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There are not so many organisms that are so well studied and researched as the bacterium Escherichia coli(E. coli). Since its discovery in 1885, it was used in research, and by end of 2018, there are now already 368,071 publications in PubMed about E. coli. Figure 1, presenting data about number of publications found in PubMed for the search term “Escherichia coli” in the time frame from 1932 to 2018, clearly demonstrates the high and still growing research interest in this microbe.
The bacterium E. coliwas discovered by the German-Austrian pediatrician Dr. Theodor Escherich (1857–1911) in 1885 . He conducted examinations of neonate’s meconium and feces of breast-fed infants with the aim to gain insight into the development of intestinal “flora.” In preparations of meconium and stool samples under the microscope, he observed “slender short rods” of the size of 1–5 μm in length and 0.3–0.4 μm in width, which he named Bacterium coli commune(Figure 2). Further, he cultured these bacteria on agar and blood serum plates, where these bacteria grew as white, non-liquefying colonies. He also showed that these bacteria slowly cause milk to be clotted, as a result of acid formation, and demonstrated that these bacteria have fermentative ability. He also performed the Gram method of staining and revealed that these bacteria rapidly take color with all aniline dyes but lose the color after treatment with potassium iodide and alcohol . Later, in 1919, the bacterium was renamed after its discoverer by Castellani and Chalmers and became Escherichia coli.
3. Characteristics of Escherichia coli
3.1 Basic characteristics
The bacterium E. coli(Figure 3) belongs into the family of Enterobacteriaceae. It is a Gram-negative rod-shaped bacterium, non-sporulating, nonmotile or motile by peritrichous flagella, chemoorganotrophic, facultative anaerobic, producing acid from glucose, catalase positive, oxidase negative, and mesophilic .
E. coliis a well-known commensal bacterium that is among the first colonizing bacteria of the gut after birth. It is a highly successful competitor in the human gut and is comprising the most abundant facultative anaerobe of the human intestinal microbiota . As it is a facultative anaerobe, it survives when released to the environment and can be spread to new hosts. E. coliis thus an important component of the biosphere .
Even though E. coliis a well-known commensal bacterium, many pathogenic strains of E. colido exist. Several highly adapted E. coliclones have acquired specific virulence factors, which confer an increased ability to adapt to new niches and allow them to cause a broad spectrum of disease, and intestinal and also extraintestinal infections .
3.2 The E. coligenome
The first complete E. coligenome sequence was the sequence of the K-12 MG1655 strain of E. coli, published in 1997. The sequenced strain has been maintained as a laboratory strain with minimal genetic manipulation, having only been cured of the temperate bacteriophage lambda and F plasmid. The published genome has 4,639,221 base pairs. Protein-coding genes account for 87.8% of the genome, 0.8% encodes stable RNAs, and 0.7% consists of noncoding repeats. Eleven percent of the genome are involved in regulation of gene expression and also other functions . A circular map of the E. coligenome is represented in Figure 4.
The map is based on the K-12 MG1655 sequence data as deposited in GenBank (Accession number NC_000913) . The multiplier for the ticks is 1e-6 (1.0 represents 1,000,000). In blue, the forward genes are shown, in purple the reverse genes, tRNA genes in orange, and rRNA genes in red. The map was drawn with the online tool ClicO FS, available at the Internet site http://www.codoncloud.com:3000/home [11, 12].
Genomes of pathogenic E. colistrains are general bigger, as the pathogenic strains need several special properties, so-called virulence factors. These are encoded in the virulence-associated genes (VAGs), which are frequently clustered in DNA regions called pathogenicity islands (PAIs) . Often the pathogenic strains possess also extrachromosomal DNA elements, i.e., plasmids, that can also carry additional VAGs . Some examples of genomes of pathogenic strains in comparison with the K-12 MG1655 strain are given in Table 1.
Associated with infection
Chromosome size (Mbp)
Number of genes in the chromosome
Plasmid size (bp)
Number of genes on the plasmid
Urinary tract infection
O83:H1 NRG 857C
O104:H4 2011C-3493 ASM29945v1
Urinary tract infection
Genomes of different E. colistrains.
