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Escherichia coli: An Overview of Main Characteristics

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Chapter

Escherichia coli: An Overview of

Main Characteristics
M. Basavaraju and B.S. Gunashree

Abstract

Escherichia coli is a type of bacteria that lives in many places in the environment,
including the gastrointestinal system of humans and warm-blooded animals, where
it is part of the gut microbiota. Some strains of E. coli can be administered as probi-
otics and are known to have a positive effect on host health. However, some strains
can be pathogenic, causing intestinal and extraintestinal infections in humans as
well as animals. E. coli is hence a bacterium with a wide range of different natural
types of strains, each with its own set of features. Because of its unique qualities,
such as simplicity of handling, availability of the entire genome sequence, and
capacity to grow in both aerobic and anaerobic conditions, E. coli is also a popular
bacterium for laboratory research and biotechnology. So, E. coli is considered to be
the utmost widely utilized microbe in the field of recombinant DNA technology,
and it is used in a wide range of industrial and medical applications.

Keywords: Escherichia coli, Gram-negative bacteria, growth, infection, model

organism, pathogenesis

1. Introduction

The bacteria Escherichia coli was discovered by German pediatrician Theodor

Escherich (1857–1911), who isolated it from babies' feces in 1885 [1]. E. coli is a
gram-negative, non-sporulating, rod-shaped, facultative anaerobic, and coli-
form bacterium pertaining to the genus Escherichia that commonly inhabits the
environment, foods, and warm-blooded animals' lower gut [2]. In the domains
of biotechnology and microbiology, it is the most widely studied prokaryotic
model organism. It can live for long periods of time in feces, soil, and water, and
is frequently used as a water contamination indicator organism. For 2–3 days, the
bacterium multiplies rapidly in fresh feces under aerobic circumstances, but its
numbers gradually fall after that. E. coli is gram-negative, straight, rod-shaped,
non-sporing, non-acid fast, and bacilli that exist in single and pairs. Cells are
typically rod-shaped, with 1–3 μm × 0.4–0.7 μm (micrometer) in size around
1 μm long, 0.35 μm wide, and 0.6–0.7 μm in volume [3]. It is motile due to
peritrichous flagellar arrangement, and very few strains are non-motile. The
optimal growth of E. coli occurs at 37°C (98°F) but some laboratory strains can
multiply at temperatures of up to 49°C (120.2°F). It takes as little as 20 min to
reproduce in favorable conditions [4]. Fimbriated strains exist both as motile
and non-motile. A polysaccharide capsule has been discovered in some E. coli
strains isolated from extraintestinal infections. The E. coli capsules can be clearly
seen using negative staining procedures, which produce a bright halo over a dark

1
Escherichia coli

backdrop. They have a thin cell wall with only one or two layers of peptidoglycan
[5] as shown in Figure 1.
It colonizes a newborn’s gastrointestinal (GI) tract within hours after birth and
even helps to keep our digestive tract healthy. Several strains of E. coli have been
identified as good and effective probiotics and are currently employed in phar-
maceuticals. It truly is a facultative anaerobic chemoorganotroph capable of both
respiratory and fermentative metabolism [7]. Although most strains of E. coli are
safe, some serotypes can induce diarrhea when consumed through contaminated
food or drink, while others might cause urinary tract infections (UTIs), anemia,
and respiratory or kidney infections [8]. However, certain strains have developed
into pathogenic E. coli by using plasmids, transposons, bacteriophages, and/or
pathogenicity islands to acquire virulence factors [9]. Serogroups, pathogenicity
mechanisms, clinical signs, and virulence factors can all be used to classify the
pathogenic strain of E. coli [10].
The bacterium can be grown easily and inexpensively in a laboratory setting
under appropriate conditions. It takes as little as 20 min to reproduce and has been
intensively investigated for over 60 years [11]. E. coli is the most widely studied
prokaryotic model organism and an important species in the field of biotechnology
and microbiology, where it serves as the host organism for recombinant DNA and
experimental workhorse for DNA manipulation and protein production [12].

