogenic Escherichia coli#Serotypes}}

[[File:Escherichia coli on agar.jpg|alt=E.coli colonies on agar.|thumb|''E. coli'' on sheep blood agar]]
A common subdivision system of ''E. coli'', but not based on evolutionary relatedness, is by serotype, which is based on major surface [[antigen]]s (O antigen: part of [[lipopolysaccharide]] layer; H: [[flagellin]]; K [[antigen]]: capsule), e.g. [[O157:H7]]).<ref name="pmid334154">{{cite journal | vauthors = Orskov I, Orskov F, Jann B, Jann K | title = Serology, chemistry, and genetics of O and K antigens of ''Escherichia coli'' | journal = Bacteriological Reviews | volume = 41 | issue = 3 | pages = 667–710 | date = September 1977 | pmid = 334154 | pmc = 414020 | doi =  10.1128/MMBR.41.3.667-710.1977}}</ref> It is, however, common to cite only the [[serogroup]], i.e. the [[O antigen|O-antigen]]. At present, about 190 serogroups are known.<ref>{{cite journal | vauthors = Stenutz R, Weintraub A, Widmalm G | title = The structures of ''Escherichia coli'' O-polysaccharide antigens | journal = FEMS Microbiology Reviews | volume = 30 | issue = 3 | pages = 382–403 | date = May 2006 | pmid = 16594963 | doi = 10.1111/j.1574-6976.2006.00016.x | doi-access = free }}</ref> The common laboratory strain has a mutation that prevents the formation of an [[O antigen|O-antigen]] and is thus not typeable.

===Genome plasticity and evolution===
Like all lifeforms, new strains of ''E. coli'' [[evolution|evolve]] through the natural biological processes of [[mutation]], [[gene duplication]], and [[horizontal gene transfer]]; in particular, 18% of the genome of the [[Escherichia coli in molecular biology|laboratory strain MG1655]] was horizontally acquired since the divergence from ''[[Salmonella]]''.<ref name="pmid9689094">{{cite journal | vauthors = Lawrence JG, Ochman H | title = Molecular archaeology of the ''Escherichia coli'' genome | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 95 | issue = 16 | pages = 9413–17 | date = August 1998 | pmid = 9689094 | pmc = 21352 | doi = 10.1073/pnas.95.16.9413 | bibcode = 1998PNAS...95.9413L | doi-access = free }}</ref> [[E. coli K-12|''E. coli'' K-12]] and ''E. coli'' B strains are the most frequently used varieties for laboratory purposes. Some strains develop [[Trait (biology)|traits]] that can be harmful to a host animal. These [[Virulence|virulent]] strains typically cause a bout of [[diarrhea]] that is often [[Self-limiting (biology)|self-limiting]] in healthy adults but is frequently lethal to children in the developing world.<ref name=Nataro>{{cite journal | vauthors = Nataro JP, Kaper JB | title = Diarrheagenic ''Escherichia coli'' | journal = Clinical Microbiology Reviews | volume = 11 | issue = 1 | pages = 142–201 | date = January 1998 | pmid = 9457432 | pmc = 121379 | doi = 10.1128/CMR.11.1.142 }}</ref> More virulent strains, such as [[Escherichia coli O157:H7|O157:H7]], cause serious illness or death in the elderly, the very young, or the [[immunocompromised]].<ref name=Nataro/><ref name=Viljanen>{{cite journal | vauthors = Viljanen MK, Peltola T, Junnila SY, Olkkonen L, Järvinen H, Kuistila M, Huovinen P | s2cid = 23087850 | title = Outbreak of diarrhoea due to ''Escherichia coli'' O111:B4 in schoolchildren and adults: association of Vi antigen-like reactivity | journal = Lancet | volume = 336 | issue = 8719 | pages = 831–34 | date = October 1990 | pmid = 1976876 | doi = 10.1016/0140-6736(90)92337-H }}</ref>

The genera ''[[Escherichia]]'' and ''[[Salmonella]]'' diverged around 102&nbsp;million years ago (credibility interval: 57–176&nbsp;mya), an event unrelated to the much earlier (see ''[[Synapsid]]'') divergence of their hosts: the former being found in mammals and the latter in birds and reptiles.<ref name="pmid15535883">{{cite journal | vauthors = Battistuzzi FU, Feijao A, Hedges SB | title = A genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land | journal = BMC Evolutionary Biology | volume = 4 | pages = 44 | date = November 2004 | pmid = 15535883 | pmc = 533871 | doi = 10.1186/1471-2148-4-44 | doi-access = free }}</ref> This was followed by a split of an ''Escherichia'' ancestor into five species (''[[Escherichia albertii|E. albertii]]'', ''E. coli'', ''[[Escherichia fergusonii|E. fergusonii]]'', ''[[Escherichia hermannii|E. hermannii]]'', and ''[[Escherichia vulneris|E. vulneris]]'').<!--Dates unavailable--> The last ''E. coli'' ancestor split between 20 and 30&nbsp;million years ago.<ref name="pmid9866203">{{cite journal | vauthors = Lecointre G, Rachdi L, Darlu P, Denamur E | title = Escherichia coli molecular phylogeny using the incongruence length difference test | journal = Molecular Biology and Evolution | volume = 15 | issue = 12 | pages = 1685–95 | date = December 1998 | pmid = 9866203 | doi = 10.1093/oxfordjournals.molbev.a025895 | doi-access = free }}</ref>

The [[E. coli long-term evolution experiment|long-term evolution experiments using ''E. coli'']], begun by [[Richard Lenski]] in 1988, have allowed direct observation of genome evolution over more than 65,000 generations in the laboratory.<ref>{{cite web | vauthors = Holmes B | date = 9 June 2008 | url = https://www.newscientist.com/channel/life/dn14094-bacteria-make-major-evolutionary-shift-in-the-lab.html | title = Bacteria make major evolutionary shift in the lab | archive-url = https://web.archive.org/web/20080828030920/http://www.newscientist.com/channel/life/dn14094-bacteria-make-major-evolutionary-shift-in-the-lab.html | archive-date=28 August 2008 | work = New Scientist }}</ref> For instance, ''E. coli'' typically do not have the ability to grow aerobically with [[citrate]] as a [[carbon source (biology)|carbon source]], which is used as a diagnostic criterion with which to differentiate ''E. coli'' from other, closely, related bacteria such as ''Salmonella''. In this experiment, one population of ''E. coli'' unexpectedly evolved the ability to aerobically metabolize [[citrate]], a major evolutionary shift with some hallmarks of microbial [[speciation]].[[File:Scanning electron micrograph of an E. coli colony.jpg|thumb|Scanning electron micrograph of an ''E. coli'' colony]]

In the microbial world, a relationship of predation can be established similar to that observed in the animal world. Considered, it has been seen that ''E. coli'' is the prey of multiple generalist predators, such as ''[[Myxococcus xanthus]]''. In this predator-prey relationship, a parallel evolution of both species is observed through genomic and phenotypic modifications, in the case of ''E. coli'' the modifications are modified in two aspects involved in their virulence such as mucoid production (excessive production of exoplasmic acid alginate ) and the suppression of the [[OmpT]] gene, producing in future generations a better adaptation of one of the species that is counteracted by the evolution of the other, following a co-evolutionary model demonstrated by the [[Red Queen hypothesis]].<ref name="pmid31541093">{{cite journal | vauthors = Nair RR, Vasse M, Wielgoss S, Sun L, Yu YN, Velicer GJ | title = Bacterial predator-prey coevolution accelerates genome evolution and selects on virulence-associated prey defences | journal = Nature Communications | volume = 10 | issue = 1 | pages = 4301 | date = September 2019 | pmid = 31541093 | pmc = 6754418 | doi = 10.1038/s41467-019-12140-6 | bibcode = 2019NatCo..10.4301N }}</ref>

===Neotype strain===
''E. coli'' is the type species of the genus (''Escherichia'') and in turn ''Escherichia'' is the type genus of the family [[Enterobacteriaceae]], where the family name does not stem from the genus ''[[Enterobacter]]'' + "i" (sic.) + "[[Bacterial taxonomy|aceae]]", but from "enterobacterium" + "aceae" (enterobacterium being not a genus, but an alternative trivial name to enteric bacterium).<ref name=Bergey2B /><ref name="pmid9103655">{{cite journal | vauthors = Euzéby JP | title = List of Bacterial Names with Standing in Nomenclature: a folder available on the Internet | journal = International Journal of Systematic Bacteriology | volume = 47 | issue = 2 | pages = 590–2 | date = April 1997 | pmid = 9103655 | doi = 10.1099/00207713-47-2-590 | doi-access = free }}</ref><ref>{{cite journal |title=Conservation of the family name Enterobacteriaceae, of the name of the type genus, and designation of the type species |journal=International Bulletin of Bacteriological Nomenclature and Taxonomy |date=1 January 1958 |volume=8 |issue=1 |pages=73–74 |doi=10.1099/0096266X-8-1-73 |doi-access=free }}</ref>

The original strain described by Escherich is believed to be lost, consequently a new type strain (neotype) was chosen as a representative: the neotype strain is U5/41<sup>T</sup>,<ref name="Meier-Kolthoff14">{{cite journal | vauthors = Meier-Kolthoff JP, Hahnke RL, Petersen J, Scheuner C, Michael V, Fiebig A, Rohde C, Rohde M, Fartmann B, Goodwin LA, Chertkov O, Reddy T, Pati A, Ivanova NN, Markowitz V, Kyrpides NC, Woyke T, Göker M, Klenk HP | display-authors = 6 | title = Complete genome sequence of DSM 30083(T), the type strain (U5/41(T)) of ''Escherichia coli'', and a proposal for delineating subspecies in microbial taxonomy | journal = Standards in Genomic Sciences | volume = 9 | pages = 2 | year = 2013 | pmid = 25780495 | pmc = 4334874 | doi = 10.1186/1944-3277-9-2 | doi-access = free }}</ref> also known under the deposit names [[DSMZ|DSM 30083]],<ref>{{cite web|url=http://www.dsmz.de/catalogues/details/culture/DSM-30083.html|title=Details: DSM-30083|work=dsmz.de|access-date=10 January 2017}}</ref> [[American Type Culture Collection|ATCC 11775]],<ref>{{cite web|url=http://www.atcc.org/ATCCAdvancedCatalogSearch/ProductDetails/tabid/452/Default.aspx?ATCCNum=11775&Template=bacteria|title=Escherichia coli (Migula) Castellani and Chalmers ATCC 11775&tra|work=atcc.org|access-date=10 January 2017|archive-date=4 December 2012|archive-url=https://web.archive.org/web/20121204005421/http://www.atcc.org/ATCCAdvancedCatalogSearch/ProductDetails/tabid/452/Default.aspx?ATCCNum=11775&Template=bacteria|url-status=dead}}</ref> and NCTC 9001,<ref>{{cite web|url=https://lpsn.dsmz.de/genus/escherichia|title=Escherichia|publisher=LPSN|access-date=6 February 2011}}</ref> which is pathogenic to chickens and has an O1:K1:H7 [[serotype]].<ref>{{cite web|url=http://www.jcm.riken.go.jp/cgi-bin/jcm/jcm_number?JCM=1649 |title=Escherichia coli (Migula 1895) Castellani and Chalmers 1919 |work=JCM Catalogue }}</ref> However, in most studies, either [[O157:H7]], K-12 MG1655, or K-12 W3110 were used as a representative ''E. coli''. The genome of the type strain has only lately (2013) been sequenced.<ref name="Meier-Kolthoff14"/>

