_ Bacillus coli communis_ Escherich 1885
_ESCHERICHIA COLI_ (/ˌɛʃᵻˈrɪkiə ˈkoʊlaɪ/ ; also known as
_E. COLI_) is a gram-negative , facultatively anaerobic , rod-shaped ,
coliform bacterium of the genus _
_E. coli_ and other facultative anaerobes constitute about 0.1% of gut flora , 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 organisms to test environmental samples for fecal contamination . A growing body of research, though, has examined environmentally persistent _E. coli_ which can survive for extended periods outside of 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 model organism , and an important species
in the fields of biotechnology and microbiology , where it has served
as the host organism for the majority of work with recombinant
* 1 Biology and biochemistry
* 1.1 Type and morphology * 1.2 Metabolism * 1.3 Culture growth * 1.4 Cell cycle * 1.5 Genetic adaptation
* 2 Diversity
* 3 Genomics * 4 Gene nomenclature
* 5 Proteomics
* 6 Normal microbiota
* 6.1 Therapeutic use
* 7 Role in disease
* 7.1 Incubation period * 7.2 Treatment * 7.3 Prevention * 7.4 Causes and risk factors
* 8 Model organism in life science research
* 8.1 Role in biotechnology * 8.2 Model organism
* 9 History * 10 See also * 11 References * 12 Further reading
* 13 External links
* 13.1 Databases * 13.2 General databases with _E. coli_-related information
BIOLOGY AND BIOCHEMISTRY
_ Model of successive binary fission in E. coli_ _ A colony of E. coli_ growing
TYPE AND MORPHOLOGY
_E. coli_ is a Gram-negative, facultative anaerobic (that makes ATP by aerobic respiration if oxygen is present, but is capable of switching to fermentation or anaerobic respiration if oxygen is absent) and nonsporulating 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.
_E. coli_ stains Gram-negative because its cell wall is composed of a thin peptidoglycan layer and an outer membrane. During the staining process, _E. coli_ picks up the color of the counterstain safranin and stains pink. The outer membrane surrounding the cell wall provides a barrier to certain antibiotics such that _E. coli_ is not damaged by penicillin.
Strains that possess flagella are motile . The flagella have a peritrichous arrangement.
_E. coli_ can live on a wide variety of substrates and uses mixed-acid fermentation in anaerobic conditions, producing lactate , succinate , ethanol , acetate , and carbon dioxide . Since many pathways in mixed-acid fermentation produce hydrogen gas, these pathways require the levels of hydrogen to be low, as is the case when _E. coli_ lives together with hydrogen-consuming organisms, such as methanogens or sulphate-reducing bacteria .
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 , or any medium that contains glucose, ammonium phosphate, monobasic, sodium chloride, magnesium sulfate, potassium phosphate, dibasic, and water. Growth can be driven by aerobic or anaerobic respiration , using a large variety of redox pairs , including the oxidation of pyruvic acid , formic acid , hydrogen , and amino acids , and the reduction of substrates such as oxygen , nitrate , fumarate , dimethyl sulfoxide , and trimethylamine N-oxide . _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.
Main article: Cell cycle
The bacterial cell cycle is divided into three stages. The B period
occurs between the completion of cell division and the beginning of
Unlike eukaryotes, prokaryotes do not rely upon either changes in gene expression or changes in protein synthesis to control the cell cycle. This probably explains why they do not have similar proteins to those used by eukaryotes to control their cell cycle, such as cdk1 . This has led to research on what the control mechanism is in prokaryotes. Recent evidence suggests that it may be membrane- or lipid-based.
_E. coli_ and related bacteria possess the ability to transfer DNA
via bacterial conjugation or transduction , which allows genetic
material to spread horizontally through an existing population. The
process of transduction, which uses the bacterial virus called a
bacteriophage , is where the spread of the gene encoding for the
Shiga toxin from the _
_ Scanning electron micrograph of an E. coli_ colony.
