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'{{redirect|E. coli|the protozoan commensal|Entamoeba coli}} {{about|Escherichia coli as a species|E. coli in medicine|Pathogenic Escherichia coli|E. coli in molecular biology|Escherichia coli (molecular biology)}} {{good article}} {{Taxobox | image = EscherichiaColi NIAID.jpg | image_width = 250px | domain = [[Bacteria]] | regnum = [[Eubacteria]] | phylum = [[Proteobacteria]] | classis = [[Gammaproteobacteria]] | ordo = [[Enterobacteriales]] | familia = [[Enterobacteriaceae]] | genus = ''[[Escherichia]]'' | species = '''''E. coli''''' | binomial = ''Escherichia coli'' | binomial_authority = ([[Walter Migula|Migula]] 1895)<br />[[Castellani]] and [[Chalmers (surname)|Chalmers]] 1919 | synonyms = ''Bacillus coli communis'' <small>[[Theodor Escherich|Escherich]] 1885</small> | status = NE | status_system = iucn3.1 }} '''''Escherichia coli''''' ({{IPAc-en|ˌ|ɛ|ʃ|i-|ˈ|r|ɪ|k|i|ə|_|ˈ|k|oʊ|l|aɪ}};<ref>{{OED|coli}}</ref> also known as '''''E. coli''''') is a [[gram-negative]], [[Facultative anaerobic organism|facultatively anaerobic]], [[Bacillus (shape)|rod-shaped]] [[bacterium]] of the [[genus]] ''[[Escherichia]]'' that is commonly found in the lower [[intestine]] of [[warm-blooded]] organisms (endotherms).<ref name=Singleton>{{cite book | author = Singleton P| title = Bacteria in Biology, Biotechnology and Medicine | edition = 5th | publisher = Wiley | year = 1999 | pages= 444–454| isbn = 0-471-98880-4}}</ref> Most ''E. coli'' [[Strain (biology)|strains]] are harmless, but some [[serotype]]s can cause serious [[Foodborne illness|food poisoning]] in their hosts, and are occasionally responsible for [[product recall]]s due to [[food contamination]].<ref name=CDC>{{cite web | title=''Escherichia coli''| work=CDC National Center for Emerging and Zoonotic Infectious Diseases| url=http://www.cdc.gov/ecoli/index.html/ | accessdate=2012-10-02}}</ref><ref name=Vogt>{{cite journal | vauthors = Vogt RL, Dippold L | title = Escherichia coli O157:H7 outbreak associated with consumption of ground beef, June-July 2002 | journal = Public Health Reports | volume = 120 | issue = 2 | pages = 174–8 | year = 2005 | pmid = 15842119 | pmc = 1497708 }}</ref> The harmless strains are part of the [[Human flora|normal flora]] of the [[Gut (zoology)|gut]], and can benefit their hosts by producing [[vitamin k|vitamin K₂]],<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 = Sep 1982 | pmid = 6127606 | pmc = 281544 | url = http://mmbr.asm.org/cgi/pmidlookup?view=long&pmid=6127606 }}</ref> and preventing colonization of the intestine with [[pathogenic bacteria]].<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 = Jul 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 = 424–428 | date = Sep 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 conditions for 3 days, but its numbers decline slowly afterwards.<ref name=Russell2001>{{cite journal |vauthors=Russell JB, Jarvis GN |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 |year=2001 |pmid=11321582 |doi= |url=}}</ref> ''E. coli'' and other facultative [[anaerobic organism|anaerobes]] constitute about 0.1% of [[gut flora]],<ref name="pmid15831718">{{cite journal | vauthors = Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, Sargent M, Gill SR, Nelson KE, Relman DA | title = Diversity of the human intestinal microbial flora | journal = Science | volume = 308 | issue = 5728 | pages = 1635–8 | date = Jun 2005 | pmid = 15831718 | pmc = 1395357 | doi = 10.1126/science.1110591 | bibcode = 2005Sci...308.1635E }}</ref> and [[fecal–oral route|fecal–oral transmission]] is the major route through which pathogenic strains of the bacterium cause disease. 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 |author1=Feng P |author2=Weagant S |author3=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= 2002-09-01 | url=http://www.cfsan.fda.gov/~ebam/bam-4.html | accessdate=2007-01-25}}</ref><ref name=Thompson>{{cite news |first=Andrea |last=Thompson |title=E. coli Thrives in Beach Sands |url=http://www.livescience.com/health/070604_beach_ecoli.html |work= |publisher=Live Science |date=2007-06-04 |accessdate=2007-12-03 }}</ref> A growing body of research, though, has examined environmentally persistent ''E. coli'' which can survive for extended periods outside of a host.