Escherichia coli
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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 that do not retain the Crystal violet, crystal violet stain used in the Gram staining method of bacterial differentiation. They are characterized by their cell envelopes, which are composed of a thin peptidogly ...
, facultative anaerobic, rod-shaped, 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 gastroint ...
'' 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 that leads from the mouth to the anus. The GI tract contains all the major organ (biology), organs of the digestive syste ...
of
warm-blooded Warm-blooded is an informal term referring to animal species which can maintain a body temperature higher than their environment. In particular, homeothermy, homeothermic species maintain a stable body temperature by regulating metabolic proce ...
organisms. Most ''E. coli'' strains are harmless, but some
serotype A serotype or serovar is a distinct variation within a species of bacteria or virus or among immune cells of different individuals. These microorganisms, viruses, or Cell (biology), cells are classified together based on their surface antigens, ...
s ( EPEC, ETEC etc.) can cause serious
food poisoning Foodborne illness (also foodborne disease and food poisoning) is any Disease, illness resulting from the spoilage of food contaminant, contaminated food by pathogenic bacteria, viruses, or parasites that contaminate food, as well as prions (the ...
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. Most strains do not cause disease in humans and are part of the normal microbiota of the gut; such strains are harmless or even beneficial to humans (although these strains tend to be less studied than the pathogenic ones). For example, some strains of ''E. coli'' benefit their hosts by producing vitamin K2 or by preventing the colonization of the intestine by
pathogenic bacteria Pathogenic bacteria are bacteria that can cause disease. This article focuses on the bacteria that are pathogenic to humans. Most species of bacteria are harmless and are often Probiotic, beneficial but others can cause infectious diseases. The n ...
. These mutually beneficial relationships between ''E. coli'' and humans are a type of mutualistic biological relationship — where both the humans and the ''E. coli'' are benefitting each other. ''E. coli'' is expelled into the environment within fecal matter. The bacterium grows massively in fresh faecal matter under aerobic conditions for three 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, fungi and helminth eggs are being used for various purposes. Types Indicator bacteria ...
s to test environmental samples for fecal contamination. 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 whose chemically defined medium must include a source of carbon and energy. ''E. coli'' is the most widely studied
prokaryotic A prokaryote () is a Unicellular organism, single-celled organism that lacks a cell nucleus, nucleus and other membrane-bound organelles. The word ''prokaryote'' comes from the Greek language, Greek wikt:πρό#Ancient Greek, πρό (, 'before') a ...
model organism A model organism (often shortened to model) is a non-human species that is extensively studied to understand particular biology, biological phenomena, with the expectation that discoveries made in the model organism will provide insight into th ...
, and an important species in the fields of
biotechnology Biotechnology is the integration of Natural science, natural sciences and Engineering Science, engineering sciences in order to achieve the application of organisms, cells, parts thereof and molecular analogues for products and services. The te ...
and
microbiology Microbiology () is the scientific study of microorganisms, those being unicellular (single cell), multicellular (cell colony), or acellular (lacking cells). Microbiology encompasses numerous sub-disciplines including virology, bacteriolog ...
, where it has served as the
host organism In biology and medicine, a host is a larger organism that harbours a smaller organism; whether a parasite, parasitic, a mutualism (biology), mutualistic, or a commensalism, commensalist ''guest'' (symbiont). The guest is typically provided with ...
for the majority of work with
recombinant DNA Recombinant DNA (rDNA) molecules are DNA molecules formed by laboratory methods of genetic recombination (such as molecular cloning) that bring together genetic material from multiple sources, creating DNA sequence, sequences that would not othe ...
. Under favourable 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 that do not retain the Crystal violet, crystal violet stain used in the Gram staining method of bacterial differentiation. They are characterized by their cell envelopes, which are composed of a thin peptidogly ...
, facultative anaerobe, nonsporulating coliform bacterium. Cells are typically rod-shaped, and are about 2.0 μm long and 0.25–1.0 μm in diameter, with a cell volume of 0.6–0.7 μm3. 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 certain plant and animal sperm cells, and from a wide range of microorganisms to provide Motility#Cellular level, motility. Many protists with flagella are termed as flagellates. A m ...
which allow the bacteria to swim have a peritrichous arrangement. It also attaches and effaces to the microvilli of the intestines via an adhesion molecule known as intimin.