_E. coli_ encompasses an enormous population of bacteria that exhibit a very high degree of both genetic and phenotypic diversity. Genome sequencing of a large number of isolates of _E. coli_ and related bacteria shows that a taxonomic reclassification would be desirable. However, this has not been done, largely due to its medical importance, 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 evolutionary point of view, the members of genus
_Shigella_ (_S. dysenteriae_, _S. flexneri_, _S. boydii_, and _S.
sonnei_) should be classified as _E. coli_ strains, a phenomenon
termed taxa in disguise . Similarly, other strains of _E. coli_ (e.g.
the K-12 strain commonly used in recombinant
A strain is a subgroup within the species that has unique characteristics that distinguish it from other strains. These differences are often detectable only at the molecular level; however, they may result in changes to the physiology or lifecycle of the bacterium. For example, a strain may gain pathogenic capacity , the ability to use a unique carbon source, the ability to take upon a particular ecological niche , or the ability to resist antimicrobial agents. Different strains of _E. coli_ are often host-specific, making it possible to determine the source of fecal contamination in environmental samples. For example, knowing which _E. coli_ strains are present in a water sample allows researchers to make assumptions about whether the contamination originated from a human, another mammal , or a bird .
Main article: Pathogenic Escherichia coli § Serotypes
A common subdivision system of _E. coli_, but not based on evolutionary relatedness, is by serotype, which is based on major surface antigens (O antigen: part of lipopolysaccharide layer; H: flagellin ; K antigen: capsule), e.g. O157:H7). 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 , gene duplication , and horizontal gene transfer ; in particular, 18% of the genome of the laboratory strain MG1655 was horizontally acquired since the divergence from _ Salmonella _. _E. coli_ K-12 and _E. coli_ B strains are the most frequently used varieties for laboratory purposes. Some strains develop traits that can be harmful to a host animal. These virulent strains typically cause a bout of diarrhea that is often self-limiting in healthy adults but is frequently lethal to children in the developing world. More virulent strains, such as O157:H7 , cause serious illness or death in the elderly, the very young, or the immunocompromised .
The genera _
The long-term evolution experiments using _E. coli_ , begun by Richard Lenski in 1988, have allowed direct observation of major evolutionary shifts in the laboratory. In this experiment, one population of _E. coli_ unexpectedly evolved the ability to aerobically metabolize citrate , which is extremely rare in _E. coli_. As the inability to grow aerobically is normally used as a diagnostic criterion with which to differentiate _E. coli_ from other, closely related bacteria, such as _Salmonella_, this innovation may mark a speciation event observed in the laboratory.
_E. coli_ is the type species of the genus (_Escherichia_) and in turn _Escherichia_ is the type genus of the family Enterobacteriaceae, where the family name does not stem from the genus _Enterobacter_ + "i" (sic.) + "aceae ", but from "enterobacterium" + "aceae" (enterobacterium being not a genus, but an alternative trivial name to enteric bacterium).
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 DSM 30083 , 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
A large number of strains belonging to this species have been isolated and characterised. In addition to serotype (_vide supra_), they can be classified according to their phylogeny , i.e. the inferred evolutionary history, as shown below where the species is divided into six groups. Particularly the use of 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 of this group. Indeed, all _Shigella_ species were placed within a single subspecies of _E. coli_ in a phylogenomic study that included the type strain, and for this reason an according reclassification is difficult. All commonly used research strains of _E. coli_ belong to group A and are derived mainly from Clifton's K-12 strain (λ⁺ F⁺; O16) and to a lesser degree from d\'Herelle 's _ Bacillus coli _ strain (B strain)(O7).