2. Habitat of E. coli

Escherichia coli can live on a wide variety of substrates. The availability of

nutrients within the intestine of host species determines E. coli niche. The (GI) tract
of humans and many other warm-blooded animals is the principal niche for E. coli.
It cycles between two major habitats-warm-blooded animal intestines and the

Figure 1.
Structure of E. coli [6].

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Escherichia coli: An Overview of Main Characteristics
DOI: http://dx.doi.org/10.5772/intechopen.105508

environment (water, sediment, and soil), which is considerably different in terms

of physical conditions, the range, and quantity of nutrients availability. E. coli form
a mutual relationship with its host. E. coli in the colon synthesizes K and B complex
vitamins and protects the GI tract against colonization with pathogenic microbes,
while the host offers an ecological niche and nutrients. E. coli is the most common
type of facultative anaerobes in the intestine, accounting for around 0.1% of the gut
microbiota [13]. E. coli can also be found in hotter conditions, such as on the edge of
hot springs and on-ground meats due to slaughterhouse processing [14].

3. Scientific classification

Domain: Bacteria [15]

Kingdom: Bacteria
Phylum: Proteobacteria
Class: Gamma proteobacteria
Order: Enterobacterales
Family: Enterobacteriaceae
Genus: Escherichia
Species: Escherichia coli (E. coli)

4. Antigenic Structure of E. coli

E. coli is classified into 150–200 serotypes or serogroups based on 3 antigens,

somatic (O) or cell wall antigen, capsular (K) antigen, and flagellar (H) antigen.
Seventy five types of the H or flagellar antigen and 173 types of O or somatic anti-
gens 103 types of the K or capsular antigens have been recognized [16] (Figure 2).

5. Cultural requirements of Escherichia coli

E. coli cells may grow on a solid or in a liquid growth medium under laboratory
conditions. It may be grown in a basic minimum of media, which includes glucose
as a carbon and energy source, ammonium salts as a nitrogen source, other salts,
and trace elements [18]. As E. coli have simple nutritional requirements it can be

Figure 2.
Antigenic structure of E. coli [17].

3
Escherichia coli

easily cultured on a common medium, such as Nutrient agar, Mac Conkey agar, and
EMB agar [19].
E. coli can grow at temperatures ranging from 10°C to 40°C, although the
optimum temperature for most strains is 37°C (98.6°F), however, some laboratory
strains can proliferate at temperatures as high as 49°C (120.2°F) [20]. E. coli can
survive at 4.5–9.5 pH but the maximum growth is observed at 7.0, i.e., neutral pH.
Also, the pH requirements vary with the strains of E. coli; [21]. The cultural charac-
teristics of E. coli are presented in Table 1.

5.1 Nutrient agar

E. coli, on NAM, forms large, thick, greyish white, moist, smooth, opaque,
or translucent discs like colonies as shown in Figure 3. The smooth forms (S) of
colonies seen in fresh isolation are easily emulsifiable in saline. The rough forms
(R) of colonies seen in older cultures, with dull surfaces often auto-agglutinable in
saline. S-R variation occurs as a result of repeated subcultures and is associated with
the loss of surface antigens and usually of virulence [24].

5.2 Blood agar

Some of the strains show beta hemolysis, especially those that are isolated from
the pathologic conditions, whereas those which are isolated from normal persons
may or may not show hemolysis on blood agar [25, 26] shown in Figure 4.

Cultural Nutrient agar Eosin methylene MacConkey agar Blood agar

characteristics medium (NAM) blue (EMB) agar medium medium
medium

Shape Circular Circular Circular Circular

Size 1–3 mm 2–3 mm 2–3 mm 1–3 mm

Elevation Convex Convex Convex Convex

Surface Smooth (fresh Smooth fresh Smooth fresh Smooth fresh
isolation); isolation rough isolation rough isolation rough
rough (repeated repeated repeated repeated
subculture, subculture subculture subculture mucoid
mucoid mucoid mucoid (capsulated
(capsulated (capsulated (capsulated strains)
strains) strains) strains)
Color Grayish white Green metallic Pink Green metallic
sheen sheen

Structure Translucent Opaque Opaque Opaque

Opaque

Hemolysis — — — Beta-hemolysis (in

some strains)

Emulsifiability Smooth Smooth Smooth Smooth

from-easily, from-easily, from-easily, from-easily,
emulsifiable; emulsifiable; emulsifiable; emulsifiable;
roughly forms roughly forms roughly forms roughly forms
auto agglutinable auto agglutinable auto agglutinable auto agglutinable
hence do not hence do not hence do not hence do not
emulsify easily emulsify easily emulsify easily emulsify easily

Table 1.
Cultural characteristics of E. coli [22].