Data in the table are based on data available in the genome database of the National Center for Biotechnology Information (Internet site: www.ncbi.nlm.nih.gov) .
The most famous E. coliplasmid is the plasmid F (Figure 5). It is the paradigm plasmid for plasmid-specified transfer systems, as bacterial conjugation was first identified as a function of the F plasmid. Further, this plasmid was used to develop many of the genetic techniques commonly used to dissect prokaryotic systems, and F product analysis has been central in elucidating the basic mechanisms of plasmid replication and transmission .
F plasmid has two functional replication regions, RepFIA and RepFIB. The RepFIA region is believed to be primarily responsible for the typical replication properties of F . The secondary replication region, RepFIB, is independently functional and can perform replication in the absence of RepFIA. F plasmid has also remnants of a third replication region, RepFIC, whose function was abolished by transposition of Tn1000into this replication region . Apart from Tn1000also insertion sequences IS2 and IS3 are carried on F plasmid . The plasmid-specified transfer system is encoded in the traregion, starting with the origin of transfer (oriT) .
3.3 The phylogenetic groups of E. coli
The E. colispecies has an extensive genetic substructure and the methods to assess the phylogenetic relationship among E. colistrains evolved during the time. In the pre-molecular era, the E. colidiversity was studied by serotyping. Serotyping studies showed that the somatic (O) antigen, the flagellar (H) antigen, and to a lesser extent the capsular (K) antigen are useful in distinguishing E. colistrains . The E. coliserotyping is complex—173 O antigens, 80 K antigens, and 56 H antigens are known—and the O, K, and H antigens can be found in nature in many of the possible combinations. The final number of E. coliserotypes is therefore very high, 50,000–100,000 or more .
The molecular studies of E. colidiversity began with the measurement of variations in electrophoretic mobility of enzymes derived from different E. colistrains . In 1980s the multi-locus enzyme electrophoresis (MLEE) became the common technique for the study of bacterial diversity. It was found that E. colipopulations evolve in a clonal manner, with recombination playing a limited role, and it also became clear that genetically distant strains can have the same serotype and that closely related strains may have different serotypes . Based on the MLEE studies of 38 enzyme loci, four major phylogenetic groups among E. coliwere found: A, B1, B2, and D . Clermont et al.  established a method of rapid and simple determination of the E. coliphylogenetic groups by a triplex PCR. This genotyping method is based on the amplification of a 279 bp fragment of the chuAgene; a 211 bp fragment of the yjaAgene; and a 152 bp fragment of TSPE4.C2, a noncoding region of the genome. The presence or absence of combinations of these three amplicons is used to assign the E. colito the phylogenetic groups: A, B1, B2, or D (Figure 6).
However, subsequently, on the basis of multi-locus sequence typing and complete genome data, additional E. coliphylogenetic groups were recognized [24, 25]. The number of defined phylogenetic groups thus rose to eight (A, B1, B2, C, D, E, F that belongs to E. colisensu stricto, and the eighth—the Escherichiacryptic clade I). Clermont et al.  thus revised their method to encompass the newly described phylogenetic groups. To enable identification of the F phylogenetic group, the new extended PCR phylotyping method employs an additional gene target, arpA, which serves also as an internal control for DNA quality. Thus, the revised PCR method is based on a quadruplex PCR, and if required, additional single PCR reactions are employed to distinguish between E and clade I, A or C, and D or E phylo-group  (Figure 7).
Two collections of human fecal isolates were screened using the quadruplex phylo-group assignment method demonstrating that 12.8% of E. coliisolates belonged to the newly described phylo-groups C, E, F, and clade I and that strains assigned to phylo-groups A and D by the triplex method are worth to be retested by the quadruplex method, as it is likely that they are going to be reclassified . Logue et al.  performed a comparative analysis of phylogenetic assignment of human and avian extraintestinal pathogenic (ExPEC) and fecal commensal E. coli(FEC) strains and showed that a total 13.05% of studied human E. colistrains and 40.49% of avian E. colistrains had to be reclassified. Another study using human E. colistrains isolated from skin and soft-tissue infections and fecal E. colistrains from healthy humans and also avian and brown bear fecal strains revealed that 27.60% of human, 23.33% of avian, and 70.93% of brown bear strains had to be reclassified. Moreover, a high number (12.22%) of reclassifications from the previous phylo-groups to the non-typeable (NT) group were observed among the avian fecal strains of this study. Further, a survey performed on other published data by Starčič Erjavec et al.  showed that also a number of other studies report occurrence of NT strains by the quadruplex method, for example, a study including 140 uropathogenic E. colistrains from Iran reported 27.14% of NT strains . These data emphasizes that there is a need to search for more E. colistrains from novel environments (new hosts in not yet explored geographic regions) and to revise the PCR phylotyping method again in order to type these NT strains.