<ref name="pmid21558695">{{cite journal | vauthors = Ishii S, Sadowsky MJ | title = Escherichia coli in the Environment: Implications for Water Quality and Human Health | journal = Microbes and Environments / JSME | volume = 23 | issue = 2 | pages = 101–8 | year = 2008 | pmid = 21558695 | doi = 10.1264/jsme2.23.101 }}</ref> The bacterium can be 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=":0" /> ''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 favorable conditions, it takes only 20 minutes to reproduce.<ref>{{cite web|title=Bacteria|url=http://www.microbiologyonline.org.uk/about-microbiology/introducing-microbes/bacteria|publisher=Microbiologyonline|accessdate=27 February 2014}}</ref> ==Biology and biochemistry== [[Image:Life cycle of Escherichia coli.png|thumb|350px|Model of successive binary [[Fission (biology)|fission]] in ''E. coli'']] [[Image:E.-coli-growth.gif|thumb|200px|A colony of ''E. coli'' growing]] ===Type and morphology=== ''E. coli'' is a [[Gram-negative bacteria|gram-negative]], [[Facultative anaerobic organism|facultative anaerobic]] (that makes [[Adenosine triphosphate|ATP]] by [[aerobic respiration]] if [[oxygen]] is present, but is capable of switching to [[Fermentation (biochemistry)|fermentation]] or [[anaerobic respiration]] if oxygen is absent) and [[Endospore|nonsporulating]] bacterium.<ref>{{cite web|title=E.Coli|url=http://www.redorbit.com/education/reference_library/health_1/bacteria/2584144/escherichia_coli/|publisher=Redorbit|accessdate=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;μm³.<ref>{{cite web|url=http://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: – Britannica Online Encyclopedia |publisher=Britannica.com |accessdate=2015-06-25}}</ref><ref name="pmid24287933">{{cite journal| vauthors = Yu AC, Loo JF, Yu S, Kong SK, Chan TF | title=Monitoring bacterial growth using tunable resistive pulse sensing with a pore-based technique |journal=Appl Microbiol Biotechnol. |volume=98| issue=2 |pages=855–862|year=2014|doi = 10.1007/s00253-013-5377-9|pmid=24287933}}</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 = Jan 1990 | pmid = 2403552 | pmc = 208405 | url = http://jb.asm.org/cgi/pmidlookup?view=long&pmid=2403552 }}</ref> ''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.<ref name=":0" /> Strains that possess [[flagellum|flagella]] are [[Motility|motile]]. The flagella 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 = Mar 2007 | pmid = 17189361 | pmc = 1855780 | doi = 10.1128/JB.01501-06 }}</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 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=0-13-196893-9| edition=11th}}</ref> ===Culture growth=== Optimum growth of ''E. coli'' occurs at 37&nbsp;°C (98.6&nbsp;°F), but some laboratory strains can multiply at temperatures of up to 49&nbsp;°C (120.2&nbsp;°F).<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 = 403–4 | year = 2005 | pmid = 16187264 | doi = 10.1002/jobm.200410542 }}</ref> ''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 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 = Sep 1984 | pmid = 6387427 | pmc = 373010 }}</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. 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=":0">{{Cite book|title = Microbiology: An Introduction|last = Tortora|first = Gerard|publisher = Benjamin Cummings|year = 2010|isbn = 0-321-55007-2|location = San Francisco, CA|pages = 85–87, 161, 165,}}</ref> ===Cell cycle=== {{main article|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.<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=822–7 |year=2009 |pmid=19806155 |pmc=2887316 |doi=10.1038/nrmicro2202 |url=}}</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 |year=1968 |pmid=4866337 |doi= 10.1016/0022-2836(68)90425-7|url=}}</ref> Unlike eukaryotes, prokaryotes do not rely upon either changes in gene expression<ref>{{cite journal |vauthors=Arends SR, Weiss DS |title=Inhibiting Cell Division in Escherichia coli Has Little If Any Effect on Gene Expression |journal=J. Bacteriol. |volume=186 |issue=3 |pages=880–884 |date=February 2004 |pmid= 14729718|pmc=321490 |doi=10.1128/JB.186.3.880-884.2004 |issn= |bibcode=}}</ref> or changes in protein synthesis<ref>{{cite journal |vauthors=Rueda S, Vicente M, Mingorance J |title=Concentration and Assembly of the Division Ring Proteins FtsZ, FtsA, and ZipA during the Escherichia coli Cell Cycle |journal=J. Bacteriol. |volume=185 |issue=11 |pages=3344–3351 |date=June 2003 |pmid= 12754232|pmc= 155373|doi=10.1128/JB.185.11.3344-3351.2003 |issn= |bibcode=}}</ref> to control the cell cycle. This probably explains why they do not have similar proteins to those used by eukaryotes to control their cell cycle, such as [[cdk1]]. This has led to research on what the control mechanism is in prokaryotes. Recent evidence suggests that it may be membrane- or lipid-based.