Editing Escherichia coli (section)

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

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

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

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