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Escherichia coli: An Overview of Main Characteristics
DOI: http://dx.doi.org/10.5772/intechopen.105508

Figure 3.
Growth of E. coli on nutrient agar [23].

Figure 4.
A. A non-hemolytic E. coli strain on blood agar [25]. B. A beta-hemolytic E. coli strain on blood agar [26].

5.3 Mac Conkey agar

The colonies are pink in color due to lactose fermentation, which is

important for distinguishing E. coli from other bacteria in the specimen, par-
ticularly gram-positive bacteria and Salmonella species, which are non–lactose
fermenters and produce colorless colonies on MacConkey agar media [27] shown
in Figure 5.

5.4 E. coli on Mueller Hinton agar

Starch is added to absorb any toxic metabolites produced and starch hydrolysis
yields dextrose, which serves as a source of energy. The use of a suitable medium for
testing the susceptibility of microorganisms to sulfonamides and trimethoprim [28]
is shown in Figure 6.

5
Escherichia coli

Figure 5.
Colonies of E. coli on MacConkey agar plate are pink to dark pink, [27].

Figure 6.
E. coli on Mueller Hinton Agar (MHA) tested for susceptibility for five different types of antibiotics [29].

5.5 Eosin methylene blue agar

The colonies of E. coli grow with a green metallic sheen, which is due to the
metachromatic property of dyes (eosin and methylene blue in the ratio of 6:1) and
the lactose fermenting property of E. coli, which changes the pH of the medium to
acidic. Hence, making the medium more selective for E. coli makes the identifica-
tion much more easier [30] as shown in Figure 7.

5.6 E. coli on m-ENDO agar

Coliforms appear as red colonies with a metallic green sheen. In E. coli, this
reaction is so intense that the fuchsin crystallizes out giving the colonies a metallic
green sheen. The selective agents contained in the medium, sodium deoxycholate
and sodium lauryl sulfate help to inhibit non-coliforms metabolize lactose with the
production of aldehyde and acid [31] shown in Figure 8.

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Escherichia coli: An Overview of Main Characteristics
DOI: http://dx.doi.org/10.5772/intechopen.105508

Figure 7.
E. coli on EMB agar showing green metallic sheen colonies [30].

Figure 8.
E. coli on ENDO agar with green metallic sheen colonies [31].

5.7 E. coli on violet red bile agar

Violet red bile agar (VRBA) is a selective medium used to detect and enumerate
lactose-fermenting coliform. Lactose-fermenting microorganisms produce pink to
red colonies that are generally surrounded by a reddish zone of precipitated bile.
Bluish fluorescence is seen around colonies under UV [32] as shown in Figure 9.

5.8 E. coli on cystine lactose electrolyte-deficient agar

It promotes the growth and enumeration of UTIs however due to a shortage of

electrolytes; it prevents excessive swarming of Proteus species. On cystine lactose
electrolyte-deficient (CLED) agar, lactose fermenters form yellow colonies, while
non-lactose fermenters form blue colonies [33] as shown in Figure 10.

7
Escherichia coli

Figure 9.
VRBA agar, A: E. coli, pinkish red with bile precipitate B: Salmonella gallinarium, fair to good growth;
colorless colonies [32].

Figure 10.
Growth of E. coli on cysteine lactose electrolyte-deficient agar, [34].

6. E. coli in liquid media

Within 12–18 h, they demonstrate homogeneous murky development because of

the increasing quantity of bacteria, the broth gets hazy. Pellicles grow on the surface
of a liquid medium after a long period of incubation (>72 h). Heavy deposits occur,
which disperse when shaken [19] as seen in Figure 11.