<ref>{{cite journal |vauthors=Furse S, Wienk H, Boelens R, de Kroon AI, Killian JA |title=E. coli MG1655 modulates its phospholipid composition through the cell cycle |journal=FEBS Lett. |volume= 589|issue= 19PartB|pages= 2726–2730|date=August 2015 |pmid= |pmc= |doi=10.1016/j.febslet.2015.07.043 |issn= |bibcode=}}</ref> ===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 : MMBR | volume = 68 | issue = 3 | pages = 560–602 | date = Sep 2004 | pmid = 15353570 | pmc = 515249 | doi = 10.1128/MMBR.68.3.560-602.2004 | url = http://mmbr.asm.org/cgi/pmidlookup?view=long&pmid=15353570 }}</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== ''Escherichia coli'' encompasses an enormous population of bacteria that exhibit a very high degree of both genetic and phenotypic diversity. Genome sequencing of a large number of 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 |editor1-first=N. R. |editor1-last=Krieg |editor2-first=J. G. |editor2-last=Holt |title=Bergey's Manual of Systematic Bacteriology |edition=First |volume=1 |publisher=The Williams & Wilkins Co |location=Baltimore |year=1984 |pages=408–420 |isbn=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 = Nov 2010 | pmid = 20623278 | pmc = 2974192 | doi = 10.1007/s00248-010-9717-3 }}</ref> In fact, from the evolutionary 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 / Institut Pasteur | volume = 4 | issue = 11 | pages = 1125–32 | date = Sep 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 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, 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 article|Pathogenic Escherichia coli#Serotypes}} 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).<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 = Sep 1977 | pmid = 334154 | pmc = 414020 | doi = }}</ref> It is, however, common to cite only the serogroup, i.e. the 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 | postscript = <!-- Bot inserted parameter. Either remove it; or change its value to "." for the cite to end in a ".", as necessary. -->{{inconsistent citations}} }}</ref> The common laboratory strain has a mutation that prevents the formation of an 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 (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 = 9413–7 | date = Aug 1998 | pmid = 9689094 | pmc = 21352 | doi = 10.1073/pnas.95.16.9413 | bibcode = 1998PNAS...95.9413L }}</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 unpleasant in healthy adults and is often 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 = Jan 1998 | pmid = 9457432 | pmc = 121379 }}</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 | 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 = 831–4 | date = Oct 1990 | pmid = 1976876 | doi = 10.1016/0140-6736(90)92337-H }}</ref> The genera ''[[Escherichia]]'' and ''[[Salmonella]]'' diverged around 102 million years ago (credibility interval: 57–176&nbsp;mya) which coincides with the 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 = Nov 2004 | pmid = 15535883 | pmc = 533871 | doi = 10.1186/1471-2148-4-44 }}</ref> This was followed by a split of the escherichian ancestor into five species (''E. albertii'', ''E. coli'', ''E. fergusonii'', ''E. hermannii'', and ''E. vulneris'').<!--Dates unavailable--> The last ''E. coli'' ancestor split between 20 and 30 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 = Dec 1998 | pmid = 9866203 | doi = 10.1093/oxfordjournals.molbev.a025895 }}</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 major evolutionary shifts in the laboratory.<ref>[http://www.newscientist.com/channel/life/dn14094-bacteria-make-major-evolutionary-shift-in-the-lab.html Bacteria make major evolutionary shift in the lab] ''New Scientist''</ref> In this experiment, one population of ''E. coli'' unexpectedly evolved the ability to aerobically metabolize [[citrate]], which is extremely rare in ''E. coli''. As the inability to grow aerobically is normally used as a diagnostic criterion with which to differentiate ''E. coli'' from other, closely related bacteria, such as ''Salmonella'', this innovation may mark a [[speciation]] event observed in the laboratory. === 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>{{lpsn|e/enterobacteriaceae|Discussion of nomenclature of Enterobacteriaceae}}</ref><ref>International Bulletin of Bacteriological Nomenclature and Taxonomy 8:73–74 (1958)<!