3.4 The commensal E. coli
As E. coliis a facultative anaerobe, and among the first gut colonizers, these bacteria help to establish the anaerobic environment of the gut that enables the further colonization of the gut by anaerobic bacteria . After the E. colicolonization, usually the host and E. colicoexist in mutual benefit for decades . E. coligets “food and shelter,” and the host benefits due to the E. colivitamin K production and the so-called colonization resistance. Colonization resistance is the phenomenon of protection against colonization by pathogenic bacteria, including pathogenic E. coli. The niche of the commensal E. coliis the mucous layer of the colon . On average five different commensal E. colistrains colonize a human host at any given time . As host and the E. coliprofits from their association, these E. colicould be also designated as mutualistic E. coli.
3.5 The pathogenic E. coli
E. coliis also a medically important species, as it is involved in many different types of infections. Two major groups of pathogenic E. coliexists: the intestinal pathogenic E. coli(IPEC), associated with infections of the gastrointestinal tract, and the extraintestinal pathogenic E. coli(ExPEC), associated with infections of extraintestinal anatomic sites . The medical diversity of this species is nicely exhibited by its classification of pathogenic E. coli(Figure 8), the so-called E. colipathotypes.
The versatility of pathogenic E. colistrains depends on their genetic makeup, on the presence of so-called virulence genes, and possession of such genes distinguishes pathogenic from nonpathogenic bacteria . Virulence factors help bacteria to (1) invade the host, (2) cause disease, and (3) evade host defenses .
3.5.1 Adhesins and invasins
Once a bacterium reaches the host surface, in order to colonize, it must adhere to host cells. For this purpose bacteria have different fimbrial and afimbrial adhesins. Fimbrial adhesins are rod-shaped protein structures, which consists primarily of an ordered array of single protein subunits, which build a long cylindrical structure. At the top, there are proteins, adhesins, which mediate the adherence to the host’s molecules. A fimbrial adhesin is thus a structure that extends outward from the bacterial surface and establishes the contact between the bacterial surface and the surface of the host cells. Afimbrial adhesins are surface proteins important for tighter binding of bacteria to host cells. Some bacteria have evolved mechanisms for entering nonphagocytic host cells. Bacterial surface proteins that provoke actin rearrangements and thereby incite the phagocytic ingestion of the bacterium by host cells are called invasins . The most known E. coliadhesins and invasins are presented in Table 2.
Most commonly tested virulence (associated) genes
Type 1 fimbriae (Fim)
P fimbriae (Pap/Prf)
S/F1C fimbriae (Sfa/Foc)
N-Acetyl-d-glucosamine-specific fimbriae (Gaf)
Bifunctional enterobactin receptor/adhesin (Iha)
Afimbrial adhesin (Afa)
Invasion of brain endothelium (IbeA)
Colonization factor antigen I (CFA/I)
Bundle-forming pili (BFP)
Aggregative adherence fimbriae (AAF/I)
Typical adhesins and invasins of pathogenic E. colistrains.
3.5.2 Iron acquisition mechanisms
Iron is essential for bacterial growth, but iron concentrations in nature are generally quite low, particularly low in host organism. To survive in the host organism, bacteria must have some mechanisms for acquiring iron. The best studied type of bacterial iron acquisition is the siderophores. These are low-molecular-weight compounds that chelate iron with very high affinity . The most known E. coliiron uptake systems are presented in Table 3.