===Phylogeny of ''E. coli'' strains===
{{Update|section|inaccurate=yes|reason=Cladogram uses an [[WP:OR|OR]] extension of Sims & Kim 2011, which is outdated anyways and should be replaced by Meier-Kolthoff et al. 2014 (fig 6).|talk=Phylogeny|date=January 2021}}
Many strains belonging to this species have been isolated and characterised. In addition to serotype (''vide supra''), they can be classified according to their [[phylogeny]], i.e. the inferred evolutionary history, as shown below where the species is divided into six groups as of 2014.<ref name="comparison02">{{cite journal | vauthors = Sims GE, Kim SH | title = Whole-genome phylogeny of ''Escherichia coli/Shigella'' group by feature frequency profiles (FFPs) | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 108 | issue = 20 | pages = 8329–34 | date = May 2011 | pmid = 21536867 | pmc = 3100984 | doi = 10.1073/pnas.1105168108 | bibcode = 2011PNAS..108.8329S | doi-access = free }}</ref><ref name="pmid21713444">{{cite journal | vauthors = Brzuszkiewicz E, Thürmer A, Schuldes J, Leimbach A, Liesegang H, Meyer FD, Boelter J, Petersen H, Gottschalk G, Daniel R | display-authors = 6 | title = Genome sequence analyses of two isolates from the recent ''Escherichia coli'' outbreak in Germany reveal the emergence of a new pathotype: Entero-Aggregative-Haemorrhagic ''Escherichia coli'' (EAHEC) | journal = Archives of Microbiology | volume = 193 | issue = 12 | pages = 883–91 | date = December 2011 | pmid = 21713444 | pmc = 3219860 | doi = 10.1007/s00203-011-0725-6 | bibcode = 2011ArMic.193..883B }}</ref> Particularly the use of [[Whole genome sequencing|whole genome sequences]] yields highly supported phylogenies.<ref name="Meier-Kolthoff14" /> The [[phylogroup]] structure remains robust to newer methods and sequences, which sometimes adds newer groups, giving 8 or 14 as of 2023.<ref>{{cite journal | vauthors = Koh XP, Shen Z, Woo CF, Yu Y, Lun HI, Cheung SW, Kwan JK, Lau SC | display-authors = 6 | title = Genetic and Ecological Diversity of ''Escherichia coli'' and Cryptic ''Escherichia'' Clades in Subtropical Aquatic Environments | journal = Frontiers in Microbiology | volume = 13 | pages = 811755 | date = 2022 | pmid = 35250929 | pmc = 8891540 | doi = 10.3389/fmicb.2022.811755 | doi-access = free }}</ref><ref>{{cite journal | vauthors = Abram K, Udaondo Z, Bleker C, Wanchai V, Wassenaar TM, Robeson MS, Ussery DW | title = Mash-based analyses of Escherichia coli genomes reveal 14 distinct phylogroups | journal = Communications Biology | volume = 4 | issue = 1 | pages = 117 | date = January 2021 | pmid = 33500552 | pmc = 7838162 | doi = 10.1038/s42003-020-01626-5 }}</ref>

The link between phylogenetic distance ("relatedness") and pathology is small,<ref name="Meier-Kolthoff14" /> ''e.g.'' the [[O157:H7]] serotype strains, which form a [[clade]] ("an exclusive group")—group E below—are all enterohaemorragic strains (EHEC), but not all EHEC strains are closely related. In fact, four different species of ''Shigella'' are nested among ''E. coli'' strains (''vide supra''), while ''[[Escherichia albertii|E. albertii]]'' and ''[[Escherichia fergusonii|E. fergusonii]]'' are outside this group. Indeed, all ''Shigella'' species were placed within a single subspecies of ''E. coli'' in a phylogenomic study that included the type strain.<ref name="Meier-Kolthoff14" /> All commonly used [[Escherichia coli (molecular biology)|research strains]] of ''E. coli'' belong to group A and are derived mainly from Clifton's K-12 strain (λ<sup>+</sup> F<sup>+</sup>; O16) and to a lesser degree from [[Félix d'Herelle|d'Herelle]]'s "[[Bacillus coli]]" strain (B strain; O7).

There have been multiple proposals to revise the taxonomy to match phylogeny.<ref name="Meier-Kolthoff14" /> However, all these proposals need to face the fact that ''Shigella'' remains a widely used name in medicine and find ways to reduce any confusion that can stem from renaming.<ref>{{cite journal |vauthors = Cobo-Simón M, Hart R, Ochman H |title = Escherichia Coli: What Is and Which Are? |journal = Molecular Biology and Evolution |volume = 40 |issue = 1 |pages = msac273 |date = January 2023 |pmid = 36585846 |pmc = 9830988 |doi = 10.1093/molbev/msac273 }}</ref>

{{clade|style=font-size:80%;line-height:80%
 |1=''[[Salmonella enterica]]''
 |2={{clade
  |1=[[Escherichia albertii|''E. albertii'']]
  |2={{clade
   |1=[[Escherichia fergusonii|''E. fergusonii'']]
   |2={{clade
     |1={{clade
      |label1=Group&nbsp;B2
      |1={{clade
       |1=[[E. coli SE15|''E. coli'' SE15]] (O150:H5. Commensal)
       |2=[[E. coli E2348/69|''E. coli'' E2348/69]] (O127:H6. Enteropathogenic)
      }}
     |2={{clade
      |1=[[E. coli ED1a|''E. coli'' ED1a]] O81 (Commensal)
      |2={{clade
       |1={{clade
        |1=[[E. coli CFT083|''E. coli'' CFT083]] (O6:K2:H1. UPEC)
        |2={{clade
         |1=[[E. coli APEC O1|''E. coli'' APEC O1]] (O1:K12:H7. APEC
         |2=[[E. coli UTI89|''E. coli'' UTI89]] O18:K1:H7. UPEC)
         |3=[[E. coli S88|''E. coli'' S88]]  (O45:K1. Extracellular pathogenic)
         }}
        }}
       |2={{clade
        |1=[[E. coli F11|''E. coli'' F11]]
        |2=[[E. coli 536|''E. coli'' 536]]
        }}
       }}
      }}
    |3={{clade
     |label1=Group&nbsp;D
     |1={{clade
      |1=[[E. coli UMN026|''E. coli'' UMN026]] (O17:K52:H18. Extracellular pathogenic)
      |2={{clade
       |1=[[E. coli SMS-3-5|''E. coli'']] (O19:H34. Extracellular pathogenic)
       |2=[[E. coli IAI39|''E. coli'']] (O7:K1. Extracellular pathogenic)
       }}
      }}
     |2={{clade
      |label1=Group&nbsp;E
      |1={{clade
       |1={{clade
        |1=[[E. coli EDL933|''E. coli'' EDL933]] (O157:H7  EHEC)
        |2=[[E. coli Sakai|''E. coli'' Sakai]] (O157:H7 EHEC)
        }}
       |2={{clade
        |1=[[E. coli EC4115|''E. coli'' EC4115]] (O157:H7 EHEC)
        |2=[[E. coli TW14359|''E. coli'' TW14359]] (O157:H7 EHEC)
        }}
       }}
      |2={{clade
       |label1=Shigella
       |1={{clade
        |1={{clade
         |1=''[[Shigella dysenteriae]]''
         |2={{clade
          |1=''[[Shigella sonnei]]''
          |2={{clade
           |1=''[[Shigella boydii]]''
           |2=''[[Shigella flexneri]]''
           }}
          }}
         }}
        }}
       |2={{clade
        |label1=Group&nbsp;B1
        |1={{clade
         |1={{clade
          |1=[[E. coli E24377A|''E. coli'' E24377A]] (O139:H28. Enterotoxigenic)
          |2={{clade
           |1={{clade
            |1={{clade
             |1=[[E. coli E110019|''E. coli'' E110019]] <!-- what is this? -->
             |2={{clade
              |1=[[E. coli 11368|''E. coli'' 11368]] (O26:H11. EHEC)
              |2=[[E. coli 11128|''E. coli'' 11128]] (O111:H-. EHEC)
              }}
             }}
            |2={{clade
             |1={{clade
              |1=[[E. coli IAI1|''E. coli'' IAI1]] O8 (Commensal)
              |2=[[E. coli 53638|''E. coli'' 53638]] (EIEC)
              }}
             |2={{clade
              |1=[[E. coli SE11|''E. coli'' SE11]] (O152:H28. Commensal)
              |2=[[E. coli B7A|''E. coli'' B7A]]
              }}
             }}
            }}
           |2={{clade
            |1={{clade
             |1={{clade
              |1=[[E. coli 12009|''E. coli'' 12009]] (O103:H2. EHEC)
              |2=[[E. coli O104:H4|''E. coli'' GOS1]] (O104:H4 EAHEC) German 2011 outbreak
              }}
             |2=[[E. coli E22|''E. coli'' E22]]
             }}
            |2={{clade
             |1=[[E. coli Oslo O103|''E. coli'' Oslo O103]]
             |2=[[E. coli 55989|''E. coli'' 55989]] (O128:H2. Enteroaggressive)
             }}
            }}
           }}
          }}
         }}
        |label2=Group&nbsp;A
        |2={{clade
         |1={{clade
          |1=[[E. coli HS|''E. coli'' HS]] (O9:H4. Commensal)
          |2=[[E. coli ATCC8739|''E. coli'' ATCC8739]] (O146. Crook's E.coli used in phage work in the 1950s)
          }}
         |2={{clade
          |label1=K-12 strain derivatives
          |1={{clade
           |1=[[E. coli K-12 W3110|''E. coli'' K-12 W3110]] (O16. λ<sup>−</sup> F<sup>−</sup> "wild type" molecular biology strain)
           |2=[[E. coli K-12 DH10b|''E. coli'' K-12 DH10b]] (O16. high electrocompetency molecular biology strain)
           |3=[[E. coli K-12 DH1|''E. coli'' K-12 DH1]]  (O16. high chemical competency molecular biology strain)
           |4=[[E. coli K-12 MG1655|''E. coli'' K-12 MG1655]] (O16. λ<sup>−</sup> F<sup>−</sup> "wild type" molecular biology strain)
           |5=[[E. coli BW2952|''E. coli'' BW2952]] (O16. competent molecular biology strain)
           }}
          |2={{clade
            |1=[[E. coli 101-1|''E. coli'' 101-1]] (O? H?. EAEC)
            |label2=B strain derivatives
            |2={{clade
             |1=[[E. coli B REL606|''E. coli'' B REL606]] (O7. high competency molecular biology strain)
             |2=[[E. coli BL21-DE3|''E. coli'' BL21-DE3]] (O7. expression molecular biology strain with T7 polymerase for pET system)
            }}
           }}
          }}
         }}
        }}
       }}
      }}
     }}
    }}
   }}
  }}
 }}
}}

