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''Escherichia coli'' (),Wells, J. C. (2000) Longman Pronunciation Dictionary. Harlow ngland Pearson Education Ltd. also known as ''E. coli'' (), is a
Gram-negative Gram-negative bacteria are bacteria Bacteria (; common noun bacteria, singular bacterium) are a type of Cell (biology), biological cell. They constitute a large domain (biology), domain of prokaryotic microorganisms. Typically a few microm ...
, facultative anaerobic,
rod-shaped A bacillus (plural bacilli), or bacilliform bacterium, is a rod-shaped bacterium Bacteria (; common noun bacteria, singular bacterium) are a type of Cell (biology), biological cell. They constitute a large domain (biology), domain of prok ...
, coliform bacterium of the genus ''
Escherichia ''Escherichia'' is a genus of Gram-negative, non-Endospore, spore-forming, Facultative anaerobic organism, facultatively anaerobic, rod-shaped bacteria from the family Enterobacteriaceae. In those species which are inhabitants of the gastrointest ...
'' that is commonly found in the lower
intestine The gastrointestinal tract (GI tract, digestive tract, alimentary canal) is the tract or passageway of the digestive system The human digestive system consists of the gastrointestinal tract The gastrointestinal tract, (GI tract, GIT, d ...

intestine
of warm-blooded organisms. Most ''E. coli'' strains are harmless, but some
serotype A serotype or serovar is a distinct variation within a species In biology, a species is the basic unit of biological classification, classification and a taxonomic rank of an organism, as well as a unit of biodiversity. A species is often d ...

serotype
s ( EPEC, ETEC etc.) can cause serious
food poisoning Foodborne illness (also foodborne disease and colloquially referred to as food poisoning) is any Disease, illness resulting from the spoilage of food contaminant, contaminated food, pathogenic bacteria, viruses, or parasites that contaminate food, ...
in their hosts, and are occasionally responsible for
food contamination Food contamination refers to the presence of harmful chemicals and microorganisms in food, which can cause consumer illness. This article addresses the chemical contamination of foods, as opposed to microbiological contamination, which can be found ...
incidents that prompt product recalls. The harmless strains are part of the normal microbiota of the gut, and can benefit their hosts by producing vitamin K2, and preventing colonisation of the intestine with
pathogenic bacteria Pathogenic bacteria are bacteria Bacteria (; common noun bacteria, singular bacterium) are a type of Cell (biology), biological cell. They constitute a large domain (biology), domain of prokaryotic microorganisms. Typically a few micrometr ...
, having a mutualistic relationship. ''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. ''E. coli'' and other facultative anaerobes constitute about 0.1% of gut microbiota, and 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 Indicator organisms are used as a proxy to monitor conditions in a particular environment, ecosystem, area, habitat, or consumer product. Certain bacteria Bacteria (; common noun bacteria, singular bacterium) are a type of Cell (biology), bi ...
s to test environmental samples for . A growing body of research, though, has examined environmentally persistent ''E. coli'' which can survive for many days and grow outside a host. 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
chemoheterotroph Chemotrophs are organisms that obtain energy In physics Physics (from grc, φυσική (ἐπιστήμη), physikḗ (epistḗmē), knowledge of nature, from ''phýsis'' 'nature'), , is the natural science that studies matter, ...
whose chemically defined medium must include a source of carbon and energy. ''E. coli'' is the most widely studied
prokaryotic A prokaryote () is a single-celled organism A unicellular organism, also known as a single-celled organism, is an organism In biology, an organism (from Ancient Greek, Greek: ὀργανισμός, ''organismos'') is any individual conti ...
model organism A model organism (often shortened to model) is a non-human species In biology, a species is the basic unit of biological classification, classification and a taxonomic rank of an organism, as well as a unit of biodiversity. A species is ...
, and an important species in the fields of
biotechnology Biotechnology is a broad area of biology, involving the use of living systems and organisms to develop or make products. Depending on the tools and applications, it often overlaps with related scientific fields. In the late 20th and early 21st c ...

biotechnology
and
microbiology Microbiology (from Greek#REDIRECT Greek Greek may refer to: Greece Anything of, from, or related to Greece Greece ( el, Ελλάδα, , ), officially the Hellenic Republic, is a country located in Southeast Europe. Its population is appro ...

microbiology
, where it has served as the
host organism In biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular interactions, Physiology, physiological mechanisms ...
for the majority of work with
recombinant DNA Recombinant DNA (rDNA) molecules are DNA Deoxyribonucleic acid (; DNA) is a molecule File:Pentacene on Ni(111) STM.jpg, A scanning tunneling microscopy image of pentacene molecules, which consist of linear chains of five carbon rings ...

recombinant DNA
. Under favorable conditions, it takes as little as 20 minutes to reproduce.