Iron uptake system
Most commonly tested virulence (associated) genes
Siderophore receptor IreA
Temperature sensitive hemagglutinin (Tsh)—in birds, Hemoglobin protease (Hbp)—in humans
Periplasmic iron binding protein (SitA)
Ferrichrome-iron receptor (Fhu)
Typical iron uptake systems of pathogenic E. colistrains.
3.5.3 Systems to evade host immune response
The healthy host usually has multilayered defenses that prevent the establishment of bacterial infection. Among the most effective of these defenses is the immune response. However, bacteria have evolved systems to avoid, subvert, or circumvent innate host defenses and to evade acquired specific immune responses of the host . A capsule is a loose, relatively unstructured network of polymers that covers the surface of a bacterium. The role of capsules in bacterial virulence is to protect bacteria from the host’s inflammatory response . Further, increased serum resistance is often found among pathogenic bacteria, especially those associated with systemic infections . Serum resistance is the ability to prevent complement activation on the bacterial cell surface and to inhibit insertion of the membrane attack complex into the bacterial membrane . The feature is often based on the modifications in lipopolysaccharide (LPS), which can be of two types: either attachment of sialic acid to LPS O antigen or changes in the LPS O antigen side chain . However, other proteins can also be implicated in increased serum resistance; for example, the TraT protein of the surface exclusion complex involved in conjugation . Another important protein of pathogenic E. coliis the Toll/interleukin-1 receptor domain-containing protein (Tcp) that interferes with the TLR signaling system of the innate immunity . The most known E. colisystems to evade host immune response are presented in Table 4.
Host immunity evading system
Most commonly tested virulence (associated) genes
Group II capsule including K1 and K5 capsules
Conjugal transfer surface exclusion protein (TraT)
Outer membrane protease T (OmpT)
Increased serum survival (Iss)
Suppression of innate immunity (Toll/interleukin-1 receptor domain-containing protein Tcp)
Typical host immunity evading systems of pathogenic E. colistrains.
Toxins are the virulence factors that damage the host. Exotoxins are toxic bacterial proteins that are excreted into the medium by growing bacteria or localized in the bacterial cytoplasm or periplasm and released during bacterial lysis. Exotoxins vary considerably in their activities and the target host cell types . The most known E. colitoxins (exotoxins) are presented in Table 5.
Most commonly tested virulence (associated) genes
Cytotoxic necrotizing factor 1 (CNF-1)
Cytolethal distending toxin IV (CDT 1)
Uropathogenic specific protein (Usp)
Serine protease autotransporters Sat, Pic
Heat-stable toxins (STa, STb)
Heat-labile toxin I (LTI), heat-labile toxin II (LTII)
Shiga toxin 1 (Stx1), Shiga toxin 2 (Stx2)
EHEC hemolysin (Ehx)
Low-MW heat-stable toxin (EAST1)
Typical toxins (exotoxins) of pathogenic E. colistrains.
However, E. colipossess also an endotoxin, namely, the lipopolysaccharide, which is an integral component of the outer membrane of Gram-negative bacteria. The lipid portion (lipid A) is embedded in the outer membrane, with the core and O antigen portions extending outward from the bacterial surface. Lipid A is the toxic portion of the molecule, and it exerts its effects only when bacteria are lysed. The toxicity of lipid A resides primarily in its ability to activate, complement, and stimulate the release of bioactive host proteins, such as cytokines .
3.6 The antibiotic-resistant E. coli
Antibiotics are low-molecular-weight compounds that kill or inhibit growth of bacteria . Antibiotic treatment is one of the main approaches of modern medicine to combat bacterial infections, including also E. coliinfections . However, bacteria evolved different mechanisms that confer resistances to antibiotics. Resistant bacteria are able to either (i) modify/degrade the antibiotic, (ii) actively transport the antibiotic out of the cell or prevent its intake, (iii) sequester the antibiotic by special proteins, or (iv) modify, bypass, or protect the target . The emergence, spread, and persistence of resistant and even multidrug-resistant (MDR) bacteria or “superbugs”, also among E. coli, are now posing a serious global health threat of growing concern . The antimicrobial resistance surveillance data of European Centre for Disease Prevention and Control (ECDC) also showed the increase in antibiotic resistance among invasive E. coliisolates (Figure 9).
