How is a bacterial strain defined?

How is a bacterial strain defined?

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When a species of bacteria is referred to by its strain, are they a clone of single founder or is a certain amount variation allowed?

In theory they're clones, but depending on the age of the strain(some strains are surprisingly old: ~40 years) there's variation inside strains.

The reverse is also true. Bacteria from a single species are isolated twice and named different things by different labs and the mistake can take years to even find, much less correct.

Bacteria effectively clone themselves so theoretically all clones are identical. However like every organism they're subject to Darwinian evolution so there's always a chance a random mutation happens. Since bacteria usually reproduce fast the rate of these mutations can happen fast resulting in the strain evolving to a (slightly) different strain.

Whereas a clone (or clonal population) is the current population of individuals descended from a single particular ancestral individual, a strain can be understood as the whole line of individuals down and up to that single particular individual.

But as noted in the other answers, even though the isogenic character is often taken as a more or less tacit approximation, none of those two concepts forbid genetic variation or assume that all the individuals of the said clone or strain are isogenic.

The concept of species for microbial organisms is more intricate.


cell strain
A population of cultured cells, of plant or animal origin, that has a finite life span, in contrast to a cell line. (Figure 6-5)
Full glossary .

electronic strain
The distorted distribution of electrons in a substrate induced by the proximity of a strong dipole in the enzyme, e.g. Zn2+ in carboxypeptidase.
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Different bacteria strains produce different types of exopolysaccharides in different rates from varied types of sources. There are possibilities in discovering novel exopolysaccharides that can be utilized for different applications. Bacterial exopolysaccharides production is affected by the growth conditions.

grows faster than its wild counterpart, and is said to be very high in minerals, vitamins and antioxidants, containing up to 16 percent protein by dry weight. Abalone did well on a diet of it, growing at rates "that exceeded those previously reported in the literature." .

An organism that is different from other organisms of the same species due to genetic differences.

s are tradenamed GloFish other cultivated varieties include "golden", "sandy", "longfin" and "leopard".

: Population of cells, all of which arise from a single pure isolate.
Substrate: A base on which an organism is grown. They can also be the substances on which compounds and enzymes act.

behaving as recipients during conjugation (female). It lacks the F factor.

s that differ in their incubation period, symptoms, and effects on different brain regions. Skeptics argue that these differences are due to mutations in nucleic acid and is evidence that prions do indeed have genetic material.

of resistant bacteria shows up in a community, let's say it shows up in a school. What should the public health people be doing to control it?

s together.
Hybrid vigor. Heterosis.
Hypomorph. A mutant allele that does not eliminate the wild-type function of a gene and may give a less severe phenotype than a loss-of-function mutant.

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, .

of mice used for cancer research, called Oncomouse, was the first mammal to be patented!
This cloned sheep, Dolly, foretells the prospect of human cloning, one of many reproductive possibilities under debate.
The Tech Museum of Innovation
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of a species that has certain biological characters separating it from other individuals of that species.
Bacterial blight lesions on stems.

mating preferences.
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s are named after their types of hemagglutinin and neuraminidase surface proteins , so they will be called, for example, H3N2 for type-3 hemagglutinin and type-2 neuraminidase.

of human papillomavirus that causes plantar warts and other warts is very common in the environment. It is not known why some people develop warts and others don't.

s of Streptococcus have a toxin on their surface call streptolysin-s. When a white blood cell attacks these bacteria, what happens?

), DH5a (ditto), JM101 and JM109 (suitable for growing M13 phages), XL1-Blue (general-purpose, good for blue/white lacZ screening).

s of lice were always there " and are just more frequent now because all the non-resistant lice died a sudsy death.
Exposure to lice shampoo actually caused mutations for resistance to the shampoo.

that is lac Z met bio and carrying an F' episome with the plac O lac Z DNA sequence on the episome, and cultured for several hours.

congenital trait /kən-JEHN-ə-təl/ A trait present at birth, and not produced by environmental influences.

produced by inbreeding
Source: Jenkins, John B. 1990. Human Genetics, 2nd Edition. New York: Harper & Row

from the Keio collection which is reported to grow on glucose with growth defect (see Supplementary Information, S3 and S7) is not adequate. Therefore it is irrelevant to state ".

on the heart as the heart muscle receives less oxygen and carbon monoxide can damage directly, the linings of arteries.
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2. The Live R had been transformed into Live S by some "transforming factor".
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in which the joining together of Okazaki fragments is impaired and suspect that a mutation has occurred in an enzyme found at the replication fork. Which enzyme is most likely to be mutated?
Telomere Replication .