Biology and biochemistry


Type and morphology

''E. coli'' is a
Gram-negative Gram-negative bacteria are bacteria Bacteria (; common noun bacteria, singular bacterium) are a type of Cell (biology), biological cell. They constitute a large domain (biology), domain of prokaryotic microorganisms. Typically a few microm ...
,
facultative anaerobe 300px, Aerobic and anaerobic bacteria can be identified by growing them in test tubes of thioglycolate broth: 1: Obligate aerobes need oxygen because they cannot ferment or respire anaerobically. They gather at the top of the tube where the oxygen ...
, nonsporulating coliform bacterium. Cells are typically rod-shaped, and are about 2.0 long and 0.25–1.0 μm in diameter, with a cell volume of 0.6–0.7 μm3. Antibiotics can effectively treat ''E. coli'' infections outside the digestive tract and most intestinal infections but are not used to treat intestinal infections by one strain of these bacteria. The
flagella A flagellum (; ) is a hairlike appendage that protrudes from a wide range of microorganism A microorganism, or microbe,, ''mikros'', "small") and ''organism In biology Biology is the natural science that studies life and ...
which allow the bacteria to swim have a
peritrichous A flagellum (; plural: flagella) is a lash-like appendage that protrudes from the cell body of certain cells termed as flagellate 's '' Artforms of Nature'', 1904 (''Giardia lamblia'') ('' Chlamydomonas'') A flagellate is a cell or organism ...
arrangement. It also attaches and effaces to the microvilli of the intestines via an adhesion molecule known as
intimin Intimin is a virulence factor (Bacterial adhesin, adhesin) of Pathogenic Escherichia coli, EPEC (''e.g.'' ''E. coli'' O127:H6) and EHEC (''e.g. E. coli'' O157, O157:H7) ''E. coli'' strains. It is an attaching and effacing (A/E) protein, which with o ...
.


Metabolism

''E. coli'' can live on a wide variety of substrates and uses
mixed acid fermentation Mixed acid fermentation is the biological process by which a six-carbon sugar e.g. glucose Glucose is a simple sugar with the Chemical formula#Molecular formula, molecular formula . Glucose is the most abundant monosaccharide, a subcategory of car ...
in anaerobic conditions, producing ,
succinate Succinic acid () is a dicarboxylic acidA dicarboxylic acid is an organic compound , CH4; is among the simplest organic compounds. In chemistry Chemistry is the scientific discipline involved with Chemical element, elements and chemical co ...

succinate
,
ethanol Ethanol (also called ethyl alcohol, grain alcohol, drinking alcohol, or simply alcohol) is an organic Organic may refer to: * Organic, of or relating to an organism, a living entity * Organic, of or relating to an anatomical organ (anatomy), ...

ethanol
,
acetate An acetate is a salt formed by the combination of acetic acid with a base (e.g. alkaline, earthy, metallic, nonmetal image:Simple Periodic Table Chart-en.svg, upright=1.75, Nonmetals (and metalloids) in the periodic table: Metalloids are i ...

acetate
, and
carbon dioxide Carbon dioxide (chemical formula A chemical formula is a way of presenting information about the chemical proportions of s that constitute a particular or molecule, using symbols, numbers, and sometimes also other symbols, such as pare ...

carbon dioxide
. Since many pathways in mixed-acid fermentation produce
hydrogen Hydrogen is the chemical element with the Symbol (chemistry), symbol H and atomic number 1. Hydrogen is the lightest element. At standard temperature and pressure, standard conditions hydrogen is a gas of diatomic molecules having the che ...

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 Methanogens are microorganisms that produce methane Methane (, ) is a chemical compound with the chemical formula (one carbon atom bonded to four hydrogen atoms). It is a group-14 hydride, the simplest alkane, and the main constituent of n ...
s or sulphate-reducing bacteria. In addition, ''E. colis metabolism can be rewired to solely use 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 Carbon fixation or сarbon assimilation is the process by which inorganic carbon (particularly in the form of carbon dioxide Carbon dioxide (chemical formula ) is a colorless gas with a density about 53% higher than that of dry air. Carbon ...
genes as well as
formate dehydrogenase Formate dehydrogenases are a set of enzymes that catalyse the oxidation of formate to carbon dioxide, donating the electrons to a second substrate, such as Nicotinamide adenine dinucleotide, NAD+ in formate:NAD+ oxidoreductase (EC 1.2.1.2) or to a ...
and conducting laboratory evolution experiments. This may be done by using
formate Formate (IUPAC The International Union of Pure and Applied Chemistry (IUPAC ) is an international federation of National Adhering Organizations that represents chemists in individual countries. It is a member of the International Science Coun ...

formate
to reduce electron carriers and supply the ATP required in anabolic pathways inside of these synthetic autotrophs. ''E. coli'' have three native glycolytic pathways: EMPP, , and . The EMPP employs ten enzymatic steps to yield two pyruvates, two
ATP ATP may refer to: Companies and organizations * Association of Tennis Professionals * American Technical Publishers * ', a Danish pension * Armenia Tree Project * Association for Transpersonal Psychology * ATP architects engineers office * ATP ...