7. Pathogenicity of E. coli

The majority of E. coli strains in the colon are not harmful, however pathogenic
E. coli isolates cause intestinal or extraintestinal infections, depending on the array

8
Escherichia coli: An Overview of Main Characteristics
DOI: http://dx.doi.org/10.5772/intechopen.105508

Figure 11.
Growth of E. coli on LB liquid medium. (Photo: M. Basavaraju.)

of virulence-associated genes that they harbor. The intestinal pathogenic E. coli

(IPEC) strains are divided and classified into several pathotypes (Table 2). Diseases
associated with various intestinal pathogenic E. coli pathotypes in animals are as
shown in Table 3. E. coli is linked also to a number of extraintestinal diseases and
is the most prevalent cause of cholecystitis, bacteremia, cholangitis, UTI, traveler's
diarrhea, and septicemia as well as neonatal meningitis, etc., [37]. Most infections,
with the exception of infant meningitis and gastroenteritis, are endogenous, like
E. coli from the patient's normal microbiota, cause infection when the patient's
defenses are impaired, e.g., through trauma or immune suppression [38]. In order to
cause disease E. coli to possess several different types of virulence factors: fimbrial
and fimbrial adhesins, capsules, toxins (exotoxins, hemolysins, and enterotoxins),
iron up-take systems, etc., [39]. Important ExPEC virulence-associated genes, their
encoded proteins, function, and connection to different ExPEC pathotypes are
given in Table 4 [41].

8. Antibiotic-resistant E. coli

Antibiotic resistance genes have been generated in many gram-negative bacteria

and E. coli is not an exception. These bacteria evolved different mechanisms that
confer resistance to anti-biotics. E. coli can produce extended-spectrum beta-lactamase
(ESBL) that makes the bacteria resistant to beta lactams (e.g., cephalosporins,
monobactams, etc.). Carbapenemase-producing E. coli strains, on the other hand,
have genes that confer carbapenem resistance (e.g., imipenem, ertapenem, and
meropenem). ESBL producing E. coli are a rapidly evolving group of β-lactamases,
produced by certain types of bacteria where E. coli are the major ones. These
enzymes can break down the active ingredients by cleaving the beta-lactam ring
of penicillin’s and cephalosporin antibiotics, resulting in the inactivation of these

9
10

Escherichia coli
Category Clinical manifestations Susceptible population Virulence factors Diagnostic Treatment
ETEC Watery stool (without blood Children 0–5 years of age and ST, LT, CFs Culture, detection of ST Self-limited, responsive to oral
(enteropathogenic or inflammatory cells) leading adults traveling to developing (STa, STb) and LT, CFAs rehydration therapy (low response
E. coli) to dehydration, headache, countries. using ELISA and PCR-based in children <2 years). Antimicrobial
fever, nausea and vomiting methods. therapy on individual cases
EPEC Secretory and persistent Children 0–2 years of age, pEAF, BFP, LEE Culture, adherence patterns Self-limited, responsive to oral
(enteropathogenic diarrhea, anorexia, low fever, occasionally adults and Nle effectors (LA LAL, etc.), serotyping, rehydration therapy. Antimicrobial
E. coli) and rapid wasting PCR-based methods. therapy on individual cases.

EAEC Persistent and acute diarrhea, People of all ages in developing EAST Pet Pic Culture, adherence pattern Self-limited, responsive to oral
(enteroaggregative mucoid stools, abdominal and industrialized countries, ShET-1 Aap AAF/II (stacked-brick pattern), rehydration therapy. Antimicrobial
E. coli) pain, nausea, vomiting, HIV-infected adults pAA DNA probe, multiplex therapy on individual cases
occasionally fever and real-time PCR assays.

STEC/VTE/ Mild uncomplicated diarrhea During the summer, it's Stx 1 and 2 Shiga toxins rather and A/E To drink plenty of fluids to prevent
EHEC (a hybrid to hemorrhagic colitis with the most common, and the verotoxins (VT) cytopathology. dehydration and blood transfusions and
Pathotypes) severe abdominal pain and incidence is higher in children kidney dialysis.
bloody diarrhea. under the age of five.