==Genomics==
[[File:E.coli image.jpg|thumb|An image of ''E. coli'' using early [[electron microscopy]]]]
The first complete [[DNA sequence]] of an ''E. coli'' [[genome]] (laboratory strain K-12 derivative MG1655) was published in 1997. It is a circular [[DNA]] molecule 4.6&nbsp;million [[base pair]]s in length, containing 4288 annotated protein-coding genes (organized into 2584 [[operons]]), seven [[ribosomal RNA]] (rRNA) operons, and 86 [[transfer RNA]] (tRNA) genes. Despite having been the subject of intensive genetic analysis for about 40 years, many of these genes were previously unknown. The coding density was found to be very high, with a mean distance between genes of only 118 base pairs. The genome was observed to contain a significant number of [[transposon|transposable genetic elements]], repeat elements, cryptic [[prophages]], and [[bacteriophage]] remnants.<ref name="Blattner_1997">{{cite journal | vauthors = Blattner FR, Plunkett G, Bloch CA, Perna NT, Burland V, Riley M, Collado-Vides J, Glasner JD, Rode CK, Mayhew GF, Gregor J, Davis NW, Kirkpatrick HA, Goeden MA, Rose DJ, Mau B, Shao Y | display-authors = 6 | title = The complete genome sequence of ''Escherichia coli'' K-12 | journal = Science | volume = 277 | issue = 5331 | pages = 1453–62 | date = September 1997 | pmid = 9278503 | doi = 10.1126/science.277.5331.1453 | doi-access = free }}</ref> Most genes have only a single copy.<ref>{{Cite web |last=Philips |first=Ron Milo & Ron |title=» How many ribosomal RNA gene copies are in the genome? |url=https://book.bionumbers.org/how-many-ribosomal-rna-gene-copies-are-in-the-genome/ |access-date=2024-06-20 |website=book.bionumbers.org |language=en}}</ref>

More than three hundred complete genomic sequences of ''Escherichia'' and ''Shigella'' species are known. The genome sequence of the type strain of ''E. coli'' was added to this collection before 2014.<ref name="Meier-Kolthoff14" /> Comparison of these sequences shows a remarkable amount of diversity; only about 20% of each genome represents sequences present in every one of the isolates, while around 80% of each genome can vary among isolates.<ref name="comparison" /> Each individual genome contains between 4,000 and 5,500 genes, but the total number of different genes among all of the sequenced ''E. coli'' strains (the pangenome) exceeds 16,000. This very large variety of component genes has been interpreted to mean that two-thirds of the ''E. coli'' [[pangenome]] originated in other species and arrived through the process of horizontal gene transfer.<ref name="pmid21481756">{{cite journal | vauthors = Zhaxybayeva O, Doolittle WF | s2cid = 14499247 | title = Lateral gene transfer | journal = Current Biology | volume = 21 | issue = 7 | pages = R242–46 | date = April 2011 | pmid = 21481756 | doi = 10.1016/j.cub.2011.01.045 | doi-access = free | bibcode = 2011CBio...21.R242Z }}</ref>

== Gene nomenclature ==
{{see also|Gene nomenclature#Bacterial genetic nomenclature}}
Genes in ''E. coli'' are usually named in accordance with the uniform nomenclature proposed by Demerec et al.<ref>{{cite journal | vauthors = Demerec M, Adelberg EA, Clark AJ, Hartman PE | title = A proposal for a uniform nomenclature in bacterial genetics | journal = Genetics | volume = 54 | issue = 1 | pages = 61–76 | date = July 1966 | pmid = 5961488 | pmc = 1211113 | doi = 10.1093/genetics/54.1.61 }}</ref> Gene names are 3-letter acronyms that derive from their function (when known) or mutant phenotype and are italicized. When multiple genes have the same acronym, the different genes are designated by a capital later that follows the acronym and is also italicized. For instance, ''recA'' is named after its role in [[homologous recombination]] plus the letter A. Functionally related genes are named ''recB'', ''recC'', ''recD'' etc. The proteins are named by uppercase acronyms, e.g. [[RecA]], [[RecBCD|RecB]], etc. When the genome of ''E. coli'' strain K-12 substr. MG1655 was sequenced, all known or predicted protein-coding genes were numbered (more or less) in their order on the genome and abbreviated by b numbers, such as b2819 (= ''recD''). The "b" names were created after Fred <u>B</u>lattner, who led the genome sequence effort.<ref name="Blattner_1997" /> Another numbering system was introduced with the sequence of another ''E. coli'' K-12 substrain, W3110, which was sequenced in Japan and hence uses numbers starting by JW... (<u>J</u>apanese <u>W</u>3110), e.g. JW2787 (= ''recD'').<ref name="Hayashi">{{cite journal | vauthors = Hayashi K, Morooka N, Yamamoto Y, Fujita K, Isono K, Choi S, Ohtsubo E, Baba T, Wanner BL, Mori H, Horiuchi T | display-authors = 6 | title = Highly accurate genome sequences of ''Escherichia coli'' K-12 strains MG1655 and W3110 | journal = Molecular Systems Biology | volume = 2 | pages = 2006.0007 | year = 2006 | pmid = 16738553 | pmc = 1681481 | doi = 10.1038/msb4100049 }}</ref>  Hence, ''recD'' = b2819 = JW2787. Note, however, that most databases have their own numbering system, e.g. the EcoGene database<ref name="Ecogene">{{cite journal | vauthors = Zhou J, Rudd KE | title = EcoGene 3.0 | journal = Nucleic Acids Research | volume = 41 | issue = Database issue | pages = D613–24 | date = January 2013 | pmid = 23197660 | pmc = 3531124 | doi = 10.1093/nar/gks1235 }}</ref>  uses EG10826 for ''recD''. Finally, ECK numbers are specifically used for alleles in the MG1655 strain of ''E. coli'' K-12.<ref name="Ecogene" /> Complete lists of genes and their synonyms can be obtained from databases such as EcoGene or [[UniProt|Uniprot]].

==Proteomics==

===Proteome===
The genome sequence of ''E. coli'' predicts 4288 protein-coding genes, of which 38 percent initially had no attributed function. Comparison with five other sequenced microbes reveals ubiquitous as well as narrowly distributed gene families; many families of similar genes within ''E. coli'' are also evident. The largest family of paralogous proteins contains 80 ABC transporters. The genome as a whole is strikingly organized with respect to the local direction of replication; guanines, oligonucleotides possibly related to replication and recombination, and most genes are so oriented. The genome also contains insertion sequence (IS) elements, phage remnants, and many other patches of unusual composition indicating genome plasticity through horizontal transfer.<ref name = "Blattner_1997" />

Several studies have experimentally investigated the [[proteome]] of ''E. coli''. By 2006, 1,627 (38%) of the predicted proteins ([[open reading frames]], ORFs) had been identified experimentally.<ref name="HanLee">{{cite journal | vauthors = Han MJ, Lee SY | title = The ''Escherichia coli'' proteome: past, present, and future prospects | journal = Microbiology and Molecular Biology Reviews | volume = 70 | issue = 2 | pages = 362–439 | date = June 2006 | pmid = 16760308 | pmc = 1489533 | doi = 10.1128/MMBR.00036-05 }}</ref> Mateus et al. 2020 detected 2,586 proteins with at least 2 peptides (60% of all proteins).<ref>{{cite journal | vauthors = Mateus A, Hevler J, Bobonis J, Kurzawa N, Shah M, Mitosch K, Goemans CV, Helm D, Stein F, Typas A, Savitski MM | display-authors = 6 | title = The functional proteome landscape of ''Escherichia coli'' | journal = Nature | volume = 588 | issue = 7838 | pages = 473–478 | date = December 2020 | pmid = 33299184 | pmc = 7612278 | doi = 10.1038/s41586-020-3002-5 | bibcode = 2020Natur.588..473M }}</ref>

=== Post-translational modifications (PTMs) ===
Although much fewer bacterial proteins seem to have [[post-translational modification]]s (PTMs) compared to [[Eukaryote|eukaryotic]] proteins, a substantial number of proteins are modified in ''E. coli''. For instance, Potel et al. (2018) found 227 [[phosphoprotein]]s of which 173 were phosphorylated on [[histidine]]. The majority of phosphorylated [[amino acid]]s were [[serine]] (1,220 sites) with only 246 sites on [[histidine]] and 501 phosphorylated [[threonine]]s and 162 [[tyrosine]]s.<ref>{{cite journal | vauthors = Potel CM, Lin MH, Heck AJ, Lemeer S | title = Widespread bacterial protein histidine phosphorylation revealed by mass spectrometry-based proteomics | journal = Nature Methods | volume = 15 | issue = 3 | pages = 187–190 | date = March 2018 | pmid = 29377012 | doi = 10.1038/nmeth.4580 | hdl = 1874/362159 | s2cid = 3367416 | hdl-access = free }}</ref>

===Interactome===
The [[interactome]] of ''E. coli'' has been studied by [[affinity purification]] and [[mass spectrometry]] (AP/MS) and by analyzing the binary interactions among its proteins.