A cross between an animal that is heterozygous for alleles obtained from two parental

s. Also used to describe the breeding protocol of an outcross followed by a backcross.
See also: model organisms (ORNL)
Bacterial artificial chromosome (BAC) .

s are also capable of diazotrophic growth. Genome sequencing has provided a large amount of information on the genetic basis of nitrogen metabolism and its control in different cyanobacteria.

Genetic reassortment between various flu viruses occurs in these animals, and if humans live in close quarters with the animals, flu viruses containing RNA segments from all sorts of different

s can start infecting humans.

Mutations in the antigenic structure of the influenza virus have resulted in a number of different influenza subtypes and

Actin fibers in a cell stained with a fluorescent

specific for actin
Unlike the nuclear membrane, the plasma membrane surrounding the cell is single and it has no pores.

of crop is an example of agricultural biotechnology: a range of tools that include both traditional breeding techniques and more modern lab-based methods.

One of the most dangerous

Ossification of muscular tissue as a result of repeated

or injury is not infrequent. It is oftenest found about the tendon of the Adductor longus and Vastus medialis in horsemen, or in the Pectoralis major and Deltoideus of soldiers. It may take the form of exostoses firmly fixed to the bone"e.g.

Found in the intestines of humans and animals, this bacterium is usually harmless, but some

known as O157:H7 is considered a potential biological weapon.

The process introduces a plant to a mild

of that same or very closely related pathogen. Eventually, the plant may build resistance to the virus.

ing in the toilet
Processed food diet high in sugar and refined carbohydrates like bread, cake, jams, breakfast cereal, sweets etc. Lack of fresh vegetables and fruit, unprocessed whole grain cereals and brown rice
Genetic - more common in women and runs in families
Obesity .

Restriction enzymes are found in many different

s of bacteria where their biological role is to participate in cell defense. These enzymes "restrict" foreign (e.g. viral) DNA that enters the cell, by destroying it.

s that are typically used for molecular mapping are generally recombinant inbred lines. RI lines are derived from a cross between parents with polymorphic genotypes.

of a microorganism that lacks the ability to synthesize one or more essential growth factors, which therefore must be included in the medium to allow growth.

The vaccine against the flu is a vaccine made of the attenuated virus of three different

s should compose the vaccine. This is a strategy to combat the high mutation rate of the virus.

Mysticetes are filter feeders,

ing water through their baleen to capture prey items. Mysticetes include the largest of the whales, the fin and blue whales. The blue whale is the largest animal ever to have lived on earth. ( 2. Any right whale, or whalebone whale. ( 3.

Harmful algal bloom. A bloom of (usually) planktonic microalgae belonging to a

of a species that has a toxic harmful to marine organisms or humans consuming marine organisms.
Heritable character. A morphological character whose given state can be explained partially in terms of the genotype of the individual .

(2) That which purposefully direct, manipulate, manage, regulate, re

, or cause change.
(science) A subject or a group in an experiment where the factor being tested is not applied, hence, serves as a standard for comparison against another group where the factor is applied.
verb .

And this third phosphate it's going in to this region of great negativity so there is a lot of

on that bond and so very easily dink, you can break it off and it flies off kind of like one of those old sucker dart guns where you push it back load up a spring and then pull the trigger and doink, .

Figure 2. Immunohistochemical

ing of ribosomal protein RPL17 in liver, showing the cytosolic localization of the protein.
Metabolism .

