Escherichia coli

File:Life cycle of Escherichia coli.png in E. coli]]

E. coli is a gram-negative, facultative anaerobe, nonsporulating coliform bacterium.{{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}} Cells are typically rod-shaped, and are about 2.0 μm long and 0.25–1.0 μm in diameter, with a cell volume of 0.6–0.7 μm³.{{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}}{{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 }}{{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 }}

E. coli stains gram-negative because its cell wall is composed of a thin peptidoglycan layer and an 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.

The flagella which allow the bacteria to swim have a peritrichous arrangement.{{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 }} It also attaches and effaces to the microvilli of the intestines via an adhesion molecule known as intimin.{{cite web | url=https://microbewiki.kenyon.edu/index.php/E._coli_O157_in_North_America | title=E. coli O157 in North America – microbewiki}}

E. coli can live on a wide variety of substrates and uses mixed acid fermentation in anaerobic conditions, producing lactate, succinate, ethanol, acetate, and carbon dioxide. Since many pathways in 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 methanogens or sulphate-reducing bacteria.{{cite book | title=Brock Biology of microorganisms|vauthors=Madigan MT, Martinko JM | year=2006| publisher=Pearson| isbn=978-0-13-196893-6| edition=11th}}

In addition, E. coli{{'}}s metabolism can be rewired to solely use CO₂ 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 carriers and supply the ATP required in anabolic pathways inside of these synthetic autotrophs.{{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 }}File:Ecoli_Metabolism.webp

E. coli has three native glycolytic pathways: EMPP, EDP, and OPPP. The EMPP employs ten enzymatic steps to yield two pyruvates, two 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.{{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 }}

When growing in the presence of a mixture of sugars, bacteria will often consume the sugars sequentially through a process known as 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.{{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 }}

Image:e.coli-colony-growth.gifOptimum growth of E. coli occurs at {{convert|37|C}}, but some laboratory strains can multiply at temperatures up to {{convert|49|C}}.{{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 }} E. coli grows in a variety of defined laboratory media, such as lysogeny broth, or any medium that contains glucose, ammonium phosphate monobasic, sodium chloride, magnesium sulfate, potassium phosphate dibasic, and water. Growth can be driven by aerobic or anaerobic respiration, using a large variety of redox pairs, including the oxidation of pyruvic acid, formic acid, hydrogen, and amino acids, and the reduction of substrates such as oxygen, nitrate, fumarate, dimethyl sulfoxide, and trimethylamine N-oxide.{{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 }} 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.{{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}}

{{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 chromosomal DNA. The D period refers to the stage between the conclusion of DNA replication and the end of cell division.{{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 }} 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.{{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 }}

The number of replication forks in fast growing E. coli typically follows 2n (n = 1, 2 or 3). This only happens if replication is initiated simultaneously from all origins of replications, and is referred to as synchronous replication. However, not all cells in a culture replicate synchronously. In this case cells do not have multiples of two replication forks. Replication initiation is then referred to being asynchronous.{{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 }} However, asynchrony can be caused by mutations to for instance DnaA or DnaA initiator-associating protein DiaA.{{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 }}

Although E. coli reproduces by 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.{{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 }} 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.{{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 }} Cellular aging is a general process, affecting prokaryotes and eukaryotes alike.

E. coli and related bacteria possess the ability to transfer DNA via bacterial conjugation or transduction, which allows genetic material to spread horizontally through an existing population. The process of transduction, which uses the bacterial virus called a bacteriophage,{{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 }} is where the spread of the gene encoding for the Shiga toxin from the Shigella bacteria to E. coli helped produce E. coli O157:H7, the Shiga toxin-producing strain of E. coli. One of the key envelope stress regulators is IgaA, a membrane-associated protein that inhibits activation of the Rcs phosphorelay system, thereby controlling expression of capsule synthesis and virulence-related genes.{{cite journal | vauthors = Rinken R, Thomas B, Wackernagel W | title = Evidence that recBC-dependent degradation of duplex DNA in Escherichia coli recD mutants involves DNA unwinding | journal = Journal of Bacteriology | volume = 174 | issue = 16 | pages = 5424–5429 | date = August 1992 | pmid = 1322885 | doi = 10.1128/jb.174.16.5424-5429.1992 }}

File:E.coli on growing on various agar media.jpg

E. coli encompasses an enormous population of bacteria that exhibit a very high degree of both genetic and phenotypic diversity. 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,{{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 }} 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.{{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 }}

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.{{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 }} Similarly, other strains of E. coli (e.g. the K-12 strain commonly used in recombinant DNA work) are sufficiently different that they would merit reclassification.