The mechanisms of resistance to antibiotics are encoded in resistance genes. A list of typical E. coliresistance genes is given in Table 6.
As many of the resistance genes are encoded on conjugative plasmids or conjugative transposons, they are easily transferred between different bacteria and hence spread in the population .
3.7 The bacteriocinogenic E. coli
Bacteriocins are ribosomally synthesized, proteinaceous substances that inhibit the growth of closely related species through numerous mechanisms . They are a heterogeneous group of particles with different morphological and biochemical entities. They range from a simple protein to a high molecular weight complex . The bacteriocins with molecular masses below 10 kDa are designated as microcins . Bacteriocins are potent toxins that are usually produced during stressful conditions and result in the rapid elimination of neighboring bacterial cells that are not immune or resistant to their effect. The killing is exhibited after adsorption to specific receptors located on the external surface of sensitive bacteria, by one of the three primary mechanisms: forming channels in the cytoplasmic membrane, degrading cellular DNA/RNA, or inhibiting protein synthesis. Because of their narrow range of activity, it has been proposed that the primary role of bacteriocins is to mediate intraspecific, or population level, interactions . The genetic determinants of most of the bacteriocins are located on the plasmids, apart from few, which are chromosomally encoded . Bacteriocins of E. coliare usually called colicins. A relatively high frequency of colicin-encoding plasmids is found in isolates of pathogenic E. coli, for example, ~80% of O157:H7 enterohemorrhagic E. colistrains studied by Bradley and Howard were colicinogenic . Especially microcins have been associated with pathogenic strains . In a collection of E. colistrains isolated from skin and soft-tissue infections, 55% of strains possessed microcin M, and 43% possessed microcin H47 . Further, colicin insensitivity among these strains correlated with a higher prevalence of extraintestinal virulence factors . Typical E. colibacteriocins, their receptors, translocation systems, and mode of action are given in Table 7.
Mode of action
Inhibition of peptidoglycan synthesis
Typical E. colibacteriocins, their receptor, translocation system, and mode of action [59, 60].
3.8 The probiotic E. coli
Probiotics are live microorganisms that, when administered in adequate amounts, confer a health benefit on the host. Probiotic bacteria act via a variety of means, including modulation of immune function, production of organic acids and antimicrobial compounds, interaction with resident microbiota, interfacing with the host, improving the gut barrier integrity, and enzyme formation . Several E. colistrains were recognized as good and effective probiotics and are now used in drugs (see Table 8). The probiotic E. coliare applied to a variety of human conditions, including intestinal bowel diseases and diarrhea. Further it was shown that colonization of newborns led to reduced disease rates, lower incidence of allergies, and reduced mortality .
E. coliNissle 1917 strain
Six different E. colistrains (G1/2, G3/10, G4/9, G5, G6/7, and G8)
E. coliA0 34/86 strain
Powder for preparation of per oral solution
Ardeypharm GmbH, Herdecke, Germany
SymbioPharm GmbH, Herborn, Germany
Dyntec, Terezín, Czech Republic
2.5–25 × 109 CFU/capsule
1.5–4.5 × 107 CFU/ml
0.8–1.6 × 108 CFU/dosis
Recommended daily dose
1–2 capsules/day (2.5–50 × 109 CFU)
2–4 ml (3.0–18 × 107 CFU)
0.8–1.6 × 108 CFU three times/week
Isolation date of the used strain(s)
Data not available
Variable including 035,129, 0:169, rough, all H–
2 cryptic plasmids
Microcin M, H47
Data not available
Motile (flagella present)
Nonmotile (flagella absent)
Data not available
CFT073, ABU83972 (UPEC)
K12, ATCC8739 (commensals)
CFT073, 536 (UPEC)
Year of first publication describing the use in humans
E. coliNissle 1917 is nowadays often used as a reference strain or model microorganism in experimental biomedical studies, including recombinant manipulations of the strain in order to construct derivatives with novel properties . One such example is the strain ŽP, which is a genetically modified Nissle 1917 possessing a bacterial conjugation-based “kill”-“anti-kill” antimicrobial system—a conjugative plasmid carrying the “kill” gene (colicin ColE7 activity gene) and a chromosomally encoded “anti-kill” gene (ColE7 immunity gene). Hence, in the process of conjugation, the conjugative plasmid transfers the “kill” gene into a recipient cell, where it is expressed and the recipient killed [65, 66].