--PDF is easily findable...--></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^T,<ref name="doi:10.1186/1944-3277-9-2">{{cite journal|authors = Meier-Kolthoff JP, Hahnke RL, Petersen JP, Scheuner CS, Michael VM, Fiebig AF, Rohde CR, Rohde MR, Fartmann BF, Goodwin LA, Chertkov OC, Reddy TR, Pati AP, Ivanova NN, Markowitz VM, Kyrpides NC, Woyke TW, Klenk HP, Göker M|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|doi=10.1186/1944-3277-9-2|url=http://www.standardsingenomics.com/content/9/1/2}}</ref> also known under the deposit names [[DSMZ|DSM 30083]],<ref>http://www.dsmz.de/catalogues/details/culture/DSM-30083.html</ref> [[American Type Culture Collection|ATCC 11775]],<ref>http://www.atcc.org/ATCCAdvancedCatalogSearch/ProductDetails/tabid/452/Default.aspx?ATCCNum=11775&Template=bacteria</ref> and NCTC 9001,<ref>{{cite web|url=http://www.bacterio.cict.fr/e/escherichia.html|title=Escherichia|publisher=bacterio.cict.fr}}</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 |date= }}</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 been sequenced.<ref name=doi:10.1186/1944-32 ===Phylogeny of ''E. coli'' strains=== A large number of 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.<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 }}</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 | 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 = Dec 2011 | pmid = 21713444 | pmc = 3219860 | doi = 10.1007/s00203-011-0725-6 }}</ref> Particularly the use of [[Whole genome sequencing|whole genome sequences]] yields highly supported phylogenies. Based on such data, five subspecies of ''E. coli'' were distinguished.<ref name=doi:10.1186/1944-3277-9-2 /> The link between phylogenetic distance ("relatedness") and pathology is small,<ref name=doi:10.1186/1944-3277-9-2 /> ''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 of 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=doi:10.1186/1944-3277-9-2 /> and for this reason an according reclassification is difficult. 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⁺ F⁺; O16) and to a lesser degree from [[Félix d'Herelle|d'Herelle]]'s ''[[Bacillus coli]]'' strain (B strain)(O7). {{clade | style=font-size:80%;width:full; |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 Olso O103|''E. coli'' Olso 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⁻ F⁻ "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⁻ F⁻ "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|Early electron microscopy]] The first complete [[DNA sequence]] of an ''E. coli'' [[genome]] (laboratory strain K-12 derivative MG1655) was published in 1997. It was found to be a circular [[DNA]] molecule 4.6 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, a large number 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="pmid9278503">{{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 | title = The complete genome sequence of Escherichia coli K-12 | journal = Science | volume = 277 | issue = 5331 | pages = 1453–62 | date = Sep 1997 | pmid = 9278503 | doi = 10.1126/science.277.5331.1453 }}</ref> Today, several hundred complete genomic sequences of ''Escherichia'' and ''Shigella'' species are available. The genome sequence of the type strain of ''E. coli'' has been added to this collection not before 2014.<ref name="doi:10.1186/1944-3277-9-2" /> 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 | title = Lateral gene transfer | journal = Current Biology | volume = 21 | issue = 7 | pages = R242–6 | date = Apr 2011 | pmid = 21481756 | doi = 10.1016/j.cub.2011.01.045 }}</ref> == Gene nomenclature == Genes in ''E. coli'' are usually named by 4-letter acronyms that derive from their function (when known). For instance, recA is named after its role in [[homologous recombination|homologous <u>rec</u>ombination]] 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'' was sequenced, all genes were numbered (more or less) in their order on the genome and abbreviated by b numbers, such as b2819 (=recD) etc. The "b" names were created after Fred <u>B</u>lattner who led the genome sequence effort.