A strain is a subgroup within the species that has unique characteristics that distinguish it from other 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 pathogenic capacity, the ability to use a unique 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. 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.

{{main|Pathogenic Escherichia coli#Serotypes}}

File:Escherichia coli on agar.jpg

A common subdivision system of E. coli, but not based on evolutionary relatedness, is by serotype, which is based on major surface antigens (O antigen: part of lipopolysaccharide layer; H: flagellin; K antigen: capsule), e.g. O157:H7).{{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}} It is, however, common to cite only the serogroup, i.e. the O-antigen. At present, about 190 serogroups are known.{{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 }} The common laboratory strain has a mutation that prevents the formation of an O-antigen and is thus not typeable.

Like all lifeforms, new strains of E. coli evolve through the natural biological processes of mutation, gene duplication, and horizontal gene transfer; in particular, 18% of the genome of the laboratory strain MG1655 was horizontally acquired since the divergence from Salmonella.{{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 }} E. coli K-12 and E. coli B strains are the most frequently used varieties for laboratory purposes. Some strains develop traits that can be harmful to a host animal. These virulent strains typically cause a bout of diarrhea that is often self-limiting in healthy adults but is frequently lethal to children in the developing world.{{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 }} More virulent strains, such as O157:H7, cause serious illness or death in the elderly, the very young, or the immunocompromised.{{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 }}

The genera Escherichia and Salmonella diverged around 102 million years ago (credibility interval: 57–176 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.{{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 }} This was followed by a split of an Escherichia ancestor into five species (E. albertii, E. coli, E. fergusonii, E. hermannii, and E. vulneris). The last E. coli ancestor split between 20 and 30 million years ago.{{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 }}

The 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.{{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 }} For instance, E. coli typically do not have the ability to grow aerobically with citrate as a 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

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.{{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 }}

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.) + "aceae", but from "enterobacterium" + "aceae" (enterobacterium being not a genus, but an alternative trivial name to enteric bacterium).{{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 }}{{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 }}

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^T,{{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 }} also known under the deposit names DSM 30083,{{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}} ATCC 11775,{{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}} and NCTC 9001,{{cite web|url=https://lpsn.dsmz.de/genus/escherichia|title=Escherichia|publisher=LPSN|access-date=6 February 2011}} which is pathogenic to chickens and has an O1:K1:H7 serotype.{{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 }} 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.

{{Update|section|inaccurate=yes|reason=Cladogram uses an 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.{{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 }}{{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 }} Particularly the use of whole genome sequences yields highly supported phylogenies. The phylogroup structure remains robust to newer methods and sequences, which sometimes adds newer groups, giving 8 or 14 as of 2023.{{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 }}{{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 }}

The link between phylogenetic distance ("relatedness") and pathology is small, 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 E. albertii and 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. All commonly used research strains of E. coli belong to group A and are derived mainly from Clifton's K-12 strain (λ⁺ F⁺; O16) and to a lesser degree from d'Herelle's "Bacillus coli" strain (B strain; O7).