'''Protein complexes'''. A 2006 study purified 4,339 proteins from cultures of strain K-12 and found interacting partners for 2,667 proteins, many of which had unknown functions at the time.<ref name="pmid16606699">{{cite journal | vauthors = Arifuzzaman M, Maeda M, Itoh A, Nishikata K, Takita C, Saito R, Ara T, Nakahigashi K, Huang HC, Hirai A, Tsuzuki K, Nakamura S, Altaf-Ul-Amin M, Oshima T, Baba T, Yamamoto N, Kawamura T, Ioka-Nakamichi T, Kitagawa M, Tomita M, Kanaya S, Wada C, Mori H | display-authors = 6 | title = Large-scale identification of protein-protein interaction of ''Escherichia coli'' K-12 | journal = Genome Research | volume = 16 | issue = 5 | pages = 686–91 | date = May 2006 | pmid = 16606699 | pmc = 1457052 | doi = 10.1101/gr.4527806 }}</ref> A 2009 study found 5,993 interactions between proteins of the same ''E. coli'' strain, though these data showed little overlap with those of the 2006 publication.<ref name="pmid19402753">{{cite journal | vauthors = Hu P, Janga SC, Babu M, Díaz-Mejía JJ, Butland G, Yang W, Pogoutse O, Guo X, Phanse S, Wong P, Chandran S, Christopoulos C, Nazarians-Armavil A, Nasseri NK, Musso G, Ali M, Nazemof N, Eroukova V, Golshani A, Paccanaro A, Greenblatt JF, Moreno-Hagelsieb G, Emili A | display-authors = 6 | title = Global functional atlas of ''Escherichia coli'' encompassing previously uncharacterized proteins | journal = PLOS Biology | volume = 7 | issue = 4 | pages = e96 | date = April 2009 | pmid = 19402753 | pmc = 2672614 | doi = 10.1371/journal.pbio.1000096 | veditors = Levchenko A | doi-access = free }}</ref>

'''Binary interactions'''. Rajagopala ''et al.'' (2014) have carried out systematic yeast two-hybrid screens with most ''E. coli'' proteins, and found a total of 2,234 protein-protein interactions.<ref name="Rajagopala2014">{{cite journal | vauthors = Rajagopala SV, Sikorski P, Kumar A, Mosca R, Vlasblom J, Arnold R, Franca-Koh J, Pakala SB, Phanse S, Ceol A, Häuser R, Siszler G, Wuchty S, Emili A, Babu M, Aloy P, Pieper R, Uetz P | display-authors = 6 | title = The binary protein-protein interaction landscape of ''Escherichia coli'' | journal = Nature Biotechnology | volume = 32 | issue = 3 | pages = 285–90 | date = March 2014 | pmid = 24561554 | pmc = 4123855 | doi = 10.1038/nbt.2831 }}</ref> This study also integrated genetic interactions and protein structures and mapped 458 interactions within 227 [[multiprotein complex|protein complexes]].

==Normal microbiota==
''E. coli'' belongs to a group of bacteria informally known as [[coliforms]] that are found in the gastrointestinal tract of [[warm-blooded animals]].<ref name=Bergey2B>{{cite book | vauthors = Brenner DJ, Krieg NR, Staley JT |series=Bergey's Manual of Systematic Bacteriology|volume=2B|title=The Gammaproteobacteria| veditors = Garrity GM  |publisher=Springer |location= New York |edition=2nd |isbn=978-0-387-24144-9 |page=1108 |url= https://www.springer.com/life+sciences/book/978-0-387-24144-9 |date=26 July 2005| orig-year =1984 (Williams & Wilkins) |id=British Library no. GBA561951 }}</ref> ''E. coli'' normally colonizes an infant's [[gastrointestinal tract]] within 40 hours of birth, arriving with food or water or from the individuals handling the child.  In the bowel, ''E. coli'' adheres to the [[mucus]] of the [[large intestine]]. It is the primary [[Facultative anaerobic organism|facultative anaerobe]] of the human gastrointestinal tract.<ref name=Todar>{{cite web |url=http://www.textbookofbacteriology.net/e.coli.html |title=Pathogenic ''E. coli'' |access-date=30 November 2007 | vauthors = Todar K |work=Online Textbook of Bacteriology |publisher=University of Wisconsin–Madison Department of Bacteriology}}</ref> ([[Facultative anaerobic organism|Facultative anaerobes]] are organisms that can grow in either the presence or absence of oxygen.) As long as these bacteria do not acquire [[bacteriophage|genetic elements]] encoding for [[virulence factor]]s, they remain benign [[Commensalism|commensals]].<ref name=Evans>{{cite web |url=http://www.gsbs.utmb.edu/microbook/ch025.htm |title=Escherichia Coli |access-date=2 December 2007 | vauthors = Evans Jr DJ, Evans DG |work=Medical Microbiology, 4th edition |publisher=The University of Texas Medical Branch at Galveston |archive-url = https://web.archive.org/web/20071102062813/http://www.gsbs.utmb.edu/microbook/ch025.htm <!-- Bot retrieved archive --> |archive-date = 2 November 2007}}</ref>

===Therapeutic use===
Due to the low cost and speed with which it can be grown and modified in laboratory settings, ''E. coli'' is a popular expression platform for the production of [[recombinant proteins]] used in therapeutics. One advantage to using ''E. coli'' over another expression platform is that ''E. coli'' naturally does not export many proteins into the [[periplasm]], making it easier to recover a protein of interest without cross-contamination.<ref>{{cite journal | vauthors = Guerrero Montero I, Dolata KM, Schlüter R, Malherbe G, Sievers S, Zühlke D, Sura T, Dave E, Riedel K, Robinson C | display-authors = 6 | title = Comparative proteome analysis in an ''Escherichia coli'' CyDisCo strain identifies stress responses related to protein production, oxidative stress and accumulation of misfolded protein | journal = Microbial Cell Factories | volume = 18 | issue = 1 | pages = 19 | date = January 2019 | pmid = 30696436 | pmc = 6350376 | doi = 10.1186/s12934-019-1071-7 | doi-access = free }}</ref> The ''E. coli'' K-12 strains and their derivatives (DH1, DH5α, MG1655, RV308 and W3110) are the strains most widely used by the biotechnology industry.<ref>{{cite journal | vauthors = Selas Castiñeiras T, Williams SG, Hitchcock AG, Smith DC | title = ''E. coli'' strain engineering for the production of advanced biopharmaceutical products | journal = FEMS Microbiology Letters | volume = 365 | issue = 15 | date = August 2018 | pmid = 29982628 | doi = 10.1093/femsle/fny162 | s2cid = 51602230 | doi-access = free }}</ref> Nonpathogenic ''E. coli'' strain Nissle 1917 (EcN), (Mutaflor) and ''E. coli'' O83:K24:H31 (Colinfant)<ref>{{cite journal | vauthors = Wassenaar TM | title = ''E. coli'' | journal = European Journal of Microbiology & Immunology | volume = 6 | issue = 3 | pages = 147–61 | date = September 2016 | pmid = 27766164 | pmc = 5063008 | doi = 10.1556/1886.2016.00029 }}</ref><ref>{{cite journal | vauthors = Lodinová-Zádníková R, Cukrowska B, Tlaskalova-Hogenova H | s2cid = 19686481 | title = Oral administration of probiotic ''Escherichia coli'' after birth reduces frequency of allergies and repeated infections later in life (after 10 and 20 years) | journal = International Archives of Allergy and Immunology | volume = 131 | issue = 3 | pages = 209–11 | date = July 2003 | pmid = 12876412 | doi = 10.1159/000071488 }}</ref>) are used as [[probiotic]] agents in medicine, mainly for the treatment of various [[gastrointestinal disease]]s,<ref name="pmid15292145">{{cite journal | vauthors = Grozdanov L, Raasch C, Schulze J, Sonnenborn U, Gottschalk G, Hacker J, Dobrindt U | title = Analysis of the genome structure of the nonpathogenic probiotic ''Escherichia coli'' strain Nissle 1917 | journal = Journal of Bacteriology | volume = 186 | issue = 16 | pages = 5432–41 | date = August 2004 | pmid = 15292145 | pmc = 490877 | doi = 10.1128/JB.186.16.5432-5441.2004 }}</ref> including [[inflammatory bowel disease]].<ref name="pmid15867585">{{cite journal | vauthors = Kamada N, Inoue N, Hisamatsu T, Okamoto S, Matsuoka K, Sato T, Chinen H, Hong KS, Yamada T, Suzuki Y, Suzuki T, Watanabe N, Tsuchimoto K, Hibi T | s2cid = 23386584 | display-authors = 6 | title = Nonpathogenic ''Escherichia coli'' strain Nissle1917 prevents murine acute and chronic colitis | journal = Inflammatory Bowel Diseases | volume = 11 | issue = 5 | pages = 455–63 | date = May 2005 | pmid = 15867585 | doi = 10.1097/01.MIB.0000158158.55955.de }}</ref> It is thought that the EcN strain might impede the growth of opportunistic pathogens, including ''[[Salmonella]]'' and other [[Coliform bacteria|coliform]] enteropathogens, through the production of [[microcin]] proteins the production of [[siderophore]]s.<ref>{{cite journal | vauthors = Charbonneau MR, Isabella VM, Li N, Kurtz CB | title = Developing a new class of engineered live bacterial therapeutics to treat human diseases | journal = Nature Communications | volume = 11 | issue = 1 | pages = 1738 | date = April 2020 | pmid = 32269218 | pmc = 7142098 | doi = 10.1038/s41467-020-15508-1 | bibcode = 2020NatCo..11.1738C }}</ref>

==Role in disease==
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Most ''E. coli'' strains do not cause disease, naturally living in the gut,<ref>{{cite web|url=http://www.mayoclinic.org/diseases-conditions/e-coli/basics/definition/con-20032105|title=E. coli|work=Mayo Clinic|access-date=10 January 2017}}</ref> but virulent strains can cause [[gastroenteritis]], [[Uropathogenic Escherichia coli|urinary tract infections]], [[Meningitis#Bacterial|neonatal meningitis]], hemorrhagic colitis, and [[Crohn's disease]].<ref name="Baumgart_2007">{{cite journal |vauthors=Baumgart M, Dogan B, Rishniw M, Weitzman G, Bosworth B, Yantiss R, Orsi RH, Wiedmann M, McDonough P, Kim SG, Berg D, Schukken Y, Scherl E, Simpson KW |date=September 2007 |title=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 |journal=The ISME Journal |volume=1 |issue=5 |pages=403–18 |bibcode=2007ISMEJ...1..403B |doi=10.1038/ismej.2007.52 |pmid=18043660 |doi-access=free}}</ref> Common signs and symptoms include severe abdominal cramps, diarrhea, hemorrhagic colitis, vomiting, and sometimes fever. In rarer cases, virulent strains are also responsible for bowel necrosis (tissue death) and perforation without progressing to [[hemolytic-uremic syndrome]], [[peritonitis]], [[mastitis]], [[sepsis]], and gram-negative [[pneumonia]]. Very young children are more susceptible to develop severe illness, such as hemolytic uremic syndrome; however, healthy individuals of all ages are at risk to the severe consequences that may arise as a result of being infected with ''E. coli''.<ref name="Todar" /><ref>{{cite journal |vauthors = Lim JY, Yoon J, Hovde CJ |title = A brief overview of ''Escherichia coli'' O157:H7 and its plasmid O157 |journal = Journal of Microbiology and Biotechnology |volume = 20 |issue = 1 |pages = 5–14 |date = January 2010 |pmid = 20134227 |pmc = 3645889 |doi = 10.4014/jmb.0908.08007 }}</ref><ref name="who.int">{{cite web |url=https://www.who.int/mediacentre/factsheets/fs125/en/|title=E. coli |date = 7 February 2018 |work = World Health Organization }}</ref><ref name="cdc.gov">{{cite web |url=https://www.cdc.gov/features/ecoliinfection/ |archive-url = https://web.archive.org/web/20140201082843/https://www.cdc.gov/features/ecoliinfection/ |archive-date = 1 February 2014 |work = U.S. Centers for Disease Control and Prevention |title=E. coli Infection|date=2018-06-15}}</ref>