Metabolism

''E. coli'' can live on a wide variety of substrates and uses mixed acid fermentation in anaerobic conditions, producing lactate, succinate,
ethanol Ethanol (abbr. EtOH; also called ethyl alcohol, grain alcohol, drinking alcohol, or simply alcohol) is an organic compound. It is an Alcohol (chemistry), alcohol with the chemical formula . Its formula can be also written as or (an ethyl ...
,
acetate An acetate is a salt (chemistry), salt formed by the combination of acetic acid with a base (e.g. Alkali metal, alkaline, Alkaline earth metal, earthy, Transition metal, metallic, nonmetallic or radical Radical (chemistry), base). "Acetate" als ...
, and
carbon dioxide Carbon dioxide ( chemical formula ) is a chemical compound made up of molecules that each have one carbon Carbon () is a chemical element with the chemical symbol, symbol C and atomic number 6. It is nonmetallic and tetravalence, tetraval ...
. 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 chemical ...
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 as a Metabolism, metabolic byproduct in Hypoxia (environmental), hypoxic conditions. They are Prokaryote, prokaryotic and belong to the Domain (biology), domain Archaea. All known methanogens are ...
s or sulphate-reducing bacteria. In addition, ''E. coli''s metabolism can be rewired to solely use CO2 as the source of carbon for biomass production. In other words, this obligate heterotroph's metabolism can be altered to display autotrophic capabilities by heterologously expressing
carbon fixation Biological carbon fixation or сarbon assimilation is the process by which inorganic carbon (particularly in the form of carbon dioxide) is redox, converted to organic compounds by living organisms. The compounds are then used to store energy ...
genes as well as
formate dehydrogenase Formate dehydrogenases are a set of enzyme Enzymes () are proteins that act as biological catalysts by accelerating chemical reactions. The molecules upon which enzymes may act are called substrate (chemistry), substrates, and the enzyme co ...
and conducting laboratory evolution experiments. This may be done by using
formate Formate (IUPAC name: methanoate) is the conjugate base of formic acid. Formate is an anion () or its derivatives such as ester of formic acid. The salts and esters are generally colorless.Werner Reutemann and Heinz Kieczka "Formic Acid" in ''Ull ...
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, EDP, and OPPP. The EMPP employs ten enzymatic steps to yield two pyruvates, two 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 phosphat ...
per
glucose Glucose is a simple sugar with the Chemical formula#Molecular formula, molecular formula . Glucose is overall the most abundant monosaccharide, a subcategory of carbohydrates. Glucose is mainly made by plants and most algae during photosynthesis f ...
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 (biochemistry), cofactor used in anabolic reactions, such as the Calvin cycle and lipid and nucleic acid synth ...
synthesis. Although the EDP is the more thermodynamically favourable of the three pathways, ''E. coli'' do not use the EDP for
glucose metabolism Carbohydrate metabolism is the whole of the biochemistry, biochemical processes responsible for the metabolic anabolism, formation, catabolism, breakdown, and interconversion of carbohydrates in life, living organisms. Carbohydrates are central t ...
, 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 for ...
.


Catabolite repression

When growing in the presence of a mixture of sugars, bacteria will often consume the sugars sequentially through a process known as catabolite repression. By repressing the expression of the genes involved in metabolizing the less preferred sugars, cells will usually first consume the sugar yielding the highest growth rate, followed by the sugar yielding the next highest growth rate, and so on. In doing so the cells ensure that their limited metabolic resources are being used to maximize the rate of growth. The well-used example of this with ''E. coli'' involves the growth of the bacterium on glucose and lactose, where ''E. coli'' will consume glucose before lactose. Catabolite repression has also been observed in ''E. coli'' in the presence of other non-glucose sugars, such as
arabinose Arabinose is an aldopentose – a monosaccharide containing five carbon atoms, and including an aldehyde (CHO) functional group. For biosynthetic reasons, most saccharides are almost always more abundant in nature as the "D"-form, or structurally ...
and
xylose Xylose ( grc, ξύλον, , "wood") is a sugar first isolated from wood, and named for it. Xylose is classified as a monosaccharide of the aldopentose type, which means that it contains five carbon Carbon () is a chemical element with t ...
,
sorbitol Sorbitol (), less commonly known as glucitol (), is a sugar alcohol Sugar alcohols (also called polyhydric alcohols, polyalcohols, alditols or glycitols) are organic compounds, typically derivative (chemistry), derived from sugars, containing o ...
,
rhamnose Rhamnose (Rha, Rham) is a naturally occurring deoxy sugar. It can be classified as either a methyl-pentose or a 6-deoxy-hexose. Rhamnose predominantly occurs in nature in its L-form, L-form as L-rhamnose (6-deoxy-L-mannose). This is unusual, since ...
, 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 ...
. In ''E. coli'', glucose catabolite repression is regulated by the phosphotransferase system, a multi-protein
phosphorylation In chemistry Chemistry is the scientific study of the properties and behavior of matter. It is a natural science that covers the elements that make up matter to the compounds made of atoms, molecules and ions: their composition, struc ...
cascade that couples glucose uptake and metabolism.