There have been multiple proposals to revise the taxonomy to match phylogeny. 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.{{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 }}

{{clade|style=font-size:80%;line-height:80%

|1=Salmonella enterica

|2={{clade

|1=E. albertii

|2={{clade

|1=E. fergusonii

|2={{clade

|1={{clade

|label1=Group B2

|1={{clade

|1=E. coli SE15 (O150:H5. Commensal)

|2=E. coli E2348/69 (O127:H6. Enteropathogenic)

}}

|2={{clade

|1=E. coli ED1a O81 (Commensal)

|2={{clade

|1={{clade

|1=E. coli CFT083 (O6:K2:H1. UPEC)

|2={{clade

|1=E. coli APEC O1 (O1:K12:H7. APEC

|2=E. coli UTI89 O18:K1:H7. UPEC)

|3=E. coli S88 (O45:K1. Extracellular pathogenic)

}}

}}

|2={{clade

|1=E. coli F11

|2=E. coli 536

}}

}}

}}

|3={{clade

|label1=Group D

|1={{clade

|1=E. coli UMN026 (O17:K52:H18. Extracellular pathogenic)

|2={{clade

|1=E. coli (O19:H34. Extracellular pathogenic)

|2=E. coli (O7:K1. Extracellular pathogenic)

}}

}}

|2={{clade

|label1=Group E

|1={{clade

|1={{clade

|1=E. coli EDL933 (O157:H7 EHEC)

|2=E. coli Sakai (O157:H7 EHEC)

}}

|2={{clade

|1=E. coli EC4115 (O157:H7 EHEC)

|2=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 B1

|1={{clade

|1={{clade

|1=E. coli E24377A (O139:H28. Enterotoxigenic)

|2={{clade

|1={{clade

|1={{clade

|1=E. coli E110019

|2={{clade

|1=E. coli 11368 (O26:H11. EHEC)

|2=E. coli 11128 (O111:H-. EHEC)

}}

}}

|2={{clade

|1={{clade

|1=E. coli IAI1 O8 (Commensal)

|2=E. coli 53638 (EIEC)

}}

|2={{clade

|1=E. coli SE11 (O152:H28. Commensal)

|2=E. coli B7A

}}

}}

}}

|2={{clade

|1={{clade

|1={{clade

|1=E. coli 12009 (O103:H2. EHEC)

|2=E. coli GOS1 (O104:H4 EAHEC) German 2011 outbreak

}}

|2=E. coli E22

}}

|2={{clade

|1=E. coli Oslo O103

|2=E. coli 55989 (O128:H2. Enteroaggressive)

}}

}}

}}

}}

}}

|label2=Group A

|2={{clade

|1={{clade

|1=E. coli HS (O9:H4. Commensal)

|2=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 (O16. λ⁻ F⁻ "wild type" molecular biology strain)

|2=E. coli K-12 DH10b (O16. high electrocompetency molecular biology strain)

|3=E. coli K-12 DH1 (O16. high chemical competency molecular biology strain)

|4=E. coli K-12 MG1655 (O16. λ⁻ F⁻ "wild type" molecular biology strain)

|5=E. coli BW2952 (O16. competent molecular biology strain)

}}

|2={{clade

|1=E. coli 101-1 (O? H?. EAEC)

|label2=B strain derivatives

|2={{clade

|1=E. coli B REL606 (O7. high competency molecular biology strain)

|2=E. coli BL21-DE3 (O7. expression molecular biology strain with T7 polymerase for pET system)

}}

}}

}}

}}

}}

}}

}}

}}

}}

}}

}}

}}

}}

File:E.coli image.jpg]]

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 million base pairs 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 transposable genetic elements, repeat elements, cryptic prophages, and bacteriophage remnants.{{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 }} Most genes have only a single copy.{{Cite web | vauthors = Milo R, Philips R |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}}

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. 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. 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.{{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 }}

{{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.{{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 }} 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, 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 Blattner, who led the genome sequence effort. 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... (Japanese W3110), e.g. JW2787 (= recD).{{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 }} Hence, recD = b2819 = JW2787. Note, however, that most databases have their own numbering system, e.g. the EcoGene database{{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 }} uses EG10826 for recD. Finally, ECK numbers are specifically used for alleles in the MG1655 strain of E. coli K-12. Complete lists of genes and their synonyms can be obtained from databases such as EcoGene or Uniprot.

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.