Some strains of ''E. coli'', for example O157:H7, can produce [[Shiga toxin]]. The Shiga toxin causes inflammatory responses in target cells of the gut, leaving behind lesions which result in the bloody diarrhea that is a symptom of a [[Shigatoxigenic and verotoxigenic Escherichia coli|Shiga toxin-producing ''E. coli'']] (STEC) infection. This toxin further causes premature destruction of the red blood cells, which then clog the body's filtering system, the kidneys, in some rare cases (usually in children and the elderly) causing [[hemolytic-uremic syndrome]] (HUS), which may lead to kidney failure and even death. Signs of hemolytic uremic syndrome include decreased frequency of urination, lethargy, and paleness of cheeks and inside the lower eyelids. In 25% of HUS patients, complications of nervous system occur, which in turn causes [[stroke]]s.  In addition, this strain causes the buildup of fluid (since the kidneys do not work), leading to [[edema]] around the lungs, legs, and arms.  This increase in fluid buildup especially around the lungs impedes the functioning of the heart, causing an increase in blood pressure.<ref>{{cite web |title = Hemolytic uremic syndrome (HUS) |url=http://www.mayoclinic.com/health/hemolytic-uremic-syndrome/DS00876 |work = Mayo Clinic }}</ref><ref name="who.int"/><ref name="cdc.gov"/>

[[Pathogenic Escherichia coli#Urinary tract infection|Uropathogenic ''E. coli'' (UPEC)]] is one of the main causes of [[urinary tract infection]]s.<ref name=pre-eminent>{{cite web|title=Uropathogenic Escherichia coli: The Pre-Eminent Urinary Tract Infection Pathogen|url=https://www.novapublishers.com/catalog/product_info.php?products_id=25500&osCsid=3712df5600f98259a8bdc1d9baf202e9|publisher=Nova publishers|access-date=27 November 2013|archive-url=https://web.archive.org/web/20131202232432/https://www.novapublishers.com/catalog/product_info.php?products_id=25500&osCsid=3712df5600f98259a8bdc1d9baf202e9|archive-date=2 December 2013|url-status=dead}}</ref> It is part of the normal microbiota in the gut and can be introduced in many ways. In particular for females, the direction of wiping after defecation (wiping back to front) can lead to fecal contamination of the urogenital orifices. Anal intercourse can also introduce this bacterium into the male urethra, and in switching from anal to vaginal intercourse, the male can also introduce UPEC to the female urogenital system.

[[Enterotoxigenic Escherichia coli|Enterotoxigenic ''E. coli'']] (ETEC) is the most common cause of [[traveler's diarrhea]], with as many as 840&nbsp;million cases worldwide in developing countries each year. The bacteria, typically transmitted through contaminated food or drinking water, adheres to the [[Intestinal epithelium|intestinal lining]], where it secretes either of two types of [[enterotoxins]], leading to watery diarrhea. The rate and severity of infections are higher among children under the age of five, including as many as 380,000 deaths annually.<ref name=Croxen2013>{{cite journal |vauthors = Croxen MA, Law RJ, Scholz R, Keeney KM, Wlodarska M, Finlay BB |title = Recent advances in understanding enteric pathogenic Escherichia coli |journal = Clinical Microbiology Reviews |volume = 26 |issue = 4 |pages = 822–80 |date = October 2013 |pmid = 24092857 |pmc = 3811233 |doi = 10.1128/CMR.00022-13 }}</ref>

In May 2011, one ''E. coli'' strain, [[E. coli O104:H4|O104:H4]], was the subject of a [[2011 E. coli O104:H4 outbreak|bacterial outbreak]] that began in [[Germany]]. Certain strains of ''E. coli'' are a major cause of [[foodborne illness]]. The outbreak started when several people in Germany were infected with [[enterohemorrhagic|enterohemorrhagic ''E. coli'' (EHEC)]] bacteria, leading to hemolytic-uremic syndrome (HUS), a medical emergency that requires urgent treatment. The outbreak did not only concern Germany, but also 15 other countries, including regions in North America.<ref>{{cite web|url=http://www.euro.who.int/en/what-we-do/health-topics/emergencies/international-health-regulations/news/news/2011/07/outbreaks-of-e.-coli-o104h4-infection-update-29 |url-status=dead |archive-url=https://web.archive.org/web/20110808155129/http://www.euro.who.int/en/what-we-do/health-topics/emergencies/international-health-regulations/news/news/2011/07/outbreaks-of-e.-coli-o104h4-infection-update-29 |archive-date=8 August 2011 |title=Outbreaks of ''E. coli'' O104:H4 infection: update 29 |date=7 July 2011 |publisher=WHO}}</ref> On 30 June 2011, the German ''Bundesinstitut für Risikobewertung (BfR)'' (Federal Institute for Risk Assessment, a federal institute within the German [[Federal Ministry of Food, Agriculture and Consumer Protection]]) announced that seeds of [[fenugreek]] from [[Egypt]] were likely the cause of the EHEC outbreak.<ref>{{cite web|url = http://www.bfr.bund.de/cm/343/samen_von_bockshornklee_mit_hoher_wahrscheinlichkeit_fuer_ehec_o104_h4_ausbruch_verantwortlich.pdf|title = Samen von Bockshornklee mit hoher Wahrscheinlichkeit für EHEC O104:H4 Ausbruch verantwortlich|trans-title=Fenugreek seeds with high probability for EHEC O104: H4 responsible outbreak|date = 30 June 2011|publisher = Bundesinstitut für Risikobewertung (BfR) (Federal Institute for Risk Assessment) |language = de|access-date = 17 July 2011}}</ref>

Some studies have demonstrated an absence of E. ''coli'' in the gut flora of subjects with the metabolic disorder [[Phenylketonuria]]. It is hypothesized that the absence of these normal bacterium impairs the production of the key vitamins B<sub>2</sub> (riboflavin) and K<sub>2</sub> (menaquinone) – vitamins which are implicated in many physiological roles in humans such as cellular and bone metabolism – and so contributes to the disorder.<ref>{{cite journal | vauthors = Al-Zyoud W, Nasereddin A, Aljarajrah H, Saket M | title = Escherichia coli in children with phenylketonuria | journal = New Microbes and New Infections | volume = 32 | pages = 100616 | date = November 2019 | pmid = 31763047 | pmc = 6859276 | doi = 10.1016/j.nmni.2019.100616 }}</ref>

'''Carbapenem-resistant ''E. coli''''' '''(carbapenemase-producing ''E. coli'')''' that are resistant to the [[carbapenem]] class of [[antibiotics]], considered the [[Drug of last resort|drugs of last resort]] for such infections. They are resistant because they produce an [[enzyme]] called a [[carbapenemase]] that disables the drug molecule.<ref>{{cite journal | vauthors = Ghaith DM, Mohamed ZK, Farahat MG, Aboulkasem Shahin W, Mohamed HO | title = Colonization of intestinal microbiota with carbapenemase-producing Enterobacteriaceae in paediatric intensive care units in Cairo, Egypt | journal = Arab Journal of Gastroenterology | volume = 20 | issue = 1 | pages = 19–22 | date = March 2019 | pmid = 30733176 | doi = 10.1016/j.ajg.2019.01.002 | s2cid = 73444389 | url = https://zenodo.org/record/6349599 }}</ref>

=== Incubation period ===
The time between ingesting the STEC bacteria and feeling sick is called the "incubation period". The incubation period is usually 3–4 days after the exposure, but may be as short as 1 day or as long as 10 days. The symptoms often begin slowly with mild belly pain or non-bloody diarrhea that worsens over several days. HUS, if it occurs, develops an average 7 days after the first symptoms, when the diarrhea is improving.<ref>{{Cite web|url=https://www.cdc.gov/ecoli/general/|title=General Information{{!}} ''E.coli'' |publisher=U.S. Centers for Disease Control and Prevention|access-date=19 April 2017}}</ref>

=== Diagnosis ===
Diagnosis of infectious diarrhea and identification of antimicrobial resistance is performed using a [[stool culture]] with subsequent [[antibiotic sensitivity testing]]. It requires a minimum of 2 days and maximum of several weeks to culture gastrointestinal pathogens.  The sensitivity (true positive) and specificity (true negative) rates for stool culture vary by pathogen, although a number of [[human pathogen]]s can not be [[microbiological culture|cultured]]. For culture-positive samples, antimicrobial resistance testing takes an additional 12–24 hours to perform.

Current [[point of care]] [[molecular diagnostic]] tests can identify ''E. coli'' and antimicrobial resistance in the identified strains much faster than culture and sensitivity testing. Microarray-based platforms can identify specific pathogenic strains of ''E. coli'' and ''E. coli''-specific AMR genes in two hours or less with high sensitivity and specificity, but the size of the test panel (i.e., total pathogens and antimicrobial resistance genes) is limited. Newer [[Metagenomics#Infectious disease diagnosis|metagenomics-based infectious disease diagnostic]] platforms are currently being developed to overcome the various limitations of culture and all currently available molecular diagnostic technologies.

===Treatment===
The mainstay of treatment is the assessment of [[dehydration]] and replacement of fluid and electrolytes. Administration of [[antibiotics]] has been shown to shorten the course of illness and duration of excretion of enterotoxigenic ''E. coli'' (ETEC) in adults in endemic areas and in traveller's diarrhea, though the rate of resistance to commonly used antibiotics is increasing and they are generally not recommended.<ref>{{Cite web|url=https://www.cdc.gov/ecoli/etec.html|title=Enterotoxigenic E. coli (ETEC)|last=US Centers for Disease Control and Prevention|access-date=21 July 2016}}</ref> The antibiotic used depends upon susceptibility patterns in the particular geographical region. Currently, the antibiotics of choice are [[fluoroquinolone]]s or [[azithromycin]], with an emerging role for [[rifaximin]]. Rifaximin, a semisynthetic rifamycin derivative, is an effective and well-tolerated antibacterial for the management of adults with non-invasive traveller's diarrhea. Rifaximin was significantly more effective than placebo and no less effective than [[ciprofloxacin]] in reducing the duration of diarrhea. While rifaximin is effective in patients with ''E. coli''-predominant traveller's diarrhea, it appears ineffective in patients infected with inflammatory or invasive [[enteropathogen]]s.<ref>{{cite journal |vauthors = Al-Abri SS, Beeching NJ, Nye FJ |title = Traveller's diarrhoea |journal = The Lancet. Infectious Diseases |volume = 5 |issue = 6 |pages = 349–60 |date = June 2005 |pmid = 15919621 |doi = 10.1016/S1473-3099(05)70139-0 }}</ref>