Culture growth

Optimum growth of ''E. coli'' occurs at , but some laboratory strains can multiply at temperatures up to . ''E. coli'' grows in a variety of defined laboratory media, such as
lysogeny broth 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, intended LB to stand for lysogeny broth, but LB has also come to co ...
, 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 ...
or
anaerobic respiration Anaerobic respiration is respiration using electron acceptors other than molecular oxygen (O2). Although oxygen is not the final electron acceptor, the process still uses a respiratory electron transport chain. In aerobic organisms Aerobic m ...
, using a large variety of redox pairs, including the oxidation of
pyruvic acid Pyruvic acid (CH3COCOOH) is the simplest of the keto acids, alpha-keto acids, with a carboxylic acid and a ketone functional group. Pyruvate, the conjugate acid, conjugate base, CH3COCOO−, is an intermediate in several metabolic pathways throug ...
,
formic acid Formic acid (), Preferred IUPAC name, systematically named methanoic acid, is the simplest carboxylic acid, and has the chemical formula HCOOH and structure . It is an important intermediate in chemical synthesis and occurs naturally, most nota ...
,
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 chemical ...
, and
amino acid Amino acids are organic compound In chemistry, organic compounds are generally any chemical compounds that contain carbon-hydrogen or carbon-carbon chemical bond, bonds. Due to carbon's ability to Catenation, catenate (form chains with ot ...
s, and the reduction of substrates such as
oxygen Oxygen is the chemical element with the chemical symbol, symbol O and atomic number 8. It is a member of the chalcogen Group (periodic table), group in the periodic table, a highly Chemical reaction, reactive nonmetal, and an oxidizing a ...
,
nitrate Nitrate is a polyatomic ion with the chemical formula . salt (chemistry), Salts containing this ion are called nitrates. Nitrates are common components of fertilizers and explosives. Almost all inorganic nitrates are solubility, soluble in wat ...
,
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 salt (chemistry), salts and ester ...
,
dimethyl sulfoxide Dimethyl sulfoxide (DMSO) is an organosulfur compound with the chemical formula, formula (methyl, CH3)2. This colorless liquid is the sulfoxide most widely used commercially. It is an important polar solvent, polar aprotic solvent that dissolves ...
, and
trimethylamine N-oxide Trimethylamine ''N''-oxide (TMAO) is an organic compound with the formula (CH3)3NO. It is in the class of amine oxides. Although the anhydrous compound is known, trimethylamine ''N''-oxide is usually encountered as the water of crystallization, d ...
. ''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. Respiraton type is managed in part by the arc system. The ability to continue growing in the absence of oxygen is an advantage to bacteria because their survival is increased in environments where water predominates.


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 replication is initiated simultaneously from all origins of replications, and is referred to as synchronous replication. However, not all cells in a culture replicate synchronously. In this case cells do not have multiples of two
replication fork In molecular biology, DNA replication is the biological process of producing two identical replicas of DNA from one original DNA molecule. DNA replication occurs in all life, living organisms acting as the most essential part for heredity, biologi ...
s. Replication initiation is then referred to being asynchronous. However, asynchrony can be caused by mutations to for instance
DnaA Introduction Based on the Replicon Model, a positively active initiator molecule contacts with a particular spot on a circular chromosome called the replicator to start DNA replication. DnaA is a protein that activates initiation of DNA replica ...
or
DnaA Introduction Based on the Replicon Model, a positively active initiator molecule contacts with a particular spot on a circular chromosome called the replicator to start DNA replication. DnaA is a protein that activates initiation of DNA replica ...
initiator-associating protein
DiaA Diaa ( 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 footba ...
.