<ref name="Blattner">{{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 | title = The complete genome sequence of Escherichia coli K-12 | journal = Science | volume = 277 | issue = 5331 | pages = 1453–1462 | date = Sep 1997 | pmid = 9278503 | doi = 10.1126/science.277.5331.1453 }}</ref> Another numbering system was introduced with the sequence of another ''E. coli'' strain, 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 | 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 = Jan 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=== Several studies have investigated the [[proteome]] of ''E. coli''. By 2006, 1,627 (38%) of the 4,237 [[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 : MMBR | volume = 70 | issue = 2 | pages = 362–439 | date = Jun 2006 | pmid = 16760308 | pmc = 1489533 | doi = 10.1128/MMBR.00036-05 }}</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 | 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 | title = Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins | journal = PLoS Biology | volume = 7 | issue = 4 | pages = e96 | date = Apr 2009 | pmid = 19402753 | pmc = 2672614 | doi = 10.1371/journal.pbio.1000096 | editor1-last = Levchenko | editor1-first = Andre }}</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 | title = The binary protein-protein interaction landscape of Escherichia coli | journal = Nature Biotechnology | volume = 32 | issue = 3 | pages = 285–90 | date = Mar 2014 | pmid = 24561554 | 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 |series=Bergey's Manual of Systematic Bacteriology|volume=2B|title=The Gammaproteobacteria|editor=George M. Garrity |first1=Don J.|last1=Brenner|first2=Noel R.|last2=Krieg|first3= James T.|last3= Staley |publisher=Springer|location= New York|edition=2nd|isbn=978-0-387-24144-9 |pages=1108|url=http://www.springer.com/life+sciences/book/978-0-387-24144-9 |date=July 26, 2005| origyear =1984 (Williams & Wilkins) |id=British Library no. GBA561951 |name-list-format=vanc}}</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'' |accessdate=2007-11-30 |last=Todar |first=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 |accessdate=2007-12-02 |last=Evans Jr. |first=Doyle J. |author2=Dolores G. Evans |work=Medical Microbiology, 4th edition |publisher=The University of Texas Medical Branch at Galveston |archiveurl = https://web.archive.org/web/20071102062813/http://www.gsbs.utmb.edu/microbook/ch025.htm <!-- Bot retrieved archive --> |archivedate = 2007-11-02}}</ref> ===Therapeutic use=== Nonpathogenic ''E. coli'' strain Nissle 1917, also known as [[Mutaflor]], and ''E. coli'' O83:K24:H31 (known as Colinfant<ref>{{cite journal | vauthors = Lodinová-Zádníková R, Cukrowska B, Tlaskalova-Hogenova H | 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 = Jul 2003 | pmid = 12876412 | doi = 10.1159/000071488 }}</ref>) are used as [[probiotic]] agents in medicine, mainly for the treatment of various gastroenterological diseases,<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 = Aug 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 | 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> ==Role in disease== {{main article|Pathogenic Escherichia coli}} Most ''E. coli'' strains do not cause disease,<ref>http://www.mayoclinic.org/diseases-conditions/e-coli/basics/definition/con-20032105</ref> but virulent strains can cause [[gastroenteritis]], [[urinary tract infection]]s, and [[neonatal]] [[meningitis]]. It can also be characterized by severe abdominal cramps, diarrhea that typically turns bloody within 24 hours, 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]], [[septicemia]], and gram-negative [[pneumonia]].<ref name=Todar/> There is one strain, ''E.coli'' #0157:H7, that produces the [[Shiga toxin]] (classified as a bioterrorism agent). This toxin causes premature destruction of the red blood cells, which then clog the body's filtering system, the kidneys, causing hemolytic-uremic syndrome (HUS). This in turn causes [[stroke]]s due to small clots of blood which lodge in capillaries in the brain. This causes the body parts controlled by this region of the brain not to work properly. In addition, this strain causes the buildup of fluid (since the kidneys do not work), leading to edema around the lungs and 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>"E. Coli Food Poisoning." About. N.p., n.d. Web. 13 Dec. 2014. <http://www.about-ecoli.com/>.</ref><ref>"Lung Congestion." TheFreeDictionary.com. N.p., n.d. Web. 13 Dec. 2014. <http://medical-dictionary.thefreedictionary.com/Lung+Congestion>.</ref><ref>"Pulmonary Edema: Get the Facts on Treatment and Symptoms." MedicineNet. N.p., n.d. Web. 13 Dec. 2014. <http://www.medicinenet.com/pulmonary_edema/article.htm>.