_ Salmonella enterica _
_E. coli_ SE15 (O150:H5. Commensal)
_E. coli_ E2348/69 (O127:H6. Enteropathogenic)
_E. coli_ ED1a O81 (Commensal)
_E. coli_CFT083 (O6:K2:H1. UPEC)
_E. coli_ APEC O1 (O1:K12:H7. APEC
_E. coli_ UTI89 O18:K1:H7. UPEC)
_E. coli_ S88 (O45:K1. Extracellular pathogenic)
_E. coli_ F11
_E. coli_ 536
_E. coli_ UMN026 (O17:K52:H18. Extracellular pathogenic)
_E. coli_ (O19:H34. Extracellular pathogenic)
_E. coli_ (O7:K1. Extracellular pathogenic)
_E. coli_ EDL933 (O157:H7 EHEC)
_E. coli_ Sakai (O157:H7 EHEC)
_E. coli_ EC4115 (O157:H7 EHEC)
_E. coli_ TW14359 (O157:H7 EHEC)
_E. coli_ E24377A (O139:H28. Enterotoxigenic)
_E. coli_ E110019
_E. coli_ 11368 (O26:H11. EHEC)
_E. coli_ 11128 (O111:H-. EHEC)
_E. coli_ IAI1 O8 (Commensal)
_E. coli_ 53638 (EIEC)
_E. coli_ SE11 (O152:H28. Commensal)
_E. coli_ B7A
_E. coli_ 12009 (O103:H2. EHEC)
_E. coli_ GOS1 (O104:H4 EAHEC) German 2011 outbreak
_E. coli_ E22
_E. coli_ Olso O103
_E. coli_ 55989 (O128:H2. Enteroaggressive)
_E. coli_ HS (O9:H4. Commensal)
_E. coli_ ATCC8739 (O146. Crook's E.coli used in phage work in the 1950s)
K-12 strain derivatives
_E. coli_ K-12 W3110 (O16. λ⁻ F⁻ "wild type" molecular biology strain)
_E. coli_ K-12 DH10b (O16. high electrocompetency molecular biology strain)
_E. coli_ K-12 DH1 (O16. high chemical competency molecular biology strain)
_E. coli_ K-12 MG1655 (O16. λ⁻ F⁻ "wild type" molecular biology strain)
_E. coli_ BW2952 (O16. competent molecular biology strain)
_E. coli_ 101-1 (O? H?. EAEC)
B strain derivatives
_E. coli_ B REL606 (O7. high competency molecular biology strain)
_E. coli_ BL21-DE3 (O7. expression molecular biology strain with T7 polymerase for pET system)
Early electron microscopy
The first complete
Today, several hundred complete genomic sequences of _Escherichia_ and _Shigella_ species are available. The genome sequence of the type strain of _E. coli_ has been added to this collection not before 2014. 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.
Genes in _E. coli_ are usually named by 4-letter acronyms that derive from their function (when known) and italicized. For instance, _recA_ is named after its role in homologous recombination plus the letter A. Functionally related genes are named _recB_, _recC_, _recD_ etc. The proteins are named by uppercase acronyms, e.g. RecA , RecB , etc. When the genome of _E. coli_ was sequenced, all 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_ strain, 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 .
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 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 protein complexes .
_E. coli_ belongs to a group of bacteria informally known as coliforms that are found in the gastrointestinal tract of warm-blooded animals . _E. coli_ normally colonizes an infant's gastrointestinal tract within 40 hours of birth, arriving with food or water or from the individuals handling the child. In the bowel, _E. coli_ adheres to the mucus of the large intestine . It is the primary facultative anaerobe of the human gastrointestinal tract. (Facultative anaerobes are organisms that can grow in either the presence or absence of oxygen.) As long as these bacteria do not acquire genetic elements encoding for virulence factors , they remain benign commensals .
Nonpathogenic _E. coli_ strain Nissle 1917, also known as Mutaflor , and _E. coli_ O83:K24:H31 (known as Colinfant ) are used as probiotic agents in medicine, mainly for the treatment of various gastroenterological diseases, including inflammatory bowel disease .
ROLE IN DISEASE
Main article: Pathogenic Escherichia coli
Most _E. coli_ strains do not cause disease, but virulent strains can cause gastroenteritis , urinary tract infections , 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 , septicemia , 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_.