ATP
, and two
NADH Nicotinamide adenine dinucleotide (NAD) is a Cofactor (biochemistry), coenzyme central to metabolism. Found in all living cell (biology), cells, NAD is called a dinucleotide because it consists of two nucleotides joined through their phosphate ...
per
glucose Glucose is a simple with the . Glucose is the most abundant , a subcategory of s. Glucose is mainly made by and most during from water and carbon dioxide, using energy from sunlight, where it is used to make in s, the most abundant carbohydr ...

glucose
molecule while OPPP serves as an oxidation route for
NADPH Nicotinamide adenine dinucleotide phosphate, abbreviated NADP or, in older notation, TPN (triphosphopyridine nucleotide), is a cofactor used in anabolic reactions, such as the Calvin cycle The Calvin cycle, light-independent reactions, bio syn ...

NADPH
synthesis. Although the EDP is the more thermodynamically favorable of the three pathways, ''E. coli'' do not use the EDP for
glucose metabolism Carbohydrate metabolism is the whole of the biochemical Biochemistry or biological chemistry, is the study of chemical processes within and relating to living organism In biology, an organism (from Ancient Greek, Greek: ὀργανισ ...

glucose metabolism
, relying mainly on the EMPP and the OPPP. The EDP mainly remains inactive except for during growth with
gluconate Gluconic acid is an organic compound with molecular formula C6H12O7 and condensed structural formula HOCH2(CHOH)4COOH. It is one of the 16 stereoisomers of 2,3,4,5,6-pentahydroxyhexanoic acid. In aqueous solution at neutral pH, gluconic acid form ...
.


Catabolite repression

When growing in the presence of a mixture of sugars, bacteria will often consume the sugars sequentially through a process known as 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 Arabinose is an aldopentose – a monosaccharide Monosaccharides (from Greek '' monos'': single, ''sacchar'': sugar), also called simple sugars, are the simplest form of sugar Sugar is the generic name for Sweetness, sweet-tasting, soluble ...

arabinose
and
xylose Xylose ( grc, ξύλον, , "wood") is a sugar first isolated from wood, and named for it. Xylose is classified as a of the type, which means that it contains five atoms and includes an . It is derived from , one of the main constituents o ...

xylose
,
sorbitol Sorbitol (), less commonly known as glucitol (), is a sugar alcohol with a sweet taste which the human body metabolizes slowly. It can be obtained by Redox, reduction of glucose, which changes the converted aldehyde group (−CHO) to a primary alco ...

sorbitol
,
rhamnose Rhamnose (Rha, Rham) is a naturally occurring deoxy sugar Image:Alpha-L-Rhamnopyranose.svg, 150px, rhamnose Deoxy sugars are sugars that have had a hydroxyl group replaced with a hydrogen atom. Examples include: * Deoxyribose, or 2-deoxy-D-rib ...
, and
ribose Ribose is a simple sugar and carbohydrate with molecular formula C5H10O5 and the linear-form composition H−(C=O)−(CHOH)4−H. The naturally-occurring form, , is a component of the ribonucleotides from which RNA is built, and so this compoun ...

ribose
. In ''E. coli'', glucose catabolite repression is regulated by the , a multi-protein
phosphorylation In chemistry Chemistry is the study of the properties and behavior of . It is a that covers the that make up matter to the composed of s, s and s: their composition, structure, properties, behavior and the changes they undergo during ...

phosphorylation
cascade that couples glucose uptake and metabolism.


Culture growth

Optimum growth of ''E. coli'' occurs at 37 °C (98.6 °F), but some laboratory strains can multiply at temperatures up to 49 °C (120 °F). ''E. coli'' grows in a variety of defined laboratory media, such as
lysogeny broth Image:LBmedium.JPG, 200px, LB medium bottle and LB agar plate Lysogeny broth (LB) is a Nutrient, nutritionally rich Growth medium, medium primarily used for the Bacterial growth, growth of bacterium, bacteria. Its creator, Giuseppe Bertani, intende ...
, or any medium that contains glucose, ammonium phosphate monobasic, sodium chloride, magnesium sulfate, potassium phosphate dibasic, and water. Growth can be driven by
aerobic Aerobic means "requiring Earth's atmosphere, air," in which "air" usually means oxygen. Aerobic may also refer to * Aerobic exercise, prolonged exercise of moderate intensity * Aerobics, a form of aerobic exercise * Cellular respiration#Aerobic r ...
or
anaerobic respiration Anaerobic respiration is respiration Respiration may refer to: Biology * Cellular respiration, the process in which nutrients are converted into useful energy in a cell ** Anaerobic respiration, cellular respiration without oxygen ** Maintenan ...
, using a large variety of , including the oxidation of
pyruvic acid Pyruvic acid (CH3COCOOH) is the simplest of the alpha-keto acids, with a carboxylic acid A carboxylic acid is an organic acid that contains a carboxyl group (C(=O)OH) attached to an R-group. The general formula of a carboxylic acid is R ...