</ref><ref>Staff, Mayo Clinic. "Hemolytic Uremic Syndrome (HUS)." Mayo Clinic. Mayo Foundation for Medical Education and Research, 03 July 2013. Web. 13 Dec. 2014. <http://www.mayoclinic.com/health/hemolytic-uremic-syndrome/DS00876>.</ref> 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|accessdate=27 November 2013}}</ref> It is part of the normal flora 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.<ref name=pre-eminent/> For more information, see the databases at the end of the article or [[Pathogenic Escherichia coli#Urinary tract infection|UPEC pathogenicity]]. 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 11 other countries, including regions in North America.{{citation needed|date=August 2015}} 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 ''in English: Fenugreek seeds with high probability for EHEC O104: H4 responsible outbreak''|date = 30 June 2011|publisher = Bundesinstitut für Risikobewertung (BfR) ''in English: Federal Institute for Risk Assessment''|language = German|format= PDF|accessdate = 17 July 2011}}</ref> ===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 [[diarrhoea]], though the rate of resistance to commonly used antibiotics is increasing and they are generally not recommended.<ref>{{Cite web|url=http://www.cdc.gov/ecoli/etec.html|title=Enterotoxigenic E. coli (ETEC)|last=US Centers for Disease Control and Prevention|first=|date=|website=|publisher=|access-date=2016-07-21}}</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]]. [[Oral rifaximin]], a semisynthetic rifamycin derivative, is an effective and well-tolerated antibacterial for the management of adults with non-invasive traveller’s diarrhoea. Rifaximin was significantly more effective than placebo and no less effective than ciprofloxacin in reducing the duration of diarrhoea. While rifaximin is effective in patients with ''E. coli''-predominant traveller’s diarrhoea, it appears ineffective in patients infected with inflammatory or invasive [[enteropathogen]]s.<ref>{{cite journal|last1=Al-Abri|first1=Seif S|last2=Beeching|first2=Nick J|last3=Nye|first3=Fred J|title=Traveller's diarrhoea|journal=The Lancet Infectious Diseases|date=June 2005|volume=5|issue=6|pages=349–360|doi=10.1016/S1473-3099(05)70139-0|pmid=15919621|name-list-format=vanc}}</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|last=Bourgeois|first=A. Louis|last2=Wierzba|first2=Thomas F|last3=Walker|first3=Richard I|date=2016|title=Status of vaccine research and development for enterotoxigenic Escherichia coli|url=http://www.sciencedirect.com/science/article/pii/S0264410X16002875|journal=Vaccine|volume=34|issue=26|pages=2880–2886|doi=|pmid=26988259|access-date=|via=}}</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 = Feb 2011 | pmid = 21415493 | pmc = 3089050 }}</ref> <ref name="Manson's tropical diseases">{{cite book|editor-first=Jeremy |editor-last=Farrar |editor2-first=Peter |editor2-last=Hotez |editor3-first=Thomas |editor3-last=Junghanss |editor4-first=Gagandeep |editor4-last=Kang |editor5-first=David |editor5-last=Lalloo |editor6-first=Nicholas J. |editor6-last=White |title=Manson's Tropical Diseases|date=2013|publisher=Elsevier/Saunders|location=Oxford|isbn=9780702053061|edition=23rd|name-list-format=vanc}}</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.{{citation needed|date=November 2016}} ===Causes and risk factors=== * Working around livestock * Consuming unpasteurized dairy product * Eating undercooked meat * Drinking impure water{{citation needed|date=January 2016}} ==Model organism in life science research== {{main article|Escherichia coli (molecular biology)}} ===Role in biotechnology=== 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 = Mar 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 | title = The birth of biotechnology | journal = Nature | volume = 421 | issue = 6921 | pages = 456–457 | date = Jan 2003 | pmid = 12540923 | doi = 10.1038/nj6921-456a | url = http://www.nature.com/nature/journal/v421/n6921/full/nj6921-456a.html | bibcode = 2003Natur.421..456R }}</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 |accessdate=2007-11-30 |last=Tof |first=Ilanit |year=1994 |work= |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 = 13703–8 | date = Nov 1999 | pmid = 10570136 | pmc = 24128 | doi = 10.1073/pnas.96.24.13703 | bibcode = 1999PNAS...9613703B }}</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 = 494–7 | year = 2010 | pmid = 20701771 | pmc = 2927510 | doi = 10.1186/1475-2859-9-61 }}</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 | title = N-linked glycosylation in Campylobacter jejuni and its functional