Escherichia coli

Escherichia coli (commonly abbreviated E. coli) is a Gram-negative, rod-shaped bacterium that is commonly found in the lower intestine of warm-blooded organisms (endotherms). Most E. coli strains are harmless, but some serotypes can cause serious food poisoning in humans, and are occasionally responsible for product recalls. The harmless strains are part of the normal flora of the gut, and can benefit their hosts by producing vitamin K2, and by preventing the establishment of pathogenic bacteria within the intestine.

E. coli and related bacteria 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 ideal indicator organisms to test environmental samples for fecal contamination. The bacterium can also be grown easily and inexpensively in a laboratory setting, and has been intensively investigated for over 60 years. 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 DNA.

History
The genera Escherichia 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 the escherichian 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 mya.

In 1885, Theodor Escherich, a German pediatrician, first discovered this species in the feces of healthy individuals and called it Bacterium coli commune due to the fact it is found in the colon and 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 Bacteria it was reclassified as Bacillus coli by Migula in 1895 and later reclassified in the newly created genus Escherichia, named after its original discoverer.

The genus belongs in a group of bacteria informally known as "coliforms", and is a member of the Enterobacteriaceae family ("the enterics") of the Gammaproteobacteria.

Biology and biochemistry
E. coli is Gram-negative, facultative anaerobic and non-sporulating. Cells are typically rod-shaped, and are about 2.0 micrometers (μm) long and 0.5 μm in diameter, with a cell volume of 0.6 – 0.7 (μm)3. It can live on a wide variety of substrates. E. coli 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.

Optimal growth of E. coli occurs at 37°C (98.6°F) but some laboratory strains can multiply at temperatures of up to 49°C (120.2°F). 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, dimethyl sulfoxide and trimethylamine N-oxide.

Strains that possess flagella can swim and are motile. The flagella have a peritrichous arrangement.

E. coli and related bacteria possess the ability to transfer DNA via bacterial conjugation, transduction or transformation, which allows genetic material to spread horizontally through an existing population. This process led to the spread of the gene encoding shiga toxin from Shigella to E. coli O157:H7, carried by a bacteriophage.

Diversity
Escherichia coli encompasses an enormous population of bacteria that exhibit a very high degree of both genetic and phenotypic diversity. Genome sequencing of a large number of isolates of E. coli and related bacteria shows that a taxonomic reclassification would be desirable. However, this has not been done, largely due to its medical importance and Escherichia coli remains one of the most diverse bacterial species: only 20% of the genome is common to all strains. In fact, from the evolutionary point of view, the members of genus Shigella (dysenteriae, flexneri, boydii, 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 DNA work) are sufficiently different that they would merit reclassification.

A strain is a sub-group 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 faecal 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.

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) (NB: K-12, the common laboratory strain is not a serotype.)

Genome plasticity
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 diverged from Salmonella. In microbiology, all strains of E. coli derive from E. coli K-12 or E. coli B strains. Some strains develop traits that can be harmful to a host animal. These virulent strains typically cause a bout of diarrhea that is unpleasant in healthy adults and is often 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.

Neotype strain
E. coli is the type species of the genus (Escherichia) and in turn Escherichia is the type species of the family Enterobacteriaceae, where it should be noted that 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 ATCC 11775, also known as NCTC 9001, which is pathogenic to chickens and has a O1:K1:H7 serotype. However, in most studies either O157:H7 or K-12 MG1655 or K-12 W3110 are used as a representative E.coli.

Recent events
One such E. coli strain, Escherichia coli O104:H4, has been the subject of a bacterial outbreak that began in Germany in May 2011. Certain strains of E. coli are a major cause of foodborne illness. The outbreak started when several people in Germany were infected with enterohemorrhagic E. coli (EHEC) bacteria, leading to hemolytic-uremic syndrome (HUS), a medical emergency that requires urgent treatment. On 30 June 2011 announced the German Bundesinstitut für Risikobewertung (BfR) (Federal Institute for Risk Assessment, a federal, fully legal entity under public law of the Federal Republic of Germany, an institute within the German Federal Ministry of Food, Agriculture and Consumer Protection), that seeds of fenugreek from Egypt were likely the cause of the EHEC outbreak.

Phylogeny of Escherichia coli strains
Phylogeny (inferred evolutionary history) of Escherichia coli based on Note that four different species of Shigella fall within the same clade as the various Escherichia coli strains, while Escherichia albertii and Escherichia fergusonii both lie outside of the clade that contains E. coli and Shigella sp.