pyruvic acid
,
formic acid Formic acid, systematically named methanoic acid, is the simplest carboxylic acid A carboxylic acid is an organic acid An organic acid is an organic compound with acidic properties. The most common organic acids are the carboxylic acid ...

formic acid
,
hydrogen Hydrogen is the chemical element with the Symbol (chemistry), symbol H and atomic number 1. Hydrogen is the lightest element. At standard temperature and pressure, standard conditions hydrogen is a gas of diatomic molecules having the che ...

hydrogen
, and
amino acid Amino acids are organic compound In , organic compounds are generally any s that contain - . Due to carbon's ability to (form chains with other carbon s), millions of organic compounds are known. The study of the properties, reactions, a ...

amino acid
s, and the reduction of substrates such as
oxygen Oxygen is the chemical element Image:Simple Periodic Table Chart-blocks.svg, 400px, Periodic table, The periodic table of the chemical elements In chemistry, an element is a pure substance consisting only of atoms that all have the same ...

oxygen
,
nitrate Nitrate is a polyatomic ion A polyatomic ion, also known as a molecular ion, is a covalently bonded A covalent bond is a chemical bond A chemical bond is a lasting attraction between atoms, ions or molecules that enables the format ...

nitrate
,
fumarate Fumaric acid is an organic compound with the formula HO2CCH=CHCO2H. A white solid, fumaric acid occurs widely in nature. It has a fruit-like taste and has been used as a food additive. Its E number is E297. The salts and esters are known as ...

fumarate
,
dimethyl sulfoxide Dimethyl sulfoxide (DMSO) is an organosulfur compound Organosulfur compounds are organic compound , CH4; is among the simplest organic compounds. In chemistry Chemistry is the scientific discipline involved with Chemical element, elements ...

dimethyl sulfoxide
, and
trimethylamine N-oxide Trimethylamine ''N''-oxide (TMAO) is an organic compound , CH4; is among the simplest organic compounds. In chemistry, organic compounds are generally any chemical compounds that contain carbon-hydrogen chemical bond, bonds. Due to carbon's abi ...
. ''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.


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. 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. The number of replication forks in fast growing ''E. coli'' typically follows 2n (n = 1, 2 or 3). This only happens if is initiated simultaneously from all origins of replications, and is referred to as synchronous . However, not all cells in a culture replicate synchronously. In this case cells do not have multiples of two
replication fork is un'zipped' and unwound, then each separated strand (turquoise) acts as a template for replicating a new partner strand (green). Nucleotides (bases) are matched to synthesize the new partner strands into two new double helices. In molecular bio ...

replication fork
s. Replication initiation is then referred to being asynchronous. However, asynchrony can be caused by mutations to for instance
DnaA DnaA is a protein Proteins are large s and s that comprise one or more long chains of . Proteins perform a vast array of functions within organisms, including , , , providing and , and from one location to another. Proteins differ from o ...
or
DnaA DnaA is a protein Proteins are large s and s that comprise one or more long chains of . Proteins perform a vast array of functions within organisms, including , , , providing and , and from one location to another. Proteins differ from o ...
initiator-associating protein
DiaADiaa ( ar, ضياء) is an Egyptian male given name. Notable people with this name include: * Ahmed Diaa Eddine (1912–1976), Egyptian film director * Diaa al-Din Dawoud (1926-2011), Egyptian politician * Diaa Raofat (born 1988), Egyptian footballe ...
.


Genetic adaptation

''E. coli'' and related bacteria possess the ability to transfer
DNA Deoxyribonucleic acid (; DNA) is a molecule File:Pentacene on Ni(111) STM.jpg, A scanning tunneling microscopy image of pentacene molecules, which consist of linear chains of five carbon rings. A molecule is an electrically neutral gro ...