transfer into E. coli | journal = Science | volume = 298 | issue = 5599 | pages = 1790–1793 | date = Nov 2002 | pmid = 12459590 | doi = 10.1126/science.298.5599.1790 }}</ref><ref>{{cite journal | vauthors = Huang CJ, Lin H, Yang X | 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 = Mar 2012 | pmid = 22252444 | doi = 10.1007/s10295-011-1082-9 }}</ref> Modified ''E. coli'' cells have been used in [[vaccine]] development, [[bioremediation]], production of [[biofuels]],<ref>Summers, Rebecca (24 April 2013) [http://www.newscientist.com/article/dn23431-bacteria-churn-out-first-ever-petrollike-biofuel.html Bacteria churn out first ever petrol-like biofuel] New Scientist, Retrieved 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 = 450–454 | date = Oct 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=August 15, 2013|author=Nic Halverson}}</ref> ===Model organism=== ''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 = Feb 2005 | pmid = 15680764 | doi = 10.1016/j.tim.2004.11.001 }}</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 = 2442–9 | date = May 1998 | pmid = 9573197 | pmc = 107187 | doi = }}</ref> These features protect wild-type strains from [[antibody|antibodies]] and other chemical attacks, but require a large expenditure of energy and material resources. 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 |last=Lederberg |first=Joshua |author2=E.L. Tatum |date=October 19, 1946 |title=Gene recombination in E. coli |journal=Nature |volume=158 |issue= 4016|page=558 |id= |url=http://profiles.nlm.nih.gov/BB/G/A/S/Z/_/bbgasz.pdf |doi=10.1038/158558a0|format=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|pmc=1206443 |title=The Phage Course – Origins |journal=Genetics |volume=139 |issue=3 |pages=1101–1106 |year=2006 |work= |publisher=Cold Spring Harbor Laboratory |archiveurl=https://web.archive.org/web/20060916155323/https://www.cshl.edu/History/phagecourse.html |archivedate=September 16, 2006 |author1=Susman |first1=M |pmid=7768426 }}</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 | title = ON THE TOPOGRAPHY OF THE GENETIC FINE STRUCTURE | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 47 | issue = 3 | pages = 403–15 | date = Mar 1961 | pmid = 16590840 | pmc = 221592 | doi = 10.1073/pnas.47.3.403 | bibcode = 1961PNAS...47..403B }}</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|accessdate=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="pmid9278503" /> 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 = 17290–5 | date = Nov 2006 | pmid = 17090676 | pmc = 1635019 | doi = 10.1073/pnas.0607971103 | bibcode = 2006PNAS..10317290K }}</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. Studies are also 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 | title = Solving a Hamiltonian Path Problem with a bacterial computer | journal = Journal of Biological Engineering | volume = 3 | pages = 11 | date = July 24, 2009 | pmid = 19630940 | pmc = 2723075 | doi = 10.1186/1754-1611-3-11 | publisher = J Biol Eng. 2009; 3: 11. }}</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 | last = Haeckel | first = Ernst | year = 1867 | title = Generelle Morphologie der Organismen | publisher = Reimer, Berlin | isbn = 1-144-00186-2 }}</ref><ref>{{cite journal | vauthors = Escherich T | year = 1885 | title = Die Darmbakterien des Neugeborenen und Säuglinge | url = https://books.google.com/?id=o1MXAAAAYAAJ&lpg=PA135&dq=%22Die%20darmbakterien%20des%20neugeborenen%20und%20säuglings%22&pg=PA135#v=onepage&q=%22Die%20darmbakterien%20des%20neugeborenen%20und%20säuglings%22&f=false|journal = Fortschr. Med. | volume = 3 | issue = | pages = 515–522 }}</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 = 517–8 | date = May 1936 | pmid = 16559906 | pmc = 543738 | doi = }}</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.<ref>{{cite book |vauthors=Castellani A, Chalmers AJ | title = Manual of Tropical Medicine | edition = 3rd | publisher = Williams Wood and Co. | location = New York | year = 1919 }}</ref> == See also == * [[Bacteriological water analysis]] * [[Coliform bacteria]] * [[Contamination control]] * [[Dam dcm strain]] * [[Enterotoxigenic Escherichia coli|Enterotoxigenic ''Escherichia coli'']] * [[Fecal coliforms]] * [[International Code of Nomenclature of Bacteria]] * [[List of bacterial genera named after personal names]] * [[List of strains of Escherichia coli|List of strains of ''Escherichia coli'']] * [[Mannan oligosaccharide-based nutritional supplements]] * [[T4 rII system]] * [[2011 