Cell banks include master cell banks (MCBs) and working cell banks (WCBs). MCBs house primary cell

s that are kept stored and not used for production purposes. WCBs house cells used in pharmaceutical production grown from those maintained in an MCB so that their stability and uniformity are well characterized.

s of Streptococcus pneumoniae).
Adaptation: microenvironments of the host body provide habitats for bacteria that are capable of selective tissue invasion (e.g. Neisseria meningitidis vs Streptococcus pneumoniae.

The first continuously cultured cells, a human cervical cancer

taken from a woman called Henrietta Lacks (and named after her).
A parasitic worm, such as a flatworm or roundworm.

stress Physical, chemical, or emotional factors that place a

on an animal. Plants also experience physiological stress under adverse environmental conditions.
stress-related disease See stress shock.

During extraction of plasmid DNA from the bacterial cell, one strand of the DNA becomes nicked. This relaxes the torsional

needed to maintain supercoiling, producing the familiar form of plasmid.

Genetics is not the only factor that affects the physiology of animals and plants. Environmental

s wreak havoc on eukaryotic organisms as well. For organisms that do not dwell in aquatic habitats, water must be stored within their cellular environments.

A nutritional mutant that is unable to synthesize and that cannot grow on media lacking certain essential molecules normally synthesized by wild-type

s of the same species.
The vertebrate class of birds, characterized by feathers and other flight adaptations.

s are called toxigenic when they are capable of producing toxin. This terminology is typically used to indicate that a bacterial (potential) pathogen is infected with or lysogenic for a phage encoding toxin genes that are capable of expression.

The common flu virus changes (evolves) enough every year that a new flu vaccine must be produced to protect the human population from repeat infection. In addition, a significant number of bacteria

s have evolved antibiotic-resistance to the human-devised drugs that previously would have killed them.

If they eventually get someone sick, there is a chance that the antibiotics will not work again. You have incubated super bacteria! It's happening all the time in hospitals. We are killing off the easy diseases but some mutant

This relaxes the torsional

needed to maintain supercoiling, producing the familiar form of plasmid. (See Plasmid.) NIH. See National Institutes of Health. Nitrocellulose. A membrane used to immobilize DNA, RNA, or protein, which can then be probed with a labeled sequence or antibody. Nitrogen fixation.

Tumor suppressor gene -- genes that normally function to re

the growth of tumors the best understood case is for hereditary retinoblastoma.

What is a Strain

A strain is a genetic variant, subtype or culture of a biological species. They are more popularly used in microbiology. Furthermore, a strain originates from a single cell colony, and microorganisms, such as viruses, bacteria, and fungi, have several strains within a species. As an example, a “flu strain” is a certain biological form of influenza or “flu” virus characterized by their differing isoforms of surface proteins. Thereby, a strain significantly carries a particular genetic characteristic, which does not occur within the other members of the species.

Figure 1: H1N1 Viral Strain

Besides, genetic variation is the variation of genomes between individuals in the same species due to the genetic mutations, which occur during sexual reproduction. Usually, genetic variation can be caused by mutations of genes, gene flow, random mating, random fertilization, and crossing over between homologous chromosomes. In addition to that, genetic variation is an important mechanism, which forces evolution through natural selection. Also, it is important in maintaining biodiversity among species, as well.


Amplification and sequencing of gene fragments from viridans group streptococci

The primers for the amplification of internal fragments of eight house-keeping gene fragments were selected as in Methods (Table 1). The primers successfully amplified the eight gene fragments from 326 of the 375 (87%) Mitis group strains that were examined. They also amplified the correct fragments from some streptococcal species outside the Mitis group, including all strains of S. anginosus, S. vestibularis and S. pyogenes that were examined. However, the guaA gene could not be amplified from some strains (mostly S. sanguinis and S. cristatus) and this gene was eliminated to produce the final seven-locus MLSA scheme. The seven selected house-keeping genes could be amplified from all viridans group streptococci that were examined and were at least 40 kb apart on the S. pneumoniae R6 chromosome.

For each strain, the gene fragments were sequenced on both strands and trimmed to defined start and end positions. For each locus, the trimmed sequences from all strains were the same length, indicating that indels in these genes were absent, as they were in the corresponding S. agalactiae, S. mutans and S. suis sequences, and are thus likely to be uncommon among the viridans group.