DNA
via
bacterial conjugation Bacterial conjugation is the transfer of genetic material between Bacteria, bacterial cells by direct cell-to-cell contact or by a bridge-like connection between two cells. This takes place through a pilus. It is a parasexual mode of reproduction in ...
or , which allows genetic material to spread horizontally through an existing population. The process of transduction, which uses the bacterial virus called a
bacteriophage A bacteriophage (), also known informally as a ''phage'' (), is a virus A virus is a submicroscopic infectious agent In biology Biology is the natural science that studies life and living organisms, including their anatomy, ...

bacteriophage
, is where the spread of the gene encoding for the
Shiga toxin Shiga toxins are a family of related toxins with two major groups, Stx1 and Stx2, expressed by genes considered to be part of the genome In the fields of molecular biology and genetics Genetics is a branch of biology concerned ...
from the ''
Shigella ''Shigella'' is a genus Genus (plural genera) is a taxonomic rank Taxonomy (general) is the practice and science of classification of things or concepts, including the principles that underlie such classification. The term may also refer to ...
'' bacteria to ''E. coli'' helped produce ''E. coli'' O157:H7, the Shiga toxin-producing strain of ''E. coli.''


Diversity

''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, 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. 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. Similarly, other strains of ''E. coli'' (e.g. the
K-12 K-1 is a martial arts Martial arts are codified systems and traditions of combat Combat (French language, French for ''fight'') is a purposeful violence, violent conflict meant to physically harm or kill the opposition. Combat may be armed ( ...
strain commonly used in
recombinant DNA Recombinant DNA (rDNA) molecules are DNA Deoxyribonucleic acid (; DNA) is a molecule File:Pentacene on Ni(111) STM.jpg, A scanning tunneling microscopy image of pentacene molecules, which consist of linear chains of five carbon rings ...

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 In ecology Ecology (from el, οἶκος, "house" and el, -λογία, label=none, "study of") is the study of the relationships between living organisms, including humans, and their physical environment. Ecology considers organisms ...

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 Mammals (from Latin Latin (, or , ) is a classical language A classical language is a language A language is a structured system of communication Communication (from Latin ''communicare'', meaning "to share" or "to be i ...
, or a
bird Birds are a group of warm-blooded vertebrate Vertebrates () comprise all species of animal Animals (also called Metazoa) are multicellular eukaryotic organisms that form the Kingdom (biology), biological kingdom Animalia. With ...

bird
.


Serotypes

A common subdivision system of ''E. coli'', but not based on evolutionary relatedness, is by serotype, which is based on major surface
antigen In immunology Immunology is a branch of biology that covers the study of immune systems in all organisms. Immunology charts, measures, and contextualizes the Physiology, physiological functioning of the immune system in states of both health ...
s (O antigen: part of
lipopolysaccharide Lipopolysaccharides (LPS) are large molecule A molecule is an electrically Electricity is the set of physical phenomena associated with the presence and motion Image:Leaving Yongsan Station.jpg, 300px, Motion involves a change ...

lipopolysaccharide
layer; H:
flagellin '' Helicobacter pylori'' electron micrograph, showing multiple flagella on the cell surface Flagellin is a globular protein that arranges itself in a hollow cylinder to form the filament in a bacterial flagellum. It has a mass of about 30,000 to ...
; K antigen: capsule), e.g. O157:H7). It is, however, common to cite only the serogroup, i.e. the O-antigen. At present, about 190 serogroups are known. 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'' through the natural biological processes of
mutation In biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular interactions, Physiology, physiological mechan ...
,
gene duplication Gene duplication (or chromosomal duplication or gene amplification) is a major mechanism through which new genetic material is generated during molecular evolution Molecular evolution is the process of change in the sequence composition of c ...
, and
horizontal gene transfer Horizontal gene transfer (HGT) or lateral gene transfer (LGT) is the movement of genetic material between unicellular A unicellular organism, also known as a single-celled organism, is an organism In biology, an organism (from Ancient G ...
; in particular, 18% of the genome of the ''Escherichia coli'' (molecular biology), laboratory strain MG1655 was horizontally acquired since the divergence from ''Salmonella''. 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. 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. The genera ''
Escherichia ''Escherichia'' is a genus of Gram-negative, non-Endospore, spore-forming, Facultative anaerobic organism, facultatively anaerobic, rod-shaped bacteria from the family Enterobacteriaceae. In those species which are inhabitants of the gastrointest ...
'' and ''Salmonella'' diverged around 102 million years ago (credibility interval: 57–176 mya), which coincides with the divergence of their hosts: the former being found in mammals and the latter in birds and reptiles. 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. 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. 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. 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.


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). 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 U5/41T, also known under the deposit names DSMZ, DSM 30083, American Type Culture Collection, ATCC 11775, and NCTC 9001, which is pathogenic to chickens and has an O1:K1:H7 serotype. 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.


Phylogeny of ''E. coli'' strains

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. 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. 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, 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).


Genomics

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 Deoxyribonucleic acid (; DNA) is a molecule File:Pentacene on Ni(111) STM.jpg, A scanning tunneling microscopy image of pentacene molecules, which consist of linear chains of five carbon rings. A molecule is an electrically neutral gro ...