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.{{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 }} Mateus et al. 2020 detected 2,586 proteins with at least 2 peptides (60% of all proteins).{{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 }}

Although much fewer bacterial proteins seem to have post-translational modifications (PTMs) compared to eukaryotic proteins, a substantial number of proteins are modified in E. coli. For instance, Potel et al. (2018) found 227 phosphoproteins of which 173 were phosphorylated on histidine. The majority of phosphorylated amino acids were serine (1,220 sites) with only 246 sites on histidine and 501 phosphorylated threonines and 162 tyrosines.{{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 }}

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.{{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 }} 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.{{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 }}

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.{{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 }} This study also integrated genetic interactions and protein structures and mapped 458 interactions within 227 protein complexes.

E. coli belongs to a group of bacteria informally known as coliforms that are found in the gastrointestinal tract of warm-blooded animals.{{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 }} 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 anaerobe of the human gastrointestinal tract.{{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}} (Facultative anaerobes are organisms that can grow in either the presence or absence of oxygen.) As long as these bacteria do not acquire genetic elements encoding for virulence factors, they remain benign commensals.{{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 |archive-date = 2 November 2007}}

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.{{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 }} 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.{{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 }} Nonpathogenic E. coli strain Nissle 1917 (EcN), (Mutaflor) and E. coli O83:K24:H31 (Colinfant){{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 }}{{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 }}) are used as probiotic agents in medicine, mainly for the treatment of various gastrointestinal diseases,{{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 }} including inflammatory bowel disease.{{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 }} It is thought that the EcN strain might impede the growth of opportunistic pathogens, including Salmonella and other coliform enteropathogens, through the production of microcin proteins the production of siderophores.{{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 }}

{{main|Pathogenic Escherichia coli}}{{Infobox drug

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Most E. coli strains do not cause disease, naturally living in the gut,{{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}} but virulent strains can cause gastroenteritis, urinary tract infections, neonatal meningitis, hemorrhagic colitis, and Crohn's disease.{{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}} 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.{{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 }}{{cite web |url=https://www.who.int/mediacentre/factsheets/fs125/en/|title=E. coli |date = 7 February 2018 |work = World Health Organization }}{{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}}

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 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 strokes. 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.{{cite web |title = Hemolytic uremic syndrome (HUS) |url=http://www.mayoclinic.com/health/hemolytic-uremic-syndrome/DS00876 |work = Mayo Clinic }}

Uropathogenic E. coli (UPEC) is one of the main causes of urinary tract infections.{{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}} 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 E. coli (ETEC) is the most common cause of traveler's diarrhea, with as many as 840 million cases worldwide in developing countries each year. The bacteria, typically transmitted through contaminated food or drinking water, adheres to the 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.{{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 }}

In May 2011, one E. coli strain, O104:H4, was the subject of a 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 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.{{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}} 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.{{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}}

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 B₂ (riboflavin) and K₂ (menaquinone) – vitamins which are implicated in many physiological roles in humans such as cellular and bone metabolism – and so contributes to the disorder.{{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 }}

Carbapenem-resistant E. coli (carbapenemase-producing E. coli) that are resistant to the carbapenem class of antibiotics, considered the drugs of last resort for such infections. They are resistant because they produce an enzyme called a carbapenemase that disables the drug molecule.{{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 }}

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.{{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}}

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 pathogens can not be 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-based infectious disease diagnostic platforms are currently being developed to overcome the various limitations of culture and all currently available molecular diagnostic technologies.

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.{{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}} The antibiotic used depends upon susceptibility patterns in the particular geographical region. Currently, the antibiotics of choice are fluoroquinolones 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 enteropathogens.{{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 }}

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 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.{{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 }} 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.{{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 }}{{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 }}

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.{{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}}

{{main|Escherichia coli in molecular biology}}

File:Escherichia-coli-bacterium(1).tif

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.{{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 }} The work of Stanley Norman Cohen and Herbert Boyer in E. coli, using plasmids and restriction enzymes to create recombinant DNA, became a foundation of biotechnology.{{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 }}

E. coli is a very versatile host for the production of heterologous proteins, and various 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.{{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.}}

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,{{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 }} 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.{{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 }}{{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 }}{{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 }}

Modified E. coli cells have been used in vaccine development, bioremediation, production of biofuels,{{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 }} lighting, and production of immobilised enzymes.{{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 }}{{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}}

Strain K-12 is a mutant form of E. coli that over-expresses the enzyme Alkaline phosphatase (ALP).{{Cite book|title=Fundamental Laboratory Approaches for Biochemistry and Biotechnology |vauthors = Ninfa AJ, Ballou DP |publisher=Wiley |year=2009 |isbn=978-0470087664|pages=230}} 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 constitutive activity. This particular mutant form is used to isolate and purify the aforementioned enzyme.

