E-coli

''Escherichia coli'' ( )Wells, J. C. (2000) Longman Pronunciation Dictionary. Harlow ngland Pearson Education Ltd. is a gram-negative, facultative anaerobic, rod-shaped, coliform bacterium of the genus ''Escherichia'' that is commonly found in the lower intestine of warm-blooded organisms. Most ''E. coli'' strains are part of the normal microbiota of the gut, where they constitute about 0.1%, along with other facultative anaerobes. These bacteria are mostly harmless or even beneficial to humans. For example, some strains of ''E. coli'' benefit their hosts by producing vitamin K₂ or by preventing the colonization of the intestine by harmful pathogenic bacteria. 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 fecal matter under aerobic conditions for three days, but its numbers decline slowly afterwards.

Some serotypes, such as EPEC and ETEC, are pathogenic, causing serious food poisoning in their hosts. Fecal–oral transmission is the major route through which pathogenic strains of the bacterium cause disease. This transmission method is occasionally responsible for food contamination incidents that prompt product recalls. 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 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 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. Under favourable conditions, it takes as little as 20 minutes to reproduce.

Biology and biochemistry

Type and morphology

''E. coli'' is a gram-negative, 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.

''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.

The flagella 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, 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.

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 genes as well as formate dehydrogenase and conducting laboratory evolution experiments. This may be done by using formate to reduce electron carriers and supply the ATP required in anabolic pathways inside of these synthetic autotrophs.

''E. coli'' has three native glycolytic pathways: EMPP, EDP, and OPPP. The EMPP employs ten enzymatic steps to yield two pyruvates, two ATP, and two NADH per glucose molecule while OPPP serves as an oxidation route for NADPH synthesis. Although the EDP is the more thermodynamically favourable of the three pathways, ''E. coli'' do not use the EDP for glucose metabolism, relying mainly on the EMPP and the OPPP. The EDP mainly remains inactive except for during growth with gluconate.

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 and xylose, sorbitol, rhamnose, and ribose. In ''E. coli'', glucose catabolite repression is regulated by the phosphotransferase system, a multi-protein phosphorylation 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, 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. Respiration 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 forks. Replication initiation is then referred to being asynchronous. However, asynchrony can be caused by mutations to for instance ''dnaA'' or DnaA initiator-associating protein DiaA.

Although ''E. coli'' reproduces by binary fission the two supposedly identical cells produced by cell division are functionally asymmetric with the old pole cell acting as an aging parent that repeatedly produces rejuvenated offspring. When exposed to an elevated stress level, damage accumulation in an old ''E. coli'' lineage may surpass its immortality threshold so that it arrests division and becomes mortal. Cellular aging is a general process, affecting prokaryotes and eukaryotes alike.

Genetic adaptation

''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 ''Shigella'' 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 strain commonly used in recombinant DNA work) are sufficiently different that they would merit reclassification.

A strain is a subgroup within the species that has unique characteristics that distinguish it from other strains. These differences are often detectable only at the molecular level; however, they may result in changes to the physiology or lifecycle of the bacterium. For example, a strain may gain pathogenic capacity, the ability to use a unique carbon source, the ability to take upon a particular ecological niche, 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.

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 ''Escherichia'' and ''Salmonella'' diverged around 102 million years ago (credibility interval: 57–176 mya), an event unrelated to the much earlier (see ''Synapsid'') divergence of their hosts: the former being found in mammals and the latter in birds and reptiles. 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''. In this experiment, one population of ''E. coli'' unexpectedly evolved the ability to aerobically metabolize citrate, a major evolutionary shift with some hallmarks of microbial speciation.

In the microbial world, a relationship of predation can be established similar to that observed in the animal world. Considered, it has been seen that ''E. coli'' is the prey of multiple generalist predators, such as ''Myxococcus xanthus''. In this predator-prey relationship, a parallel evolution of both species is observed through genomic and phenotypic modifications, in the case of ''E. coli'' the modifications are modified in two aspects involved in their virulence such as mucoid production (excessive production of exoplasmic acid alginate ) and the suppression of the OmpT gene, producing in future generations a better adaptation of one of the species that is counteracted by the evolution of the other, following a co-evolutionary model demonstrated by the Red Queen hypothesis.

Neotype strain

''E. coli'' is the type species of the genus (''Escherichia'') and in turn ''Escherichia'' is the type genus of the family Enterobacteriaceae, where the family name does not stem from the genus ''Enterobacter'' + "i" (sic.) + " 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 U5/41^T, 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 (2013) 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 as of 2014. Particularly the use of whole genome sequences yields highly supported phylogenies. The phylogroup