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 transposon, transposable genetic elements, repeat elements, cryptic prophages, and
bacteriophage A bacteriophage (), also known informally as a ''phage'' (), is a virus A virus is a submicroscopic infectious agent In biology Biology is the natural science that studies life and living organisms, including their anatomy, ...

bacteriophage
remnants. 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.


Gene nomenclature

Genes in ''E. coli'' are usually named in accordance with the uniform nomenclature proposed by Demerec et al. Gene names are 3-letter acronyms that derive from their function (when known) or mutant phenotype and are italicized. When multiple genes have the same acronym, the different genes are designated by a capital later that follows the acronym and is also italicized. For instance, ''recA'' is named after its role in homologous recombination plus the letter A. Functionally related genes are named ''recB'', ''recC'', ''recD'' etc. The proteins are named by uppercase acronyms, e.g. RecA, RecBCD, RecB, etc. When the genome of ''E. coli'' strain K-12 substr. MG1655 was sequenced, all known or predicted protein-coding genes were numbered (more or less) in their order on the genome and abbreviated by b numbers, such as b2819 (= ''recD''). The "b" names were created after Fred 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''). Hence, ''recD'' = b2819 = JW2787. Note, however, that most databases have their own numbering system, e.g. the EcoGene database 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, 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. The 4,639,221–base pair sequence of Escherichia coli K-12 is presented. Of 4288 protein-coding genes annotated, 38 percent have 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.


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. 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. 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. 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. ''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. (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 factors, they remain benign Commensalism, commensals.


Therapeutic use

Due to the low cost and speed with which it can be grown and modified in laboratory settings, ''E. coli'' is a popular expression platform for the production of recombinant proteins used in therapeutics. One advantage to using ''E. coli'' over another expression platform is that ''E. coli'' naturally does not export many proteins into the periplasm, making it easier to recover a protein of interest without cross-contamination. 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. Nonpathogenic ''E. coli'' strain Nissle 1917 (EcN), (Mutaflor) and ''E. coli'' O83:K24:H31 (Colinfant)) are used as probiotic agents in medicine, mainly for the treatment of various gastrointestinal diseases, including inflammatory bowel disease. It is thought that the EcN strain might impede the growth of opportunistic pathogens, including ''Salmonella'' and other Coliform bacteria, coliform enteropathogens, through the production of microcin proteins the production of siderophores.


Role in disease

Most ''E. coli'' strains do not cause disease, naturally living in the gut, but virulent strains can cause gastroenteritis, Uropathogenic Escherichia coli, urinary tract infections, Meningitis#Bacterial, neonatal meningitis, hemorrhagic colitis, and Crohn's disease. 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''. Some strains of ''E. coli'', for example O157:H7, can produce
Shiga toxin Shiga toxins are a family of related toxins with two major groups, Stx1 and Stx2, expressed by genes considered to be part of the genome In the fields of molecular biology and genetics Genetics is a branch of biology concerned ...
(classified as a bioterrorism agent). The Shiga toxin causes inflammatory responses in target cells of the gut, leaving behind lesions which result in the bloody diarrhea that is a symptom of a Shigatoxigenic and verotoxigenic Escherichia coli, Shiga toxin-producing ''E. coli'' (STEC) infection. This toxin further causes premature destruction of the red blood cells, which then clog the body's filtering system, the kidneys, in some rare cases (usually in children and the elderly) causing hemolytic-uremic syndrome (HUS), which may lead to kidney failure and even death. Signs of hemolytic uremic syndrome include decreased frequency of urination, lethargy, and paleness of cheeks and inside the lower eyelids. In 25% of HUS patients, complications of nervous system occur, which in turn causes 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. Pathogenic Escherichia coli#Urinary tract infection, Uropathogenic ''E. coli'' (UPEC) is one of the main causes of urinary tract infections. It is part of the normal microbiota in the gut and can be introduced in many ways. In particular for females, the direction of wiping after defecation (wiping back to front) can lead to fecal contamination of the urogenital orifices. Anal intercourse can also introduce this bacterium into the male urethra, and in switching from anal to vaginal intercourse, the male can also introduce UPEC to the female urogenital system. Enterotoxigenic Escherichia coli, Enterotoxigenic ''E. coli'' (ETEC) is the most common cause of traveler's diarrhea, with as many as 840 million cases worldwide in developing countries each year. The bacteria, typically transmitted through contaminated food or drinking water, adheres to the Intestinal epithelium, intestinal lining, where it secretes either of two types of enterotoxins, leading to watery diarrhea. The rate and severity of infections are higher among children under the age of five, including as many as 380,000 deaths annually. In May 2011, one ''E. coli'' strain, E. coli O104:H4, O104:H4, was the subject of a 2011 E. coli O104:H4 outbreak, bacterial outbreak that began in Germany. Certain strains of ''E. coli'' are a major cause of foodborne illness. The outbreak started when several people in Germany were infected with enterohemorrhagic, enterohemorrhagic ''E. coli'' (EHEC) bacteria, leading to hemolytic-uremic syndrome (HUS), a medical emergency that requires urgent treatment. The outbreak did not only concern Germany, but also 15 other countries, including regions in North America. 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. 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. Carbapenem-resistant ''E. coli'' (carbapenemase-producing ''E. coli'') that are resistant to the carbapenem class of antibiotics, considered the Drug of last resort, drugs of last resort for such infections. They are resistant because they produce an enzyme called a carbapenemase that disables the drug molecule.