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.{{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 }} 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.

File:Escherichia coli with phages.jpg 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.{{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 }}]]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 biofilms.{{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 }}{{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}} These features protect wild-type strains from 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 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.{{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 }}

In 1946, Joshua Lederberg and Edward Tatum first described the phenomenon known as bacterial conjugation using E. coli as a model bacterium,{{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] and it remains the primary model to study conjugation.{{cite book|title=Biological Activity of Crystal|pages=169}} E. coli was an integral part of the first experiments to understand phage genetics,{{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 }} and early researchers, such as Seymour Benzer, used E. coli and phage T4 to understand the topography of gene structure.{{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 }} Prior to Benzer's research, it was not known whether the gene was a linear structure, or if it had a branching pattern.{{cite web |title=Facts about E.Coli |url=http://eol.org/pages/972688/details |publisher=Encyclopedia of Life |access-date=27 November 2013}}

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.

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",{{cite web |url=http://www.scarabgenomics.com/ |title=Scarab Genomics LLC. Company web site.}} 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, pseudogenes and phages, resulting in better maintenance of plasmid-encoded toxic genes, which are often inactivated by transposons.{{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 }}{{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 }}{{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 }} Biochemistry and replication machinery were not altered.

By evaluating the possible combination of nanotechnologies with landscape ecology, complex habitat landscapes can be generated with details at the nanoscale.{{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 }} 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.{{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}}{{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}}

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.{{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}}

Studies are being performed attempting to program E. coli to solve complicated mathematics problems, such as the Hamiltonian path problem.{{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 }}

A computer to control protein production of E. coli within yeast cells has been developed.{{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 }} A method has also been developed to use bacteria to behave as an LCD screen.{{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 }}{{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 }}

In July 2017, separate experiments with E. coli published on Nature showed the potential of using living cells for computing tasks and storing information.{{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}} A team formed with collaborators of the 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 ribonucleic acid.{{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}}{{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 = }} 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.{{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}}{{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 = }} In 2021, a team led by biophysicist Sangram Bagh realized a study with E. coli to solve 2 × 2 maze problems to probe the principle for distributed computing among cells.{{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 = }}{{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}}

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 prokaryotes 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).{{cite book |vauthors = Haeckel E | orig-date = 1867 | date = 2010 |title = Generelle Morphologie der Organismen |publisher = Reimer, Berlin |isbn = 978-1-144-00186-3 }}{{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 }}

Bacterium coli was the type species of the now invalid genus Bacterium when it was revealed that the former type species ("Bacterium triloculare") was missing.{{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}} Following a revision of Bacterium, it was reclassified as Bacillus coli by Migula in 1895{{ 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 }} and later reclassified in the newly created genus Escherichia, named after its original discoverer, by Aldo Castellani and Albert John Chalmers.{{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 }}

In 1996, an outbreak of E. coli food poisoning occurred in Wishaw, Scotland, killing 21 people.{{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}}{{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 }} This death toll was exceeded in 2011, when the 2011 Germany E. coli O104:H4 outbreak, linked to organic fenugreek sprouts, killed 53 people.

In 2024, an outbreak of E. coli food poisoning occurred across the U.S. was linked to U.S.-grown organic carrots causing one fatality and dozens of illnesses.{{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| vauthors = Mascarenhas L |date=November 17, 2024|access-date=November 17, 2024}}

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.{{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 }}{{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 }}

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• 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
• Mannan oligosaccharide-based nutritional supplements
• Overflow metabolism
• T4 rII system

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{{Reflist}}

{{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:Gut flora bacteria

Category:Tropical diseases

Category:Model organisms

Category:Bacteria described in 1919