Identification of sequence clusters

Figure 1 shows a neighbour-joining tree for all 420 concatenated sequences (402 from viridans group strains, 17 from strains of S. pyogenes and one from S. agalactiae) of the seven loci used in the new seven-locus MLSA scheme, with the strains coloured where a clear species assignment was provided by the laboratory of MK. The tree identified a number of sequence clusters that were well resolved, with ≥ 95% bootstrap confidence values for the nodes. The strains identified as S. pseudopneumoniae (including the type strain) clustered together but were not well resolved from the S. mitis cluster (bootstrap value of 92% for the node separating the S. pseudopneumoniae and S. mitis clusters on the neighbour-joining tree, but only 46% on a minimum evolution tree see below). The S. mitis cluster was unusual as it consisted of a set of closely related sub-clusters arising from the branch that separates the S. pneumoniae and S. pseudopneumoniae clusters from that of S. oralis.

Tree showing the positions of well-characterized strains and type strains within sequence clusters. A neighbour-joining radial tree was constructed using the concatenated sequences of all 420 strains. The viridans group strains that are coloured were those assigned to species in the laboratory of MK the positions on the tree of the type strains of viridans group species are indicated. Mitis, Anginosus and Salivarius group species are shown, respectively, as coloured circles, squares and diamonds. Bootstrap support values (%) for each of the nodes leading to the Mitis group sequence clusters are indicated values for the clusters within the Anginosus and Salivarius groups are shown in Figure 2C. The colour key is ordered top to bottom according to the position of the clusters on the radial tree, from S. pneumoniae to S. pyogenes.

Concordance between these clusters and the assigned species names was imperfect, in accord with the difficulties in assigning viridans group strains to species. However, almost all of the clusters contained only one designated type strain (Figure 1). Accordingly, the majority of the sequence clusters may be equated with recognized species, that is, S. anginosus, S. australis, S. constellatus, S. cristatus, S. gordonii, S. infantis, S. intermedius, S. mitis, S. oralis, S. parasanguinis, S. pseudopneumoniae, S. sanguinis, S. salivarius, S. thermophilus and S. vestibularis. The only exceptions were the S. peroris type strain which, although on an unusually long branch, fell within a cluster that otherwise included the S. infantis type strain and several reference strains of that species, and S. oligofermentans that was within a subgroup of S. oralis (see below).

For several of the sequence clusters there was complete, or almost complete, concordance with species names assigned on the basis of phenotypic examination. However, for some species (for example, S. mitis, S. infantis and S. oralis) that have been affected by changing taxonomy, or difficulties in phenotypic differentiation, there was significant discordance between the clusters and previously assigned species names. The major anomaly was that strains historically assigned as S. mitis fell into a number of different closely related sequence clusters, particularly those otherwise consisting of S. infantis and S. oralis. This anomaly was due largely to strains initially assigned as 'S. mitis biovar 2' being either part of the S. oralis cluster (see below), in agreement with a recent observation [18], or part of the subsequently described S. parasanguinis cluster [26]. Besides the anomalous clustering of some 'S. mitis' strains, there were single strains assigned as S. gordonii and S. infantis within the S. oralis cluster, a single strain of 'S. mitis biovar 2' within the S. anginosus cluster and a single strain of S. anginosus within the S. constellatus cluster.

The strains within the major sequence clusters correlated sufficiently well with the species names obtained through standard taxonomic procedures, and included the type strain of the species, that each of the sequence clusters was considered to represent a species cluster. Figure 2A shows a neighbour-joining tree for all 420 strains with the strains within each cluster coloured according to their assigned species names. Figure 2C shows the same tree with the Mitis group clusters collapsed to show better the resolution of the species clusters within the Anginosus and Salivarius groups. A few strains that were on the fringes of sequence clusters were not coloured, to represent uncertainty as to the species to which they belong. The tree shown in Figure 2A was used as the MLSA reference tree for assigning a query strain to a viridans group species from its location within one of the defined species clusters.