Incubation period

The time between ingesting the STEC bacteria and feeling sick is called the "incubation period". The incubation period is usually 3–4 days after the exposure, but may be as short as 1 day or as long as 10 days. The symptoms often begin slowly with mild belly pain or non-bloody diarrhea that worsens over several days. HUS, if it occurs, develops an average 7 days after the first symptoms, when the diarrhea is improving.


Diagnosis

Diagnosis of infectious diarrhea and identification of antimicrobial resistance is performed using a stool culture with subsequent antibiotic sensitivity testing. It requires a minimum of 2 days and maximum of several weeks to culture gastrointestinal pathogens. The sensitivity (true positive) and specificity (true negative) rates for stool culture vary by pathogen, although a number of human pathogens can not be microbiological culture, cultured. For culture-positive samples, antimicrobial resistance testing takes an additional 12–24 hours to perform. Current point of care molecular diagnostic tests can identify ''E. coli'' and antimicrobial resistance in the identified strains much faster than culture and sensitivity testing. Microarray-based platforms can identify specific pathogenic strains of ''E. coli'' and ''E. coli''-specific AMR genes in two hours or less with high sensitivity and specificity, but the size of the test panel (i.e., total pathogens and antimicrobial resistance genes) is limited. Newer Metagenomics#Infectious disease diagnosis, metagenomics-based infectious disease diagnostic platforms are currently being developed to overcome the various limitations of culture and all currently available molecular diagnostic technologies.


Treatment

The mainstay of treatment is the assessment of dehydration and replacement of fluid and electrolytes. Administration of antibiotics has been shown to shorten the course of illness and duration of excretion of enterotoxigenic ''E. coli'' (ETEC) in adults in endemic areas and in traveller's diarrhea, though the rate of resistance to commonly used antibiotics is increasing and they are generally not recommended. 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. Oral 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.


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. 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. 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, avoid cross-contamination of utensils and work spaces when preparing food.


Model organism in life science research

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. The work of Stanley Norman Cohen and Herbert Boyer in ''E. coli'', using plasmids and restriction enzymes to create
recombinant DNA Recombinant DNA (rDNA) molecules are DNA Deoxyribonucleic acid (; DNA) is a molecule File:Pentacene on Ni(111) STM.jpg, A scanning tunneling microscopy image of pentacene molecules, which consist of linear chains of five carbon rings ...

recombinant DNA
, became a foundation of biotechnology. ''E. coli'' is a very versatile host for the production of heterologous proteins, 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. 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, 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''. Modified ''E. coli'' cells have been used in vaccine development, bioremediation, production of biofuels, lighting, and production of immobilised enzymes. Strain K-12 is a mutant form of ''E. coli'' that over-expresses the enzyme Alkaline phosphatase, Alkaline Phosphatase (ALP). The mutation arises due to a defect in the gene that constantly codes for the enzyme. A gene that is producing a product without any inhibition is said to have Receptor (biochemistry), constitutive activity. This particular mutant form is used to isolate and purify the aforementioned enzyme. 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. Lack of recA decreases the possibility of unwanted restriction of the DNA of interest and lack of endA inhibit plasmid DNA decomposition. Thus, JM109 is useful for cloning and expression systems.


Model organism

''E. coli'' is frequently used as a model organism in
microbiology Microbiology (from Greek#REDIRECT Greek Greek may refer to: Greece Anything of, from, or related to Greece Greece ( el, Ελλάδα, , ), officially the Hellenic Republic, is a country located in Southeast Europe. Its population is appro ...