EIEC Invade and destroy the A small percentage of Inv plasmid, Human stool samples from Fluoroquinolones, such as ciprofloxacin,
(enteroinvasive colonic epithelium, producing patients develop dysenteric Chromosome, pInv patients with signs and macrolides, such as azithromycin, and
E. coli) a disease characterized illness, which includes fever, genes symptoms of GI infection rifaximin, are antibiotics used to treat
initially by watery diarrhea. stomach pains, and blood and non-STEC diarrheagenic E. coli.
leukocytes in stool specimens.

DAEC (diffusely Watery diarrhea Involved in diarrhea in Adhesins Afa/Dr adhesins multiplex PCR for DEP genes
adherent E. coli) children but not in adults.

AIEC (adherent- Type 1 fimbriae, cellular Associated with Crohn Persistent None Bacteria with antibacterial compounds
invasive E. coli) invasion disease. intestinal or with phage therapy, probiotics, or
inflammation. anti-adhesive molecules.
ST: heat-stable toxin, LT: heat-labile toxin, CFA: colonization factors, LEE: locus of enterocyte effacement, HIV: human immunodeficiency virus, pEAF: plasmid enteroadherente factor of EPEC, BFP:
bundle forming pilus, EAST: enteroaggregative heat-stable toxin, Pet: plasmid encoded-toxin, Pic: protein involved in colonization, ShET-1: Shigella enterotoxin-1, Aap, dispersin, AAF/II: aggregative
adherence factor II.

Table 2.
Pathotypes of human IPEC [35].
Escherichia coli: An Overview of Main Characteristics
DOI: http://dx.doi.org/10.5772/intechopen.105508

Species Disease (age) Pathotype Localization

Poultry Embryonic mortality — Egg

Swollen head, dermatitis, cellulite — Localized infections
(adult)

Diarrhea — Intestine

Cattle New born diarrhea ETEC Small intestine

Hemorrhagic dysentery (1–6 wk) EPEC Colon
STEC

Mastitis (adult) — Mammary gland

Dog and Diarrhea (young animal) ETEC Small intestine
Cat
Diarrhea (young animal) EPEC Small and large intestines

Pig Newborn diarrhea (0–1 wk) ETEC Small intestine

Young pig diarrhea (2–4 wk) ETEC Small intestine

Post-weaning diarrhea (4–8 wk) ETEC Small intestine

EPEC

Edema disease (4–8 wk) STEC Small intestine

(EDEC)

Hemorrhagic gastro-enteritis (1–8 wk) ETEC Small intestine

Rabbit Newborn diarrhea EPEC Small and large intestine

Weaning diarrhea EPEC Small and large intestine
Source: EcL, APEC: avian pathogenic Escherichia coli, SEPEC: septicemic Escherichia coli, UPEC: uropathogenic
Escherichia coli, EDEC: edema disease Escherichia coli.

Table 3.
Diseases associated with various intestinal pathogenic E. coli pathotypes in animals, [36].

Virulence Encoded Function ExPEC

gene(s) protein(s) pathotype(s)

Adhesions

fim Type 1 fimbriae Factor of colonization in extraintestinal UPEC, NMEC,

infections, biofilm formation SEPEC, APEC
afa Afimbrial adhesin The non-fibrous adhesin binds to the DAF UPEC
receptor on the cell surface epithelium,
hemagglutination capacity.

dra Dr fimbriae Binding to the DAF receptor on the UPEC

surface epithelial cells and mediation of
internalization bacteria to the host cells.

pap P fimbriae Stimulate the production of cytokines UPEC, SEPEC,

by T lymphocytes, colonization factor in APEC
extraintestinal infections.

sfa S fimbriae Adhesion to intestinal epithelial cells, UPEC, NMEC

kidney, and lower urinary tract cells;
facilitate the penetration of bacteria into
the tissues.
foc F1C fimbriae Adhesion to renal epithelial cells and UPEC
endothelial cells of the bladder and
kidneys.
iha Iha Iron-regulated-gene-homologue adhesion. UPEC

11
Escherichia coli

Virulence Encoded Function ExPEC

gene(s) protein(s) pathotype(s)
mat Mat Meningitis associated and temperature NMEC
regulated fimbriae.

crl, csg Curli fiber gene Enable biofilm formation and promote UPEC, SEPEC,
pathogenicity. APEC
agn43(flu) Antigen43 Protein of autotransporter family, UPEC
adhesion, and biofilm development.