Genetic adaptation

''E. coli'' and related bacteria possess the ability to transfer 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 i ...
or transduction, which allows genetic material to spread horizontally through an existing population. The process of transduction, which uses the bacterial virus called a
bacteriophage A bacteriophage (), also known informally as a ''phage'' (), is a duplodnaviria virus that infects and replicates within bacteria and archaea. The term was derived from "bacteria" and the Greek language, Greek φαγεῖν ('), meaning "to d ...
, is where the spread of the gene encoding for the Shiga toxin from the ''
Shigella ''Shigella'' is a genus of bacteria that is Gram-negative, facultative aerobic organism, facultative anaerobic, Endospore, non-spore-forming, nonmotile, Bacillus (shape), rod-shaped, and genetically closely related to ''Escherichia coli, E. coli ...
'' 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 professional kickboxing promotion established in 1993, well known worldwide mainly for its heavyweight division fights and Grand Prix tournaments. In January 2012, K-1 Global Holdings Limited, a company registered in Hong Kong, acquired ...
strain commonly used in
recombinant DNA Recombinant DNA (rDNA) molecules are DNA molecules formed by laboratory methods of genetic recombination (such as molecular cloning) that bring together genetic material from multiple sources, creating DNA sequence, sequences that would not othe ...
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, a niche is the match of a species to a specific environmental condition. Three variants of ecological niche are described by It describes how an organism or population responds to the distribution of Resource (biology), resources a ...
, 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 () are a group of vertebrate animals constituting the class Mammalia (), characterized by the presence of mammary glands which in females produce milk for feeding (nursing) their young, a neocortex (a region of the brain), fu ...
, or a
bird Birds are a group of warm-blooded vertebrates constituting the class (biology), class Aves (), characterised by feathers, toothless beaked jaws, the Oviparity, laying of Eggshell, hard-shelled eggs, a high Metabolism, metabolic rate, a fou ...
.


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, an antigen (Ag) is a molecule A molecule is a group of two or more atoms held together by attractive forces known as chemical bonds; depending on context, the term may or may not include ions which satisfy this criterion. ...
s (O antigen: part of
lipopolysaccharide Lipopolysaccharides (LPS) are large molecules consisting of a lipid and a polysaccharide that are bacterial toxins. They are composed of an O-antigen, an outer core, and an inner core all joined by a covalent bond, and are found in the Bacterial ...
layer; H:
flagellin 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 60,000 Atomic mass unit, daltons. Flagellin is the principal component of bacterial flagell ...
; 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'' evolve through the natural biological processes of
mutation In biology, a mutation is an alteration in the nucleic acid sequence of the genome of an organism, virus, or extrachromosomal DNA. Viral genomes contain either DNA or RNA. Mutations result from errors during DNA replication, DNA or viral repl ...
,
gene duplication Gene duplication (or chromosomal duplication or gene amplification) is a major mechanism through which new genetic material is generated during molecular evolution. It can be defined as any duplication of a region of DNA that contains a gene. ...
, and
horizontal gene transfer Horizontal gene transfer (HGT) or lateral gene transfer (LGT) is the movement of genetic material between Unicellular organism, unicellular and/or multicellular organisms other than by the ("vertical") transmission of DNA from parent to offsprin ...
; in particular, 18% of the genome of the laboratory strain MG1655 was horizontally acquired since the divergence from ''
Salmonella ''Salmonella'' is a genus of bacillus (shape), rod-shaped (bacillus) Gram-negative bacteria of the family Enterobacteriaceae. The two species of ''Salmonella'' are ''Salmonella enterica'' and ''Salmonella bongori''. ''S. enterica'' is the type s ...
''. ''E. coli'' K-12 and ''E. coli'' B strains are the most frequently used varieties for laboratory purposes. Some strains develop traits that can be harmful to a host animal. These
virulent Virulence is a pathogen In biology, a pathogen ( el, πάθος, "suffering", "passion" and , "producer of") in the oldest and broadest sense, is any organism or agent that can produce disease. A pathogen may also be referred to as an infecti ...
strains typically cause a bout of
diarrhea Diarrhea, also spelled diarrhoea, is the condition of having at least three loose, liquid, or watery bowel movements each day. It often lasts for a few days and can result in dehydration due to fluid loss. Signs of dehydration often begin ...
that is often self-limiting in healthy adults but is frequently lethal to children in the developing world. More virulent strains, such as O157:H7, cause serious illness or death in the elderly, the very young, or the
immunocompromised Immunodeficiency, also known as immunocompromisation, is a state in which the immune system's ability to fight infectious diseases and cancer is compromised or entirely absent. Most cases are acquired ("secondary") due to extrinsic factors that a ...
. 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 gastroint ...
'' and ''
Salmonella ''Salmonella'' is a genus of bacillus (shape), rod-shaped (bacillus) Gram-negative bacteria of the family Enterobacteriaceae. The two species of ''Salmonella'' are ''Salmonella enterica'' and ''Salmonella bongori''. ''S. enterica'' is the type s ...
'' diverged around 102 million years ago (credibility interval: 57–176 mya), an event unrelated to the much earlier (see ''
Synapsid Synapsids + (, 'arch') > () "having a fused arch"; synonymous with ''theropsids'' (Greek, "beast-face") are one of the two major groups of animals that evolved from basal amniotes, the other being the Sauropsida, sauropsids, the group that inc ...
'') 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 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 ''Salmonella'' is a genus of bacillus (shape), rod-shaped (bacillus) Gram-negative bacteria of the family Enterobacteriaceae. The two species of ''Salmonella'' are ''Salmonella enterica'' and ''Salmonella bongori''. ''S. enterica'' is the type s ...
''. In this experiment, one population of ''E. coli'' unexpectedly evolved the ability to aerobically metabolize
citrate Citric acid is an organic compound with the chemical formula HOC(CO2H)(CH2CO2H)2. It is a Transparency and translucency, colorless Weak acid, weak organic acid. It occurs naturally in Citrus, citrus fruits. In biochemistry, it is an intermedi ...
, a major evolutionary shift with some hallmarks of microbial
speciation Speciation is the evolutionary process by which populations evolve to become distinct species. The biologist Orator F. Cook coined the term in 1906 for cladogenesis, the splitting of lineages, as opposed to anagenesis, phyletic evolution within ...
. 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 ''Myxococcus xanthus'' is a gram-negative, rod-shaped species of myxobacteria that exhibits various forms of self-organizing behavior in response to environmental cues. Under normal conditions with abundant food, it exists as a predatory bacteria ...
''. 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 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 duplodnaviria virus that infects and replicates within bacteria and archaea. The term was derived from "bacteria" and the Greek language, Greek φαγεῖν ('), meaning "to d ...
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