There is one strain, _E. coli_ 0157:H7, that produces the Shiga toxin (classified as a bioterrorism agent). This toxin causes premature destruction of the red blood cells, which then clog the body's filtering system, the kidneys, causing hemolytic-uremic syndrome (HUS). 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 due to small clots of blood which lodge in capillaries in the brain. This causes the body parts controlled by this region of the brain not to work properly. In addition, this strain causes the buildup of fluid (since the kidneys do not work), leading to edema around the lungs and legs and arms. This increase in fluid buildup especially around the lungs impedes the functioning of the heart, causing an increase in blood pressure.
Uropathogenic _E. coli_ (UPEC) is one of the main causes of urinary tract infections . It is part of the normal flora in the gut and can be introduced in many ways. In particular for females, the direction of wiping after defecation (wiping back to front) can lead to fecal contamination of the urogenital orifices. Anal intercourse can also introduce this bacterium into the male urethra, and in switching from anal to vaginal intercourse, the male can also introduce UPEC to the female urogenital system. For more information, see the databases at the end of the article or UPEC pathogenicity .
In May 2011, one _E. coli_ strain, O104:H4 , was the subject of a
bacterial outbreak that began in
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.
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 .
ETEC is the type of _E. coli_ that most vaccine development efforts
are focused on.
Antibodies against the LT and major CFs of ETEC
provide protection against LT-producing, ETEC-expressing homologous
CFs. Oral inactivated vaccines consisting of toxin antigen and whole
cells, i.e. the licensed recombinant cholera B subunit (rCTB)-WC
cholera vaccine Dukoral, have been developed. There are currently no
licensed vaccines for ETEC, though several are in various stages of
development. 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
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.
CAUSES AND RISK FACTORS
* Working around livestock * Consuming unpasteurized dairy product * Eating undercooked meat * Drinking impure water
MODEL ORGANISM IN LIFE SCIENCE RESEARCH
Main article: Escherichia coli (molecular biology)
ROLE IN BIOTECHNOLOGY
Because of its long history of laboratory culture and ease of
manipulation, _E. coli_ plays an important role in modern biological
engineering and industrial microbiology . The work of Stanley Norman
Herbert Boyer in _E. coli_, using plasmids and restriction
enzymes to create recombinant
_E. coli_ is a very versatile host for the production of heterologous
proteins , and various protein expression systems have been developed
which allow the production of recombinant proteins in _E. coli_.
Researchers can introduce genes into the microbes using plasmids which
permit high level expression of protein, and such protein may be
mass-produced in industrial fermentation processes. One of the first
useful applications of recombinant
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 .
K-12 is a mutant form of E-coli that over-expresses the enzyme 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 constitutive activity . This particular mutant form is used to isolate and purify the aforementioned enzyme.
_E. coli_ is frequently used as a model organism in microbiology studies. Cultivated strains (e.g. _E. coli_ K12) are well-adapted to the laboratory environment, and, unlike wild-type strains, have lost their ability to thrive in the intestine. Many laboratory strains lose their ability to form biofilms . These features protect wild-type strains from antibodies and other chemical attacks, but require a large expenditure of energy and material resources.
In 1946, Joshua Lederberg and Edward Tatum first described the phenomenon known as bacterial conjugation using _E. coli_ as a model bacterium, and it remains the primary model to study conjugation. _E. coli_ was an integral part of the first experiments to understand 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.
By evaluating the possible combination of 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.
Studies are also being performed attempting to program _E. coli_ to solve complicated mathematics problems, such as the Hamiltonian path problem .
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_ 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 _
Bacteriological water analysis
Dam dcm strain
* Enterotoxigenic _
* ^ "coli". _
Oxford English Dictionary _ (3rd ed.). Oxford
University Press . September 2005. (Subscription or UK public library
* ^ Tenaillon, Olivier; Skurnik, David; Picard, Bertrand; Denamur,
Erick (2010-03-01). "The population genetics of commensal Escherichia
coli". _Nature Reviews Microbiology_. 8 (3): 207–217. ISSN 1740-1526
. doi :10.1038/nrmicro2298 .
* ^ Singleton P (1999). _