3.9 The “workhorse” E. coli
E. coliis known for its fast growing rate in chemically defined media and extensive molecular tools available for different purposes. All these make it an important model organism, which is also called the “workhorse” of molecular biology. Even though E. colilacks many interesting features appreciated in biotechnology, such as growing at extreme temperatures or pH and the capacity to degrade toxic compounds, pollutants, or difficult to degrade polymers, it is much used in biotechnology also . In Table 9 contributions of E. colito biology, medicine, and industry are listed.
Molecular biology, physiology, and genetics
Elucidation of the genetic code
Crick FH, Barnett L, Brenner S, and Watts-Tobin RJ
Lehman IR, Bessman MJ, Simms ES, and Kornberg A
Life cycle of lytic bacteriophages
Ellis EL and Delbrück M
Gene regulation of the lacoperon
Jacob F and Monod J
Gene regulation of the araoperon
Englesberg E, Irr J, Power J, and Lee N
Discovery of restriction enzymes
Linn S and Arber W
Identification of genes controlling antimicrobial drug tolerance in stationary phase
Hu Y and Coates AR
Role of global regulators and nucleotide metabolism in antibiotic tolerance
Hansen S, Lewis K, and Vulić M
Metabolic control of persister formation
Amato SM, Orman MA, and Brynildsen MP
Swarming motility behavior
Harshey RM and Matsuyama T.
Elucidation of the structure and function of ATP synthase
Capaldi RA, Schulenberg B, Murray J, and Aggeler R
Conjugal DNA transfer
Tatum EL and Lederberg J
Random nature of mutation
Luria SE and Delbrück M
Relationship between genomic evolution and adaptation
Barrick JE, Yu DS, Yoon SH, Oh TK, Schneider D, Lenski RE, and Kim JF
Role of adaption, chance, and history in evolution
Travisano M, Mongold JA, Bennet AF, and Lenski RE
Cairns J, Overbaugh J, and Miller S
Role of historical contingency in evolution
Blount ZD, Borland CZ, and Lenski RE
Origin of novel traits
Blount ZD, Barrick JE, Davidson CJ, and Lenski RE
Long-term fitness trajectories
Wiser MJ, Ribeck N, and Lenski RE
Effect of sexual recombination on adaptation
Predator-prey interactions (bacteriophage)
Chao L and Levin BR
Genetic engineering and biotechnology
Molecular cloning and recombinant DNA
Cohen S, Chang A, Boyer H, and Helling R
Generating precise deletions and insertions
Link AJ, Phillips D, and Church GM
Herring CD, Glasner JD, and Blattner FR
Contributions of E. colito biology, medicine, and industry [68, 69, 70].
The following recombinant pharmaceuticals were set up to be in vivo synthesized in E. coli: insulin, interleukin-2, human interferon-β, erythropoietin, human growth hormone, human blood clotting factors, pegloticase, taxol, and certolizumab. Further, E. coliis also used to produce biofuels and industrial chemicals such as phenol, ethanol, mannitol, and a variety of others .
To conclude, E. coliis a truly versatile microorganism possessing many facets—it is a well-known commensal bacterium, but some strains can be also pathogenic, even causing mortality, especially if the pathogenic strain acquired multiple resistance genes. However used as a probiotic it can improve health and in it can be employed as a good working “workhorse” in the laboratory as well as in biotechnological settings. The differentiation between commensal and pathogenic strains is not easy, as among the healthy gut microbiota pathogenic strains are hidden, and also commensal strains can become pathogenic due to horizontal gene transfer of mobile genetic elements possessing virulence genes . Even though E. colihas been the object of research now for already more than 100 years, its versatility warrants new possibilities for investigation also in the future.
The author is thankful to the Slovenian Research Agency (P1-0198) for its funding.
Lactic Acid Bacteria as Starter-Cultures for Cheese Processing: Past, Present and Future Developments
By J. Marcelino Kongo
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