Invasine

ibeA,B,C Ibe ABC Cell invasion into the host tissues NMEC, SEPEC,
APEC

Iron uptake

iuc,aer Aerobactin Siderophore, acquisition of Fe2+/3+ in the UPEC, APEC

host system.
irp Iron repressible Yersiniabactin synthesis NMEC
protein

iroN Salmochelin Siderophore receptor, use of Fe ions UPEC, NMEC,

obtained from the body host. SEPEC APEC

chu, hma ChuA, Hma Enable using of Fe from hemoglobin in the UPEC, SEPEC
host system.

sitA,B,C SitABC Transportation of Fe, Mn UPEC, APEC

Protectins/serum resistance

traT Transfer protein Inhibition of the classical pathway of NMEC, SEPEC

complement activity. APEC
KpsMI-neuA, Capsula antigens The protection factor against phagocytosis NMEC, SEPEC
KpsMII and the spreading factor.

omp Outer membrane Enable intracellular survival, evasion from UPEC, NMEC
protein the body’s defense.
iss Increased serum The protection factor against phagocytosis. NMEC, SEPEC,
survival APEC

colV, cvaC ColV, CvaC Factor facilitating colonization NMEC, SEPEC,

APEC
Toxins

pic Serin protease Degrades mucins, facilitates colonization UPEC

autotransporter epithelium, damages the cell membrane.

sat Secreted Proteolytic toxin, effect cytotoxic— UPEC

autotransporter influences on cell vacuolization.
toxin

vat Vacuolating Proteolytic toxin, induces host cell UPEC, APEC

autotransporter vacuolization.
toxin

hlyA Hemolysin A Creating pores in membranes of host cells UPEC

(cell lysis).

cnf Cytotoxic Engaging in cell necrosis UPEC, SEPEC

necrotizing factor

cdt Cytolethal Cytolethal distending factor SEPEC

distending toxin

Table 4.
Important ExPEC virulence-associated genes, their encoded proteins, function, and association with ExPEC
pathotype [40].

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Escherichia coli: An Overview of Main Characteristics
DOI: http://dx.doi.org/10.5772/intechopen.105508

drugs, there are at least 200 different types of ESBL enzymes, increasingly isolated
as causes of complicated UTIs and remain an important cause of failure of therapy
with cephalosporin’s and have serious infection control consequences. ESBL pro-
ducing Enterobacteriaceae have been responsible for numerous outbreaks of infec-
tion throughout the globe and pose challenging infection control issues [42]. These
organisms are associated with multidrug resistance causing a high rate of mortality
and treatment failure [43].

9. MUG (beta-glucuronidase) of E. coli

MUG is an acronym for 4-methylumbelliferyl-β-d-glucuronide, most strains of

E. coli (97%) produce the enzyme β-d-glucuronidase hence, the detection of this
enzyme is commonly employed in laboratories to identify and differentiate such
organisms [44]. β-d-glucuronidase is an enzyme that hydrolyzes the beta-d-gluco-
pyranoside-uronic derivatives to aglycons and d-glucuronic acid. In about 97% of E.
coli strains, the enzyme-glucuronidase is present [45].

10. Phylogenetic groups of E. coli

According to older phylogenetic studies, the E. coli strains were classified into
four main phylogenetic groups: A, B1, B2, and D. However, recent studies showed
that there are more phylogenetic groups seven (A, B1, B2, C, D, E, and F) belong
to E. coli sensu stricto, whereas the eighth is represented by cryptic Clade I. Apart
from clade I, also clades II, III, IV, and V are known to exist [46]. The majority of
strains that cause extraintestinal infections belong to the phylogenetic group B2,
whereas as strains belonging to the phylogenetic groups A and B1 are known to
have low extraintestinal pathogenicity potential but beside commensal strains,
strains also cause diarrhea (Figure 12). According to Doumith M, et al., E. coli
strains belonging to various phylogenetic groups displayed diverse phenotypic and
genotypic features thought to support fitness in various ecological settings, result-
ing in niche preference according to scientific findings [48]. To determine E. coli
phylogroups, several approaches have been described. Polymerase chain reaction
(PCR)-based tests, multi-locus sequence typing (MLST), ribotyping, and sequenc-
ing of the 16S rRNA gene are among them [49]. For the determination of the
original four different phylogroups (A, B1, B2, and D), the Clermont triplex PCR
phylogroup method was used [50].
However, research has revealed that this method can only confirm 80–85% of all
E. coli phylogroups, and in 2013 Clermont et al. [51], proposed a revisited method,
the quadruplex PCR, which can be used to classify E. coli in the seven phylogenetic
groups and clade I [52]. Clermont et al. [53] also proposed a PCR method for the
detection of clades II–V.