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. These features protect wild-type strains from antibody, antibodies and other chemical attacks, but require a large expenditure of energy and material resources. ''E. coli'' is often used as a representative microorganism in the research of novel water treatment and sterilisation methods, including photocatalysis. By standard Bacteriological water analysis#Plate count, plate count methods, following sequential dilutions, and growth on agar gel plates, the concentration of viable organisms or CFUs (Colony Forming Units), in a known volume of treated water can be evaluated, allowing the comparative assessment of materials performance. In 1946, Joshua Lederberg and Edward Tatum first described the phenomenon known as
bacterial conjugation Bacterial conjugation is the transfer of genetic material between Bacteria, bacterial cells by direct cell-to-cell contact or by a bridge-like connection between two cells. This takes place through a pilus. It is a parasexual mode of reproduction in ...
using ''E. coli'' as a model bacterium, and it remains the primary model to study conjugation. ''E. coli'' was an integral part of the first experiments to understand bacteriophage, phage genetics, and early researchers, such as Seymour Benzer, used ''E. coli'' and phage T4 to understand the topography of gene structure. Prior to Benzer's research, it was not known whether the gene was a linear structure, or if it had a branching pattern. ''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", 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. Biochemistry and replication machinery were not altered. By evaluating the possible combination of Nanotechnology, nanotechnologies with landscape ecology, complex habitat landscapes can be generated with details at the nanoscale. 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.


Uses in biological computing

Since 1961, scientists proposed the idea of genetic circuits used for computational tasks. Collaboration between biologists and computing scientists has allowed designing digital logic gates on the metabolism of ''E. Coli''. As Lac operon is a two-stage process, genetic regulation in the bacteria is used to realize computing functions. The process is controlled at the transcription stage of DNA into messenger RNA. Studies are being performed attempting to program ''E. coli'' to solve complicated mathematics problems, such as the Hamiltonian path problem. In 2011, researchers at ETH Zurich and the University of California used a computer to control protein production of ''E. Coli'' within Yeast cell, yeast cells. A team at the University of California achieved to program the bacteria to behave as an Liquid-crystal display, LCD screen. In July 2017, separate experiments with ''E. Coli'' published on Nature showed the potential of using living cells for computing tasks and storing information. A team formed with collaborators of the The Biodesign Institute, Biodesign Institute at Arizona State University and Harvard’s Wyss Institute for Biologically Inspired Engineering developed a biological computer inside ''E. Coli'' that responded to a dozen inputs. The team called the computer "ribocomputer", as it was composed of RNA, ribonucleic acid. 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. In 2021, a team led by biophysicist Sangram Bagh realized a study with E. coli to solve Maze, 2 x 2 maze problems to probe the principle for distributed computing among cells.


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 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). ''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. Following a revision of ''Bacterium'', it was reclassified as ''Bacillus coli'' by Migula in 1895 and later reclassified in the newly created genus ''
Escherichia ''Escherichia'' is a genus of Gram-negative, non-Endospore, spore-forming, Facultative anaerobic organism, facultatively anaerobic, rod-shaped bacteria from the family Enterobacteriaceae. In those species which are inhabitants of the gastrointest ...
'', List of bacterial genera named after personal names, named after its original discoverer. In 1996, the world's worst to date outbreak of ''E. coli'' food poisoning occurred in Wishaw, Scotland, killing 21 people. This death toll was exceeded in 2011, when the 2011 Germany E. coli O104:H4 outbreak, linked to organic fenugreek sprouts, killed 53 people.


Uses

E. coli has several practical uses besides its use as a vector for genetic experiments and processes. For example, E. coli can be used to generate synthetic propane.


See also

* Bacteriological water analysis * Carbon monoxide-releasing molecules * Contamination control * Dam dcm strain * Eijkman test * Fecal coliform * International Code of Nomenclature of Bacteria * List of strains of Escherichia coli, List of strains of ''Escherichia coli'' * Mannan oligosaccharide-based nutritional supplements * Overflow metabolism * T4 rII system


References


Databases and external links

* EcoCyc – literature-based curation of the entire genome, and of transcriptional regulation, transporters, and metabolic pathways * Membranome database provides information about single-pass transmembrane proteins from E.coli and several other organisms
''E. coli'' statistics



Bacteriome
''E. coli'' interaction database
EcoGene
(genome database and website dedicated to Escherichia coli K-12 substrain MG1655)
EcoSal
Continually updated Web resource based on the classic ASM Press publication ''Escherichia coli and Salmonella: Cellular and Molecular Biology''
ECODAB
The structure of the O-antigens that form the basis of the serological classification of ''E. coli''
Coli Genetic Stock Center
Strains and genetic information on ''E. coli'' K-12
PortEco (formerly EcoliHub)
– NIH-funded comprehensive data resource for ''E. coli'' K-12 and its phage, plasmids, and mobile genetic elements
EcoliWiki
is the community annotation component o
PortEco

RegulonDB
RegulonDB is a model of the complex regulation of transcription initiation or regulatory network of the cell ''E. coli'' K-12.


AlignACE
Matrices that search for additional binding sites in the ''E. coli'' genomic sequence
E.coli on Protein Data Bank
{{Authority control Escherichia coli, Gut flora bacteria Neglected tropical diseases Tropical diseases Model organisms Bacteria described in 1919