===Prevention===
ETEC is the type of ''E. coli'' that most vaccine development efforts are focused on. [[Antibodies]] against the LT and major CFs of ETEC provide protection against LT-producing, ETEC-expressing [[homology (biology)|homologous]] CFs. Oral inactivated vaccines consisting of toxin antigen and whole cells, i.e. the licensed recombinant cholera B subunit (rCTB)-WC cholera vaccine Dukoral, have been developed. There are currently no licensed vaccines for ETEC, though several are in various stages of development.<ref>{{cite journal | vauthors = Bourgeois AL, Wierzba TF, Walker RI | title = Status of vaccine research and development for enterotoxigenic Escherichia coli | journal = Vaccine | volume = 34 | issue = 26 | pages = 2880–86 | date = June 2016 | pmid = 26988259 | doi = 10.1016/j.vaccine.2016.02.076 | doi-access = free }}</ref> In different trials, the rCTB-WC cholera vaccine provided high (85–100%) short-term protection. An oral ETEC vaccine candidate consisting of rCTB and formalin inactivated ''E. coli'' bacteria expressing major CFs has been shown in clinical trials to be safe, immunogenic, and effective against severe [[diarrhoea]] in American travelers but not against ETEC diarrhoea in young children in [[Egypt]]. A modified ETEC vaccine consisting of recombinant ''E. coli'' strains over-expressing the major CFs and a more LT-like hybrid toxoid called LCTBA, are undergoing clinical testing.<ref>{{cite journal | vauthors = Svennerholm AM | title = From cholera to enterotoxigenic Escherichia coli (ETEC) vaccine development | journal = The Indian Journal of Medical Research | volume = 133 | pages = 188–96 | date = February 2011 | issue = 2 | pmid = 21415493 | pmc = 3089050 }}</ref><ref name="Manson's tropical diseases">{{cite book |veditors = Farrar J, Hotez P, Junghanss T, Kang G, Lalloo D, White NJ |title=Manson's Tropical Diseases |date=2013 |publisher=Elsevier/Saunders |location=Oxford |isbn=978-0702053061 |edition=23rd }}</ref>

Other proven prevention methods for ''E. coli'' transmission include handwashing and improved sanitation and drinking water, as transmission occurs through fecal contamination of food and water supplies. Additionally, thoroughly cooking meat and avoiding consumption of raw, unpasteurized beverages, such as juices and milk are other proven methods for preventing ''E. coli''. Lastly, cross-contamination of utensils and work spaces should be avoided when preparing food.<ref>{{cite web |url=https://www.cdc.gov/ecoli/general/index.html |title=General Information- ''E.coli'' |publisher=[[Centers for Disease Control and Prevention]] |access-date=25 May 2017}}</ref>

==Model organism in life science research==
{{main|Escherichia coli in molecular biology}}
[[File:Escherichia-coli-bacterium(1).tif|thumb|300px|''Escherichia coli'' bacterium, 2021, Illustration by David S. Goodsell, RCSB Protein Data Bank<br>This painting shows a cross-section through an ''Escherichia coli'' cell. The characteristic two-membrane cell wall of gram-negative bacteria is shown in green, with many lipopolysaccharide chains extending from the surface and a network of cross-linked peptidoglycan strands between the membranes. The genome of the cell forms a loosely-defined "nucleoid", shown here in yellow, and interacts with many DNA-binding proteins, shown in tan and orange. Large soluble molecules, such as ribosomes (colored in reddish purple), mostly occupy the space around the nucleoid.]]

Because of its long history of laboratory culture and ease of manipulation, ''E. coli'' plays an important role in modern [[biological engineering]] and [[industrial microbiology]].<ref name="lee1996">{{cite journal | vauthors = Lee SY | title = High cell-density culture of ''Escherichia coli'' | journal = Trends in Biotechnology | volume = 14 | issue = 3 | pages = 98–105 | date = March 1996 | pmid = 8867291 | doi = 10.1016/0167-7799(96)80930-9 }}</ref> The work of [[Stanley Norman Cohen]] and [[Herbert Boyer]] in ''E. coli'', using [[plasmid]]s and [[restriction enzyme]]s to create [[recombinant DNA]], became a foundation of biotechnology.<ref name="birth">{{cite journal | vauthors = Russo E | s2cid = 4357773 | title = The birth of biotechnology | journal = Nature | volume = 421 | issue = 6921 | pages = 456–57 | date = January 2003 | pmid = 12540923 | doi = 10.1038/nj6921-456a | bibcode = 2003Natur.421..456R | doi-access = free }}</ref>

''E. coli'' is a very versatile host for the production of [[heterologous]] [[protein]]s,<ref name="Cornelis" /> and various [[Protein expression (biotechnology)|protein expression]] systems have been developed which allow the production of [[recombinant proteins]] in ''E. coli''. Researchers can introduce genes into the microbes using plasmids which permit high level expression of protein, and such protein may be mass-produced in [[industrial fermentation]] processes. One of the first useful applications of recombinant DNA technology was the manipulation of ''E. coli'' to produce human [[insulin]].<ref>{{cite web |url=http://www.littletree.com.au/dna.htm |title=Recombinant DNA Technology in the Synthesis of Human Insulin |access-date=30 November 2007 |vauthors = Tof I |year=1994 |publisher=Little Tree Pty. Ltd.}}</ref>

Many proteins previously thought difficult or impossible to be expressed in ''E. coli'' in folded form have been successfully expressed in ''E. coli''. For example, proteins with multiple disulphide bonds may be produced in the [[periplasmic space]] or in the cytoplasm of mutants rendered sufficiently oxidizing to allow disulphide-bonds to form,<ref name="pmid10570136">{{cite journal | vauthors = Bessette PH, Aslund F, Beckwith J, Georgiou G | title = Efficient folding of proteins with multiple disulfide bonds in the ''Escherichia coli'' cytoplasm | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 96 | issue = 24 | pages = 13703–08 | date = November 1999 | pmid = 10570136 | pmc = 24128 | doi = 10.1073/pnas.96.24.13703 | bibcode = 1999PNAS...9613703B | doi-access = free }}</ref> while proteins requiring [[post-translational modification]] such as [[glycosylation]] for stability or function have been expressed using the N-linked glycosylation system of ''[[Campylobacter jejuni]]'' engineered into ''E. coli''.<ref>{{cite journal | vauthors = Ihssen J, Kowarik M, Dilettoso S, Tanner C, Wacker M, Thöny-Meyer L | title = Production of glycoprotein vaccines in ''Escherichia coli'' | journal = Microbial Cell Factories | volume = 9 | issue = 61 | pages = 61 | date = August 2010 | pmid = 20701771 | pmc = 2927510 | doi = 10.1186/1475-2859-9-61 | doi-access = free }}</ref><ref>{{cite journal | vauthors = Wacker M, Linton D, Hitchen PG, Nita-Lazar M, Haslam SM, North SJ, Panico M, Morris HR, Dell A, Wren BW, Aebi M | display-authors = 6 | title = N-linked glycosylation in ''Campylobacter jejuni'' and its functional transfer into ''E. coli'' | journal = Science | volume = 298 | issue = 5599 | pages = 1790–93 | date = November 2002 | pmid = 12459590 | doi = 10.1126/science.298.5599.1790 | bibcode = 2002Sci...298.1790W }}</ref><ref>{{cite journal | vauthors = Huang CJ, Lin H, Yang X | s2cid = 15584320 | title = Industrial production of recombinant therapeutics in ''Escherichia coli'' and its recent advancements | journal = Journal of Industrial Microbiology & Biotechnology | volume = 39 | issue = 3 | pages = 383–99 | date = March 2012 | pmid = 22252444 | doi = 10.1007/s10295-011-1082-9 | doi-access = free }}</ref>

Modified ''E. coli'' cells have been used in [[vaccine]] development, [[bioremediation]], production of [[biofuels]],<ref>{{cite web | vauthors = Summers R | date = 24 April 2013 | url = https://www.newscientist.com/article/dn23431-bacteria-churn-out-first-ever-petrollike-biofuel.html | title = Bacteria churn out first ever petrol-like biofuel | work = New Scientist | access-date = 27 April 2013 }}</ref> lighting, and production of immobilised [[enzyme]]s.<ref name="Cornelis">{{cite journal | vauthors = Cornelis P | title = Expressing genes in different Escherichia coli compartments | journal = Current Opinion in Biotechnology | volume = 11 | issue = 5 | pages = 450–54 | date = October 2000 | pmid = 11024362 | doi = 10.1016/S0958-1669(00)00131-2 }}</ref><ref>{{cite news |url=http://news.discovery.com/tech/alternative-power-sources/bacteria-powered-light-bulb-is-electricity-free-130815.htm |title=Bacteria-Powered Light Bulb Is Electricity-Free |date=15 August 2013 |author=Halverson, Nic |access-date=22 October 2013 |archive-date=25 May 2016 |archive-url=https://web.archive.org/web/20160525132633/http://news.discovery.com/tech/alternative-power-sources/bacteria-powered-light-bulb-is-electricity-free-130815.htm |url-status=dead}}</ref>

Strain K-12 is a mutant form of ''E. coli'' that over-expresses the enzyme [[Alkaline phosphatase]] (ALP).<ref name=":1">{{Cite book|title=Fundamental Laboratory Approaches for Biochemistry and Biotechnology |vauthors = Ninfa AJ, Ballou DP |publisher=Wiley |year=2009 |isbn=978-0470087664|pages=230}}</ref> The mutation arises due to a defect in the gene that constantly codes for the enzyme. A gene that is producing a product without any inhibition is said to have [[Receptor (biochemistry)|constitutive activity]]. This particular mutant form is used to isolate and purify the aforementioned enzyme.<ref name=":1" />

Strain OP50 of ''Escherichia coli'' is used for maintenance of ''[[Caenorhabditis elegans]]'' cultures.

Strain JM109 is a mutant form of ''E. coli'' that is recA and endA deficient. The strain can be utilized for blue/white screening when the cells carry the fertility factor episome.<ref>{{cite journal |vauthors = Cui Y, Zhou P, Peng J, Peng M, Zhou Y, Lin Y, Liu L |title = Cloning, sequence analysis, and expression of cDNA coding for the major house dust mite allergen, Der f 1, in ''Escherichia coli'' |journal = Brazilian Journal of Medical and Biological Research = Revista Brasileira de Pesquisas Medicas e Biologicas | volume = 41 | issue = 5 | pages = 380–388 | date = May 2008 | pmid = 18545812 | doi = 10.1590/s0100-879x2008000500006 | doi-access = free }}</ref> Lack of recA decreases the possibility of unwanted restriction of the DNA of interest and lack of endA inhibit plasmid DNA decomposition. Thus, JM109 is useful for cloning and expression systems.