11. The E. coli genome and proteome

The full genome of E. coli K12 was published by Science in 1997, making it one of
the first species to have its genome completely sequenced. E. coli has a circular DNA
molecule with 4288 annotated protein-coding genes (arranged into 2584 operons),
7 ribosomal RNA (rRNA) operons, and 86 transfer RNA (tRNA) (data for the E. coli
laboratory strain K-12 derivative MG1655) [8]. However, E. coli core genome (i.e.,
genes found in all strains) accounts for less than 20% of the pan genome's genes

13
Escherichia coli

Figure 12.
Phylogenetic tree of E. coli strains [47].

or nearly all (90%) of the genomes, leaving only a tiny fraction of genes found in
roughly half of the genomes [54]. The E. coli core genome is estimated to have less
than 1500 genes, while it has a huge pan-genome with more than 22,000 genes [55].
According to genomic analysis many of the genes of the pan-genome could be not
yet unidentified but crucial virulence factors [56]. There are 27,621 E. coli genome
assemblies and annotation sequences available to date and each genome comprises
between 4000 and 5500 genes [57]. The E. coli genome as a whole is remarkably
ordered in terms of local replication direction and oligonucleotides that may be
involved in replication and recombination [58].
The diverse behavior of this species is explained by its enormous genetic and
phenotypic diversity. With a mean distance between genes of only 118 base pairs,

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Escherichia coli: An Overview of Main Characteristics
DOI: http://dx.doi.org/10.5772/intechopen.105508

the coding density was found to be extremely high. A multitude of factors con-
tribute to the higher gene density: a. bacterial genes lack introns throughout the
genome, and neighboring genes are fairly near together, i.e., there are no many large
non-coding DNA sections between genes. There are several transposable genetic
elements, repetitive elements, cryptic prophages, and bacteriophage remnants in
the genome and a variety of additional patches with unique compositions, showing
genome plasticity due to horizontal gene transfer [58, 59].
E. coli is an excellent model for studying the general characteristics of the
bacterial proteome, such as its dynamics under different physiological situations, its
dynamic range of expression, and its changes. According to the genomic sequence
data of the E. coli K-12 strain, there are 4364 ORFs or ORF fragments in the E. coli
K-12 W3110 strain. The E. coli proteome has been used as a standard for evaluat-
ing and validating new technologies and methodologies in recent years, including
sample prefractionation, protein enrichment, two-dimensional gel electrophoresis
(2-DE), protein detection, bio-mass spectrometry (MS), combinatorial assays
with n-dimensional chromatography and image analysis. In comparison to the
proteomes of other organisms such as plants and animals, the E. coli proteome is
much smaller and with less protein modification and hence provides an excellent
model for various research needs. The usage of the E. coli proteome as a model is
further boosted by the existence of public databases such as SWISS-PROT (http://
www.expasy.ch/ch2d/) and NCBI (http://www.ncbi.nlm.nih.gov/), which contain
rich information on proteins and corresponding genes of E. coli and the existence of
the E. coli SWISS-2DPAGE maps, which are based on a large amount of biochemical
and biological data [60].