The MLSA reference tree. A. The neighbour-joining tree of Figure 1 was relabelled so that all strains within a sequence cluster were assigned to the species inferred from the positions on the tree of the type strain and other well-characterized strains. The limits of the S. mitis and S. pseudopneumoniae clusters are somewhat unclear and the strains on the flanks of this cluster are shown as white circles (uncertain species) to indicate this. Strains that were re-checked as they were outliers of species clusters, or were distinct from all other strains, are indicated by a red asterisk. B. The tree constructed from the same set of concatenated sequences using minimum evolution. C. The neighbour-joining tree with the Mitis group clusters collapsed, to show more clearly the sequence clusters within the Anginosus and Salivarius groups. The positions of the type strains and bootstrap values for the nodes are shown.

Comparing clustering patterns using different MLSA schemes and different tree-building methods

If MLSA is to be a reliable approach to identifying species as sequence clusters, the same clusters should be obtained for the same set of strains with different sets of house-keeping genes. Figure 3 shows a comparison of the trees produced from a set of 93 strains of S. pseudopneumoniae, S. pneumoniae, S. mitis and S. oralis that were characterized by both the new seven-locus MLSA scheme and the earlier scheme that used six of the pneumococcal MLST genes [11, 15]. Although these schemes used completely different house-keeping genes, the trees were remarkably similar. The genetic distances between clusters were, however, less with the new MLSA scheme than with the earlier scheme (Figure 3). There were two minor differences between the trees. Firstly, two strains on the fringes of the S. pseudopneumoniae cluster using the MLST loci were allied to the S. mitis cluster using the seven-locus MLSA scheme and were re-assigned as uncertain species. Secondly, one strain (768-1) was an outlier of the S. pneumoniae sequence cluster in the six-locus tree but not in the seven-locus tree however, its guaA gene was unusually divergent and it was also an outlier when this gene was added to the seven-locus MLSA scheme (Figure 4B).

Comparison of the clustering of strains using two different MLSA schemes. The neighbour-joining tree obtained for a set of 93 strains of S. pneumoniae, S. pseudopneumoniae, S. mitis and S. oralis using the seven-locus MLSA scheme (A) was compared with the tree obtained from the same strains using the concatenated sequences of six of the loci used in the S. pneumoniae MLST scheme (B). The two trees are drawn to the same scale.

Effect on clustering patterns of adding an additional locus ( guaA ) to the seven-locus scheme. The guaA gene was successfully sequenced from 326 of the Mitis group strains and the neighbour-joining tree obtained for these strains using the seven-locus MLSA scheme (A) was compared with that obtained from the same strains by adding the guaA sequence to the concatenated sequences of the seven loci (B). The colour code for species clusters is as in Figure 2. The positions on the tree of the type strains are indicated.

The clustering patterns were not greatly influenced by the tree-building algorithm. Figure 2B shows the tree produced by minimum evolution (a method based on local optimization of an initial neighbour-joining tree), compared with that obtained using neighbour-joining (comparisons were restricted to these two methods since both are computationally efficient, as required for the rapid generation of trees on-line with sequences from large number of strains). The assignment of strains to the sequence clusters was the same, and the only significant difference was a slightly more marked sub-division of the S. mitis group into sub-clusters using minimum evolution. As expected for sequences that are closely related, using a genetic distance correction made no difference to the clustering patterns (data not shown).

Effect of adding an eighth gene to the MLSA scheme

To assess whether the addition of an eighth gene improved the resolution of sequence clusters (particularly of S. mitis and S. pseudopneumoniae), the 326 Mitis group strains in which the guaA gene could be amplified were used to produce an eight-locus tree, that could be compared with the seven-locus tree produced for all Mitis group strains (Figure 4). There were only minor differences between the eight and seven-locus trees and, excepting the location of the S. peroris type strain as either within, or an outlier of, the S. infantis cluster, none of the differences affected the resolution of the sequence clusters, and the seven-locus scheme was chosen for all further work.