The genome sequence of ''E. coli'' predicts 4288 protein-coding genes, of which 38 percent initially had no attributed function. Comparison with five other sequenced microbes reveals ubiquitous as well as narrowly distributed gene families; many families of similar genes within ''E. coli'' are also evident. The largest family of paralogous proteins contains 80 ABC transporters. The genome as a whole is strikingly organized with respect to the local direction of replication; guanines, oligonucleotides possibly related to replication and recombination, and most genes are so oriented. The genome also contains insertion sequence (IS) elements, phage remnants, and many other patches of unusual composition indicating genome plasticity through horizontal transfer. Several studies have experimentally investigated the proteome of ''E. coli''. By 2006, 1,627 (38%) of the predicted proteins (open reading frames, ORFs) had been identified experimentally. Mateus et al. 2020 detected 2,586 proteins with at least 2 peptides (60% of all proteins).


Post-translational modifications (PTMs)

Although much fewer bacterial proteins seem to have post-translational modifications (PTMs) compared to Eukaryote, eukaryotic proteins, a substantial number of proteins are modified in ''E. coli''. For instance, Potel et al. (2018) found 227 phosphoproteins of which 173 were phosphorylated on histidine. Interestingly, the majority of phosphorylated
amino acid Amino acids are organic compound In chemistry, organic compounds are generally any chemical compounds that contain carbon-hydrogen or carbon-carbon chemical bond, bonds. Due to carbon's ability to Catenation, catenate (form chains with ot ...
s were serine (1,220 sites) with only 246 sites on histidine and 501 phosphorylated Threonine, theronines and 162 tyrosines.


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 ''Salmonella'' is a genus of bacillus (shape), rod-shaped (bacillus) Gram-negative bacteria of the family Enterobacteriaceae. The two species of ''Salmonella'' are ''Salmonella enterica'' and ''Salmonella bongori''. ''S. enterica'' is the type s ...
'' 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 (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, cross-contamination of utensils and work spaces should be avoided 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 molecules formed by laboratory methods of genetic recombination (such as molecular cloning) that bring together genetic material from multiple sources, creating DNA sequence, sequences that would not othe ...
, 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 () is the scientific study of microorganisms, those being unicellular (single cell), multicellular (cell colony), or acellular (lacking cells). Microbiology encompasses numerous sub-disciplines including virology, bacteriolog ...
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 i ...
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. A computer to control protein production of ''E. coli'' within yeast cells has been developed. A method has also been developed to use 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 × 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 gastroint ...
'', List of bacterial genera named after personal names, named after its original discoverer, by Aldo Castellani and Albert John Chalmers. 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, 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 and recombinant human growth hormone.


See also

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


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 Tropical diseases Model organisms Bacteria described in 1919