===Model organism===
[[File:Escherichia coli with phages.jpg|thumb| [[Scanning helium ion microscope|Helium ion microscopy]] image showing [[T4 phage]] infecting ''E. coli''. Some of the attached phage have contracted tails indicating that they have injected their DNA into the host. The bacterial cells are ~ 0.5 μm wide.<ref>{{cite journal | vauthors = Leppänen M, Sundberg LR, Laanto E, de Freitas Almeida GM, Papponen P, Maasilta IJ | title = Imaging Bacterial Colonies and Phage-Bacterium Interaction at Sub-Nanometer Resolution Using Helium-Ion Microscopy | journal = Advanced Biosystems | volume = 1 | issue = 8 | pages = e1700070 | date = August 2017 | pmid = 32646179 | doi = 10.1002/adbi.201700070 | s2cid = 90960276 | url = http://urn.fi/URN:NBN:fi:jyu-202006043941 }}</ref>]]''E. coli'' is frequently used as a model organism in [[microbiology]] studies. Cultivated strains (e.g. ''E. coli'' K12) are well-adapted to the laboratory environment, and, unlike [[wild-type]] strains, have lost their ability to thrive in the intestine. Many laboratory strains lose their ability to form [[biofilm]]s.<ref>{{cite journal | vauthors = Fux CA, Shirtliff M, Stoodley P, Costerton JW | title = Can laboratory reference strains mirror "real-world" pathogenesis? | journal = Trends in Microbiology | volume = 13 | issue = 2 | pages = 58–63 | date = February 2005 | pmid = 15680764 | doi = 10.1016/j.tim.2004.11.001 | s2cid = 8765887 | url = https://scholarworks.montana.edu/xmlui/handle/1/13365 }}</ref><ref>{{cite journal | vauthors = Vidal O, Longin R, Prigent-Combaret C, Dorel C, Hooreman M, Lejeune P | title = Isolation of an ''Escherichia coli'' K-12 mutant strain able to form biofilms on inert surfaces: involvement of a new ompR allele that increases curli expression | journal = Journal of Bacteriology | volume = 180 | issue = 9 | pages = 2442–49 | date = May 1998 | pmid = 9573197 | pmc = 107187 | doi =  10.1128/JB.180.9.2442-2449.1998}}</ref> These features protect wild-type strains from [[antibody|antibodies]] and other chemical attacks, but require a large expenditure of energy and material resources. ''E. coli'' is often used as a representative microorganism in the research of novel water treatment and sterilisation methods, including [[photocatalysis]]. By standard [[Bacteriological water analysis#Plate count|plate count methods]], following sequential dilutions, and growth on agar gel plates, the concentration of viable organisms or CFUs (Colony Forming Units), in a known volume of treated water can be evaluated, allowing the comparative assessment of materials performance.<ref>{{cite journal | vauthors = Hanaor D, Michelazzi M, Chenu J, Leonelli C, Sorrell CC | title = The effects of firing conditions on the properties of electrophoretically deposited titanium dioxide films on graphite substrates. | journal = Journal of the European Ceramic Society | date = December 2011 | volume = 31 | issue = 15 | pages = 2877–85 | doi = 10.1016/j.jeurceramsoc.2011.07.007 | arxiv = 1303.2757 | s2cid = 93406448 }}</ref>

In 1946, [[Joshua Lederberg]] and [[Edward Tatum]] first described the phenomenon known as [[bacterial conjugation]] using ''E. coli'' as a model bacterium,<ref>{{cite journal | vauthors = Lederberg J, Tatum EL | s2cid = 1826960 | title = Gene recombination in ''Escherichia coli'' | journal = Nature | volume = 158 | issue = 4016 | pages = 558 | date = October 1946 | pmid = 21001945 | doi = 10.1038/158558a0 | url = http://profiles.nlm.nih.gov/BB/G/A/S/Z/_/bbgasz.pdf | bibcode = 1946Natur.158..558L }} Source: [http://profiles.nlm.nih.gov/BB/G/A/S/Z/ National Library of Medicine – The Joshua Lederberg Papers]</ref> and it remains the primary model to study conjugation.<ref>{{cite book|title=Biological Activity of Crystal|pages=169}}</ref> ''E. coli'' was an integral part of the first experiments to understand [[bacteriophage|phage]] genetics,<ref>{{cite journal | vauthors = Susman M | title = The Cold Spring Harbor Phage Course (1945–1970): a 50th anniversary remembrance | journal = Genetics | volume = 139 | issue = 3 | pages = 1101–06 | date = March 1995 | doi = 10.1093/genetics/139.3.1101 | pmid = 7768426 | pmc = 1206443 | url = https://www.cshl.edu/History/phagecourse.html | archive-url = https://web.archive.org/web/20060916155323/https://www.cshl.edu/History/phagecourse.html | url-status = dead | archive-date = 16 September 2006 }}</ref> and early researchers, such as [[Seymour Benzer]], used ''E. coli'' and phage T4 to understand the topography of gene structure.<ref name="pmid16590840">{{cite journal | vauthors = Benzer S | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 47 | issue = 3 | pages = 403–15 | date = March 1961 | pmid = 16590840 | pmc = 221592 | doi = 10.1073/pnas.47.3.403 | bibcode = 1961PNAS...47..403B | title = On the Topography of the Genetic Fine Structure | doi-access = free }}</ref> Prior to Benzer's research, it was not known whether the gene was a linear structure, or if it had a branching pattern.<ref>{{cite web |title=Facts about ''E.Coli'' |url=http://eol.org/pages/972688/details |publisher=Encyclopedia of Life |access-date=27 November 2013}}</ref>

''E. coli'' was one of the first organisms to have its genome sequenced; the complete genome of ''E. coli'' K12 was published by ''Science'' in 1997.<ref name="Blattner_1997" />

==== MDS42 ====
From 2002 to 2010, a team at the Hungarian Academy of Science created a strain of ''Escherichia coli'' called MDS42, which is now sold by Scarab Genomics of Madison, WI under the name of "Clean Genome ''E. coli''",<ref>{{cite web |url=http://www.scarabgenomics.com/ |title=Scarab Genomics LLC. Company web site.}}</ref> where 15% of the genome of the parental strain (''E. coli'' K-12 MG1655) were removed to aid in molecular biology efficiency, removing [[IS elements]], [[pseudogene]]s and [[phages]], resulting in better maintenance of plasmid-encoded toxic genes, which are often inactivated by transposons.<ref>{{cite journal |vauthors = Umenhoffer K, Fehér T, Balikó G, Ayaydin F, Pósfai J, Blattner FR, Pósfai G |title = Reduced evolvability of ''Escherichia coli'' MDS42, an IS-less cellular chassis for molecular and synthetic biology applications | journal = Microbial Cell Factories | volume = 9 | pages = 38 | date = May 2010 | pmid = 20492662 | pmc = 2891674 | doi = 10.1186/1475-2859-9-38 | doi-access = free }}</ref><ref>{{cite journal | vauthors = Pósfai G, Plunkett G, Fehér T, Frisch D, Keil GM, Umenhoffer K, Kolisnychenko V, Stahl B, Sharma SS, de Arruda M, Burland V, Harcum SW, Blattner FR | s2cid = 43287314 | display-authors = 6 | title = Emergent properties of reduced-genome Escherichia coli | journal = Science | volume = 312 | issue = 5776 | pages = 1044–46 | date = May 2006 | pmid = 16645050 | doi = 10.1126/science.1126439 | bibcode = 2006Sci...312.1044P }}</ref><ref>{{cite journal | vauthors = Kolisnychenko V, Plunkett G, Herring CD, Fehér T, Pósfai J, Blattner FR, Pósfai G | title = Engineering a reduced Escherichia coli genome | journal = Genome Research | volume = 12 | issue = 4 | pages = 640–47 | date = April 2002 | pmid = 11932248 | pmc = 187512 | doi = 10.1101/gr.217202 }}</ref> Biochemistry and replication machinery were not altered.

By evaluating the possible combination of [[Nanotechnology|nanotechnologies]] with [[landscape ecology]], complex habitat landscapes can be generated with details at the nanoscale.<ref name="pmid17090676">{{cite journal | vauthors = Keymer JE, Galajda P, Muldoon C, Park S, Austin RH | title = Bacterial metapopulations in nanofabricated landscapes | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 103 | issue = 46 | pages = 17290–95 | date = November 2006 | pmid = 17090676 | pmc = 1635019 | doi = 10.1073/pnas.0607971103 | bibcode = 2006PNAS..10317290K | doi-access = free }}</ref> On such [[synthetic ecosystems]], evolutionary experiments with ''E. coli'' have been performed to study the spatial biophysics of adaptation in an [[island biogeography]] on-chip.

In other studies, non-pathogenic ''E. coli'' has been used as a model microorganism towards understanding the effects of simulated microgravity (on Earth) on the same.<ref>{{cite journal | vauthors = Tirumalai MR, Karouia F, Tran Q, Stepanov VG, Bruce RJ, Ott M, Pierson DL, Fox GE| title = The adaptation of ''Escherichia coli'' cells grown in simulated microgravity for an extended period is both phenotypic and genomic.| journal = npj Microgravity | volume =3 |issue= 15| date = May 2017 | page = 15| pmid = 28649637 | pmc = 5460176 | doi = 10.1038/s41526-017-0020-1}}</ref><ref>{{cite journal | vauthors = Tirumalai MR, Karouia F, Tran Q, Stepanov VG, Bruce RJ, Ott M, Pierson DL, Fox GE| title = Evaluation of acquired antibiotic resistance in ''Escherichia coli'' exposed to long-term low-shear modeled microgravity and background antibiotic exposure| journal = mBio | volume =10 |issue= e02637-18| date = January 2019 | pmid = 30647159 | pmc = 6336426  | doi = 10.1128/mBio.02637-18}}</ref>

== Uses in biological computing ==
Since 1961, scientists proposed the idea of genetic circuits used for computational tasks.  Collaboration between biologists and computing scientists has allowed designing digital logic gates on the metabolism of ''E. coli''. As [[Lac operon]] is a two-stage process, genetic regulation in the bacteria is used to realize computing functions. The process is controlled at the transcription stage of DNA into messenger RNA.<ref name="as">{{cite web |vauthors = Hayes B |title=Computing Comes to Life |url=https://www.americanscientist.org/article/computing-comes-to-life |website=American Scientist |access-date=28 November 2021 |date=6 February 2017}}</ref>

Studies are being performed attempting to program ''E. coli'' to solve complicated mathematics problems, such as the [[Hamiltonian path problem]].<ref>{{cite journal | vauthors = Baumgardner J, Acker K, Adefuye O, Crowley ST, Deloache W, Dickson JO, Heard L, Martens AT, Morton N, Ritter M, Shoecraft A, Treece J, Unzicker M, Valencia A, Waters M, Campbell AM, Heyer LJ, Poet JL, Eckdahl TT | display-authors = 6 | title = Solving a Hamiltonian Path Problem with a bacterial computer | journal = Journal of Biological Engineering | volume = 3 | pages = 11 | date = July 2009 | pmid = 19630940 | pmc = 2723075 | doi = 10.1186/1754-1611-3-11 | doi-access = free }}</ref>