Identification of potential new viridans group species

The MLSA scheme should be able to identify possible new species as groups of strains, or individual strains, which clearly do not fall within any of the known species clusters. We firstly checked whether strains that did not fall into known species clusters, or were outliers of species clusters, could be the result of using DNA from mixed cultures. In all cases, further sub-culturing of these strains (labelled in Figure 2A) and re-sequencing of the seven loci gave the same results as obtained initially, ruling out the possibility that the position on the concatenated tree of these strains was due to the use of DNA from mixed cultures.

One example of an unidentified cluster is provided by four closely related strains (assigned by MK as S. mitis) that arose as a distinct lineage from the branch separating the S. mitis and S. oralis clusters (unknown A in Figure 2). These four strains were isolated from members of two families included in a study of the clonal diversity of S. mitis within individuals [40]. Although the strains cannot be distinguished from S. mitis by phenotypic analysis, they may constitute a separate species.

Likewise, the two major clusters that include the type strains of S. mitis and S. oralis both include several sub-clusters, which may warrant recognition as separate species. As an example, 10 strains previously assigned to 'S. mitis biovar 2' [25], formed a sub-cluster (including strains SK34, SK79, SK96 and others) within the major S. oralis cluster (Figure 5), in agreement with recent observations [18]. These strains are phenotypically distinct from the remaining part of the S. oralis cluster by being arginine hydrolysis and α-maltosidase positive, and by expressing the Lancefield group K cell wall carbohydrate antigen (data not shown). In addition, all strains of the 'S. mitis biovar 2' sub-cluster lacked IgA1 protease activity (Figure 5).

Phenotypically distinct sub-clusters within the S. oralis species cluster. The region of the neighbour-joining tree that includes strains within the S. oralis species cluster is shown in more detail. The positions on the tree of the type strains are indicated. The sub-cluster of phenotypically distinct strains that are arginine hydrolysis and α-maltosidase positive, and which express the Lancefield group K cell wall carbohydrate antigen, is indicated (highlighted in blue). A further subgroup, which included the S. oligofermentans type strain (SK1136), consisting exclusively of IgA protease-negative strains is also indicated (highlighted in yellow). Bootstrap values for relevant nodes are shown. Green strain names indicate IgA1 protease-positive strains whereas in red they are IgA1 protease negative. The IgA1 protease status of a few strains (black strain names) was unknown.

Another sub-cluster within the major S. oralis cluster was also composed exclusively of strains that lacked IgA1 protease activity, while only six of the 59 S. oralis strains that were not in the above two sub-clusters were IgA1 protease negative (Figure 5). Surprisingly, the latter IgA1 protease-negative sub-cluster included the designated type strain of S. oligofermentans, in spite of its significantly different 16S rRNA sequences [41].

Apart from these examples, none of the other sub-clusters identified within the S. mitis and S. oralis clusters had distinguishing phenotypic properties, and their potential recognition as separate taxa should await further expansion of the eMLSA database and comprehensive phenotypic characterization of strains. A single strain (unknown B) was located on a long branch on the reference tree between S. agalactiae and the species clusters of the Salivarius group (Figure 2C) and its taxonomic status is unclear. However, from BLAST comparisons of the house-keeping genes of this strain to the nucleotide sequence databases this strain is almost certainly a member of the Bovis group streptococci.

Differences in diversity of species clusters

There were substantial differences in the extent of diversity within the species clusters and in their patterns of branching. For example, S. pneumoniae strains formed a tight sequence cluster on the tree and the average within-species diversity was only 0.3%, whereas the average diversity within several other clusters, including those of S. anginosus, S. australis, S. infantis, S. mitis and S. oralis, was 12 to 16 times greater (Table 2). Additionally, unlike S. pneumoniae and S. pyogenes, where there is a branching structure within the species clusters, with some strains being almost identical and others being more distantly related, the other species clusters typically included strains that were relatively distantly related to each other (for example, the S. infantis and S. mitis clusters), as implied by the long branch lengths from each strain in a cluster to its node (Figure 2A).