♠: E. coli B derived strains (O7. all substrains derive from d'Herelle's "Bacillus coli" strain)

♣: E. coli K-12 derived strains (O16. all substrains derive from Clifton's K-12 strain (λ⁺ F⁺))

Genomes
The first complete DNA sequence of an E. coli genome (laboratory strain K-12 derivative MG1655) was published in 1997. It was found to be a circular DNA molecule 4.6 million base 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 approximately 40 years, a large number of these genes were previously unknown. The coding density was found to be very high, with a mean distance between genes of only 118 base pairs. The genome was observed to contain a significant number of transposable genetic elements, repeat elements, cryptic prophages, and bacteriophage remnants.

Today, over 60 complete genomic sequences of Escherichia and Shigella species are available. Comparison of these sequences shows a remarkable amount of diversity; only about 20% of each genome represents sequences that are present in every one of the isolates, while approximately 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 pan-genome) exceeds 16,000. This very large variety of component genes has been interpreted to mean that two-thirds of the E. coli pan-genome originated in other species and arrived through the process of horizontal gene transfer.

Role as normal microbiota
E. coli normally colonizes an infant's gastrointestinal tract within 40 hours of birth, arriving with food or water or with the individuals handling the child. In the bowel, it 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.

Therapeutic use of nonpathogenic E. coli
Nonpathogenic Escherichia coli strain Nissle 1917 also known as Mutaflor is used as a probiotic agent in medicine, mainly for the treatment of various gastroenterological diseases, including inflammatory bowel disease.

Role in disease
Virulent strains of E. coli can cause gastroenteritis, urinary tract infections, and neonatal meningitis. In rarer cases, virulent strains are also responsible for hemolytic-uremic syndrome, peritonitis, mastitis, septicemia and Gram-negative pneumonia.

Role in biotechnology
Because of its long history of laboratory culture and ease of manipulation, E. coli also 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, became a foundation of biotechnology.

Considered a very versatile host for the production of heterologous proteins, researchers can introduce genes into the microbes using plasmids, allowing for the mass production of proteins in industrial fermentation processes. Genetic systems have also been developed which allow the production of recombinant proteins using E. coli. One of the first useful applications of recombinant DNA technology was the manipulation of E. coli to produce human insulin. Modified E. coli cells have been used in vaccine development, bioremediation, and production of immobilised enzymes. E. coli cannot, however, be used to produce some of the larger, more complex proteins which contain multiple disulfide bonds and, in particular, unpaired thiols, or proteins that also require post-translational modification for activity.

Studies are also being performed into programming E. coli to potentially solve complicated mathematics problems, such as the Hamiltonian path problem.

Model organism
E. coli is frequently used as a model organism in microbiology studies. Cultivated strains (e.g. E. coli K12) are well-adapted to the laboratory environment, and, unlike wild type strains, have lost their ability to thrive in the intestine. Many lab 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.

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 lab.

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.

Databases

 * EcoSal Continually updated Web resource based on the classic ASM Press publication Escherichia coli and Salmonella: Cellular and Molecular Biology
 * Uropathogenic Escherichia coli (UPEC)
 * ECODAB The structure of the O-antigens that form the basis of the serological classification of E. coli
 * 2DBase 2D-PAGE Database of Escherichia coli University of Bielefeld – Fermentation Engineering Group (AGFT)
 * 5S rRNA Database Information on nucleotide sequences of 5S rRNAs and their genes
 * ACLAME A CLAssification of Mobile genetic Elements
 * AlignACE Matrices that search for additional binding sites in the E. coli genomic sequence
 * ArrayExpress Database of functional genomics experiments
 * ASAP Comprehensive genome information for several enteric bacteria with community annotation
 * Bacteriome E. coli DNA-Binding Site Matrices Applied to the Complete E. coli K-12 Genome
 * BioGPS Gene portal hub
 * BRENDA Comprehensive Enzyme Information System
 * BSGI Bacterial Structural Genomics Initiative
 * CATH Protein Structure Classification
 * CBS Genome Atlas
 * CDD Conserved Domain Database
 * CIBEX Center for Information Biology Gene Expression Database
 * COGs
 * Coli Genetic Stock Center Strains and genetic information on E. coli K-12
 * coliBASE
 * EcoCyc – literature-based curation of the entire genome, and of transcriptional regulation, transporters, and metabolic pathways
 * 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 of PortEco

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