A computer to control protein production of ''E. coli'' within [[yeast cell]]s has been developed.<ref>{{cite journal | vauthors = Milias-Argeitis A, Summers S, Stewart-Ornstein J, Zuleta I, Pincus D, El-Samad H, Khammash M, Lygeros J | display-authors = 6 | title = In silico feedback for in vivo regulation of a gene expression circuit | journal = Nature Biotechnology | volume = 29 | issue = 12 | pages = 1114–1116 | date = November 2011 | pmid = 22057053 | doi = 10.1038/nbt.2018 | pmc = 4565053 }}</ref> A method has also been developed to use bacteria to behave as an [[Liquid-crystal display|LCD screen]].<ref>{{cite web | vauthors = Sawyer E |title=Computer Controlled Yeast and an E. coli LCD Screen {{!}} Bio 2.0 {{!}} Learn Science at Scitable |url=https://www.nature.com/scitable/blog/bio2.0/computer_controlled_yeast_and_an/ |website=www.nature.com |access-date=28 November 2021 }}</ref><ref>{{cite journal | vauthors = Prindle A, Samayoa P, Razinkov I, Danino T, Tsimring LS, Hasty J | title = A sensing array of radically coupled genetic 'biopixels' | journal = Nature | volume = 481 | issue = 7379 | pages = 39–44 | date = December 2011 | pmid = 22178928 | doi = 10.1038/nature10722 | pmc = 3259005 }}</ref>

In July 2017, separate experiments with ''E. coli'' published on Nature showed the potential of using living cells for computing tasks and storing information.<ref>{{cite web | vauthors = Waltz E |title=Biocomputer and Memory Built Inside Living Bacteria |url=https://spectrum.ieee.org/biocomputer-and-memory-built-inside-living-bacteria |website=IEEE Spectrum |access-date=28 November 2021 |date=23 August 2017}}</ref> A team formed with collaborators of the [[The Biodesign Institute|Biodesign Institute]] at [[Arizona State University]] and Harvard's [[Wyss Institute for Biologically Inspired Engineering]] developed a biological computer inside ''E. coli'' that responded to a dozen inputs. The team called the computer "ribocomputer", as it was composed of [[RNA|ribonucleic acid]].<ref>{{cite web | vauthors = Waltz E |title=Complex Biological Computer Commands Living Cells |url=https://spectrum.ieee.org/biological-computer-commands-living-cells-to-light-up |website=IEEE Spectrum |access-date=28 November 2021 |date=26 July 2017}}</ref><ref>{{cite journal | vauthors = Green AA, Kim J, Ma D, Silver PA, Collins JJ, Yin P | title = Complex cellular logic computation using ribocomputing devices | journal = Nature | volume = 548 | issue = 7665 | pages = 117–121 | date = August 2017 | pmid = 28746304 | doi = 10.1038/nature23271 | pmc = 6078203 | bibcode = 2017Natur.548..117G | access-date =  }}</ref> Meanwhile, Harvard researchers probed that is possible to store information in bacteria after successfully archiving images and movies in the DNA of living ''E. coli'' cells.<ref>{{cite web | vauthors = Waltz E |title=Scientists Store Video Data in the DNA of Living Organisms |url=https://spectrum.ieee.org/scientists-store-video-data-in-the-dna-of-living-organisms |website=IEEE Spectrum |access-date=28 November 2021 |date=12 July 2017}}</ref><ref>{{cite journal | vauthors = Shipman SL, Nivala J, Macklis JD, Church GM | title = CRISPR-Cas encoding of a digital movie into the genomes of a population of living bacteria | journal = Nature | volume = 547 | issue = 7663 | pages = 345–349 | date = July 2017 | pmid = 28700573 | doi = 10.1038/nature23017 | pmc = 5842791 | bibcode = 2017Natur.547..345S | access-date =  }}</ref>  In 2021, a team led by biophysicist Sangram Bagh realized a study with ''E. coli'' to solve [[Maze|2 × 2 maze problems]] to probe the principle for [[distributed computing]] among cells.<ref>{{cite journal | vauthors = Sarkar K, Chakraborty S, Bonnerjee D, Bagh S | title = Distributed Computing with Engineered Bacteria and Its Application in Solving Chemically Generated 2 × 2 Maze Problems | journal = ACS Synthetic Biology | volume = 10 | issue = 10 | pages = 2456–2464 | date = October 2021 | pmid = 34543017 | doi = 10.1021/acssynbio.1c00279 | s2cid = 237583555 | access-date =  }}</ref><ref>{{cite web | vauthors = Roberts S |title=An ''E. coli'' biocomputer solves a maze by sharing the work |url=https://www.technologyreview.com/2021/11/09/1039107/e-coli-maze-solving-biocomputer/ |website=MIT Technology Review |access-date=27 November 2021|date=9 November 2021}}</ref>

==History==
In 1885, the German-Austrian pediatrician [[Theodor Escherich]] discovered this organism in the feces of healthy individuals. He called it ''Bacterium coli commune'' because it is found in the colon. Early classifications of [[prokaryote]]s placed these in a handful of genera based on their shape and motility (at that time [[Ernst Haeckel]]'s classification of bacteria in the kingdom [[Monera]] was in place).<ref name="Manson's tropical diseases"/><ref>{{cite book |vauthors = Haeckel E |year = 1867 |title = Generelle Morphologie der Organismen |publisher = Reimer, Berlin |isbn = 978-1-144-00186-3 }}</ref><ref>{{cite journal |vauthors = Escherich T |year = 1885 |title = Die Darmbakterien des Neugeborenen und Säuglinge |url = https://books.google.com/books?id=o1MXAAAAYAAJ&q=%22Die%20darmbakterien%20des%20neugeborenen%20und%20säuglings%22&pg=PA135 |journal = Fortschr. Med. |volume = 3 |pages = 515–22 }}</ref>

''Bacterium coli'' was the type species of the now invalid genus [[Bacterium (genus)|''Bacterium'']] when it was revealed that the former type species ("''Bacterium triloculare''") was missing.<ref name=status>{{cite journal | vauthors = Breed RS, Conn HJ | title = The Status of the Generic Term Bacterium Ehrenberg 1828 | journal = Journal of Bacteriology | volume = 31 | issue = 5 | pages = 517–18 | date = May 1936 | pmid = 16559906 | pmc = 543738 | doi =  10.1128/JB.31.5.517-518.1936}}</ref> Following a revision of ''Bacterium'', it was reclassified as ''Bacillus coli'' by Migula in 1895<ref>{{ cite book | author = Migula W | chapter= Bacteriaceae (Stabchenbacterien) |veditors=Engerl A, Prantl K | title =  Die Naturlichen Pfanzenfamilien, W. Engelmann, Leipzig, Teil I, Abteilung Ia | year = 1895 | pages = 20–30 }}</ref> and later reclassified in the newly created genus ''[[Escherichia]]'', [[List of bacterial genera named after personal names|named after]] its original discoverer, by [[Aldo Castellani]] and [[Albert John Chalmers]].<ref>{{cite book |vauthors=Castellani A, Chalmers AJ | title = Manual of Tropical Medicine |url=https://archive.org/details/manualoftropical00cast | edition = 3rd | publisher = Williams Wood and Co. | location = New York | year = 1919 }}</ref>

In 1996, an outbreak of ''E. coli'' food poisoning occurred in Wishaw, Scotland, killing 21 people.<ref>{{cite web |url=http://news.bbc.co.uk/1/hi/health/154107.stm |work = BBC News |title = Sheriff criticises ''E. Coli'' butcher|date=19 August 1998}}</ref><ref>{{Cite web |title=The butcher who lied |url=https://www.heraldscotland.com/news/12363329.the-butcher-who-lied/ |access-date=2021-10-15|website=HeraldScotland |date=20 August 1998 }}</ref> This death toll was exceeded in 2011, when the [[2011 Germany E. coli O104:H4 outbreak|2011 Germany ''E. coli'' O104:H4 outbreak]], linked to organic [[Fenugreek|fenugreek sprouts]], killed 53 people.

In 2024, an outbreak of ''E. coli'' food poisoning occurred across the U.S. was linked to [[Agriculture in the United States|U.S.-grown organic]] [[carrot|carrots]] causing one fatality and dozens of illnesses.<ref>{{cite news|url=https://www.ctvnews.ca/health/e-coli-outbreak-linked-to-organic-carrots-leaves-1-dead-and-dozens-sickened-across-the-u-s-1.7113486|title=E. coli outbreak linked to organic carrots leaves 1 dead and dozens sickened across the U.S.|publisher=[[CTV News]]/[[CNN]]|last=Mascarenhas|first=Lauren|date=November 17, 2024|access-date=November 17, 2024}}</ref>

== Uses ==
''E. coli'' has several practical uses besides its use as a vector for genetic experiments and processes. For example, ''E. coli'' can be used to generate synthetic propane and recombinant human growth hormone.<ref>{{cite journal | vauthors = Song H, Jiang J, Wang X, Zhang J | title = High purity recombinant human growth hormone (rhGH) expression in Escherichia coli under phoA promoter | journal = Bioengineered | volume = 8 | issue = 2 | pages = 147–153 | date = March 2017 | pmid = 27459425 | pmc = 5398570 | doi = 10.1080/21655979.2016.1212137 }}</ref><ref>{{cite journal | vauthors = Kallio P, Pásztor A, Thiel K, Akhtar MK, Jones PR | title = An engineered pathway for the biosynthesis of renewable propane | journal = Nature Communications | volume = 5 | issue = 1 | pages = 4731 | date = September 2014 | pmid = 25181600 | pmc = 4164768 | doi = 10.1038/ncomms5731 | bibcode = 2014NatCo...5.4731K }}</ref>

== See also ==
{{Div col|colwidth=20em}}
* [[BolA-like protein family]]
* [[Carbon monoxide-releasing molecules]]
* [[Contamination control]]
* [[Dam dcm strain]]
* [[Eijkman test]]
* [[Fecal coliform]]
* [[International Code of Nomenclature of Bacteria]]
* [[List of strains of Escherichia coli|List of strains of ''Escherichia coli'']]
* [[Mannan oligosaccharide-based nutritional supplements]]
* [[Overflow metabolism]]
* [[T4 rII system]]
{{Div col end}}

== References ==
{{Reflist}}

== External links ==
{{Wikispecies}}
{{Commons category|Escherichia coli}}
* [https://pdb101.rcsb.org/sci-art/goodsell-gallery/escherichia-coli-bacterium ''E. coli'' on Protein Data Bank]

{{Antidiarrheals, intestinal anti-inflammatory and anti-infective agents}}
{{Escherichia coli}}
{{Model Organisms}}
{{Gram-negative proteobacterial diseases}}
{{Taxonbar|from=Q25419}}
{{Authority control}}

[[Category:Escherichia coli| ]]
[[Category:Gut flora bacteria]]
[[Category:Tropical diseases]]
[[Category:Model organisms]]
[[Category:Bacteria described in 1919]]