12. E. coli as a model organism

Escherichia coli is a well-known prokaryotic bacterium that is widely used as

a model organism for a variety of research due to its adaptability. E. coli is more
understood than other living species because of its minimal dietary requirements,
rapid growth rate, and, most critically, well-established genetics [61]. E. coli cells
divide once every 20–30 min on average, allowing them to adapt to their surround-
ings quickly. It also promotes the growth of numerous bacterial viruses (bacterio-
phages), allowing researchers to examine the structure and pathogenicity of viruses
in greater detail. It is a good model organism for molecular genetics because of its
ability to grow quickly on low-cost media and the availability of molecular tools to
perform genetic modifications [62].
Recent research on “wild” E. coli, for example, has revealed a lot about the
bacterial existence in the environment, its variety and genetic development, and its
function in the human microbiome and diseases [7]. Vaccine development, biore-
mediation, biofuel generation, and immobilized enzymes have all exploited modi-
fied E. coli cells [61]. Furthermore, because E. coli reproduce primarily asexually,
alterations to the genome are preserved, and the effects exhibited in these mutants
are repeatable. Because of these characteristics, E. coli is an excellent model organ-
ism for molecular genetics and microbiology research, as well as modern biological
engineering [62].

13. What discoveries were made using E. coli as a model organism

Several key inventions in the field of molecular biology, including molecu-

lar genetics, were achieved using E. coli as a model organism. This includes an

15
Escherichia coli

Year Nobel-worthy discoveries Discoverer

1958 Bacterial sex and other methods through which bacteria can Joshua Lederberg
transfer DNA

1959 The process by which life duplicates its genetic code is Arthur Kornberg
known as DNA replication

1965 Gene regulation, how genes are turned on or off Ellis Englesberg
1968 The genetic code, the language in which our DNA is written. Nirenberg and Matthaei'

1969 Viral replication is the process by which viruses reproduce Max Knoll
within cells.

1978 Restriction enzymes, also known as "molecular scissors," Werner, Nathans, and Smith
that enable scientists to cut DNA

1980 Recombinant DNA was used to make the first genetically Paul Berg
modified DNA
1982 The first licensed drug produced using recombinant DNA Developed by Genentech and
technology was human insulin licensed as well as marketed by
Eli Lilly

1989 Additional uses for RNA such as an enzyme have been Sidney Altman and Thomas R.
revealed Cech

1997 Found ATP, the energy molecule synthesis is the process by Paul Boyer and John Walker
which cells keep life going

1999 Found that protein signal sequences are one way by which Günter Blobel
cells organize themselves

2008 Scientists employed green fluorescent protein as a marker to Roger Y. Tsien, Osamu
track cell components Shimomura, and Martin Chalfie

2009 Bacteria make computers look like pocket calculators; A team of US scientists DOI:
Biologists have created a living computer from E. coli 10.1186/1754-1611-3-11
bacteria that can solve complex mathematical problems

2015 Mechanistic studies of DNA repair Tomas Lindahl, Paul Modrich,

and Aziz Sancar

Table 5.
Nobel-worthy discoveries of E. coli organism [8].

understanding of the genetic code, the mechanisms of DNA replication, the

discovery of the genetic operon systems, and the creation of a genetically modified
organism. Many proteins previously thought difficult or impossible to be expressed
in E. coli in folded form have been successfully expressed in E. coli. The process
of conjugation was discovered in E. coli in 1946 by Joshua Lederberg and Edward
L. Tatum [63]. The availability of DNA sequence information coupled with vast
biochemical and physiological data makes E. coli the organism of choice not only for
virologists, biochemists, and molecular biologists but for all researchers of biology
[8]. The most prominent discoveries made with E. coli are presented in Table 5.

14. Conclusion

E. coli is a truly resourceful microorganism possessing many facets. It is known

for its fast-growing rate in chemically defined media and its adaptability, for ease of
handling. So, E. coli is the most studied and well-understood organism on the planet.
It’s been widely used in research, employed as a model organism to investigate biologi-
cal processing protein engineering, genetic research, and used in biotechnology, its
versatility continues to open up new avenues for future investigations.

16
Escherichia coli: An Overview of Main Characteristics
DOI: http://dx.doi.org/10.5772/intechopen.105508

Author details

M. Basavaraju* and B.S. Gunashree

Department of Studies and Research in Microbiology, PG Centre, Mangalore
University, Karnataka, India

*Address all correspondence to: [email protected]

© 2022 The Author(s). Licensee IntechOpen. This chapter is distributed under the terms
of the Creative Commons Attribution License (http://creativecommons.org/licenses/
by/3.0), which permits unrestricted use, distribution, and reproduction in any medium,
provided the original work is properly cited.

17
Escherichia coli

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