E. coli O104:H4 outbreak|2011 ''E. coli'' O104:H4 outbreak]] == References == {{Reflist|35em}} == Further reading == * {{cite journal | vauthors = Jann K, Jann B | title = Capsules of Escherichia coli, expression and biological significance | journal = Canadian Journal of Microbiology | volume = 38 | issue = 7 | pages = 705–710 | date = Jul 1992 | pmid = 1393836 | doi=10.1139/m92-116}} == External links == {{wikispecies}} {{commons category|Escherichia coli}} * [http://www.aboutkidshealth.ca/En/News/NewsAndFeatures/Pages/E-coli-Protecting-Family.aspx ''E. coli'': Protecting yourself and your family from a sometimes deadly bacterium] * [http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi ''E. coli'' statistics] * [https://web.archive.org/web/20090511215840/http://www.fda.gov/oc/opacom/hottopics/spinach.html Spinach and ''E. coli'' Outbreak – U.S. FDA] * [https://web.archive.org/web/20160303193750/http://www.cdc.gov/foodborne/ecolispinach/ ''E. coli'' Outbreak From Fresh Spinach – U.S. CDC] * [http://www.micron.ac.uk/organisms/eco.html Current research on ''Escherichia coli'' at the Norwich Research Park] * ''E. coli'' gas production from glucose [http://www.tgw1916.net/movies2.html video demonstration] * [http://familydoctor.org/familydoctor/en/diseases-conditions/ecoli-infection/causes-risk-factors.html ''E. coli'' Infection | Causes & Risk Factors] ===Databases=== * [http://www.compsysbio.org/bacteriome/ Bacteriome] ''E. coli'' interaction database * [http://xbase.bham.ac.uk/colibase/ coliBASE] (subset of the comparative genomics database xBASE) * [http://www.ecogene.org/ EcoGene] (genome database and website dedicated to Escherichia coli K-12 substrain MG1655) * [http://www.ecosal.org/ EcoSal] Continually updated Web resource based on the classic ASM Press publication ''Escherichia coli and Salmonella: Cellular and Molecular Biology'' * [http://www.casper.organ.su.se/ECODAB/ ECODAB] The structure of the O-antigens that form the basis of the serological classification of ''E. coli'' * [http://cgsc.biology.yale.edu/index.php Coli Genetic Stock Center] Strains and genetic information on ''E. coli'' K-12 * [http://ecocyc.com/ EcoCyc] – literature-based curation of the entire genome, and of transcriptional regulation, transporters, and metabolic pathways * [http://porteco.org PortEco (formerly EcoliHub)] – NIH-funded comprehensive data resource for ''E. coli'' K-12 and its phage, plasmids, and mobile genetic elements * [http://ecoliwiki.net EcoliWiki] is the community annotation component of [http://porteco.org PortEco] * [http://regulondb.ccg.unam.mx/index.jsp RegulonDB] RegulonDB is a model of the complex regulation of transcription initiation or regulatory network of the cell ''E. coli'' K-12. * [http://www.genome.wisc.edu/sequencing/upec.htm Uropathogenic Escherichia coli (UPEC)] === General databases with ''E. coli''-related information === * [http://biobases.ibch.poznan.pl/5SData/ 5S rRNA Database] Information on nucleotide sequences of 5S rRNAs and their genes * [http://aclame.ulb.ac.be/ ACLAME] A CLAssification of Mobile genetic Elements * [http://arep.med.harvard.edu/ecoli_matrices/ AlignACE] Matrices that search for additional binding sites in the E. coli genomic sequence * [http://www.ebi.ac.uk/microarray-as/ae/ ArrayExpress] Database of functional genomics experiments * [https://asap.ahabs.wisc.edu/asap/home.php ASAP] Comprehensive genome information for several enteric bacteria with community annotation * [http://biogps.gnf.org/#goto=welcome BioGPS] Gene portal hub * [http://www.brenda-enzymes.info/ BRENDA] Comprehensive Enzyme Information System * [http://sgen.bri.nrc.ca/brimsg/bsgi.html BSGI] Bacterial Structural Genomics Initiative * [http://www.cathdb.info/ CATH] Protein Structure Classification * [http://www.cbs.dtu.dk/services/GenomeAtlas/ CBS Genome Atlas] * [http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml CDD] Conserved Domain Database * [http://cibex.nig.ac.jp/index.jsp CIBEX] Center for Information Biology Gene Expression Database * [http://www.ncbi.nlm.nih.gov/COG/old/ COGs] *[http://bacdive.dsmz.de/index.php?search=4907&submit=Search Type strain of ''Escherichia coli'' at Bac''Dive'' - the Bacterial Diversity Metadatabase] {{Escherichia coli}} {{Model Organisms}} {{Gram-negative proteobacterial diseases}} {{taxonbar}} {{Authority control}} [[Category:Escherichia coli| ]] [[Category:Gut flora bacteria]] [[Category:Prokaryotic model organisms]] [[Category:Bacteria described in 1919]] penis'