Clustering patterns obtained using single gene trees and identification of interspecies imports

Neighbour-joining trees were constructed from the sequences of the seven individual genes from all strains. These gene trees failed to resolve the species clusters obtained using the concatenated sequences and all individual trees showed anomalous clustering of some strains (Figure 6 Additional file 1). For example, S. mitis and S. pseudopneumoniae could only be resolved on the map and pyk gene trees (Figure 6B). Similarly, strains of S. infantis and S. australis could not be resolved on the sodA gene tree, and strains of neither of these species could be resolved from each other, or from S. parasanguinis, on the ppaC tree (Figure 6A).

Examples of individual gene trees produced from the sequences of all 420 strains. A-C shows the ppaC, pyk and tuf gene trees, which each fail to resolve some of the species clusters. Strain SK264 (assigned as S. parasanguinis labelled in Figure 2A) was used as the query strain in Figures 7 and 8. The ppaC allele of this strain is assigned as resident compatible as it falls within an unresolved cluster that includes the other S. parasanguinis sequences. For both pyk and tuf, the sequences from SK264 fall within clusters that are well resolved (bootstrap values of ≥ 80%) from the cluster that includes all (or the great majority) of the other S. parasanguinis sequences and are assigned as foreign alleles. For pyk the source of the foreign allele is unclear as its sequence falls within a cluster that includes those from several species. For tuf, the sequence appears to have been introduced from an S. australis strain. The major unresolved clusters in the trees are indicated.

Approximately 96% of strains assigned to a particular species by MLSA had alleles at all seven loci that were most similar to those of other strains of that species and, in individual gene trees, the sequences clustered with those of other strains of the species. However, 16 of the viridans group strains (4%) had alleles that were considered to be foreign (see Methods for criteria used to assign alleles as foreign). Table 3 shows the putative origins for each of the seven alleles in these 16 strains.

Assigning strains to species via the internet

The main features of the website are described in the Methods section. Figure 7 is a screenshot from the species assignment window of, showing the position of a query strain (S. parasanguinis SK264) on the reference tree, and the list of species assignments of the five strains in the database with the most similar concatenated sequences, and their sequence similarity to the query sequence. In this example the query strain is assigned as S. parasanguinis since the concatenated sequence of the seven MLSA loci clusters within this species cluster, and the top five most similar concatenated sequences are from strains assigned to this species.

Species assignment on the internet. The page returned after entering the seven gene sequences of a query strain and requesting a species assignment. The species assigned to the five most closely matching concatenated sequences are returned (left) along with an unrooted neighbour-joining radial tree indicating the position of the query strain. In this case, the query strain (SK264) is assigned as S. parasanguinis as the five most similar concatenated sequences are all from this species and the query strain falls within the S. parasanguinis species cluster on the tree.

Figure 8 shows a screenshot of the resident, resident compatible or foreign status assigned by to each of the seven individual alleles of the above query strain. In this case, five of the individual loci are most similar to sequences from S. parasanguinis (resident alleles) or are resident compatible (for example, ppaC Figure 6A). However, the pyk gene is within a cluster that is well resolved from the main S. parasanguinis cluster and which includes S. infantis, S. australis and S. cristatus (Figure 6B), and the tuf gene clusters within the well-resolved S. australis cluster (Figure 6C). These two alleles are therefore assigned by as foreign, which may explain why this strain is an outlier within the S. parasanguinis cluster (Figure 2A).

Online assignment of alleles as resident or foreign. Having assigned a query strain to a species (Figure 7), the locus view page shows the assignment of each of the seven individual sequences as resident to that species (or compatible with being resident) or foreign. In the example, the sequences of five of the genes from strain SK264 are assigned by as resident (that is, S. parasanguinis) or resident compatible, but the pyk and tuf genes are assigned as foreign. The locus view page allows the individual gene trees (in this case, the tuf tree) to be displayed to explore why the algorithm considers the sequences of an allele of a query strain to be resident, resident compatible or foreign (see Figure 6 for details). The colour codes for species clusters are as in Figure 2.

Define Conjugation in Bacteria | Genetics

In this article we will discuss about the definition of conjugation in bacteria.

The occurrence of recombination by sexual union was first shown experimentally in 1946 by Joshua Lederberg and E.L. Tatum in E. coli. They took two auxotrophic strains neither of which could grow on minimal medium due to mutation in genes controlling synthesis of vitamins thiamine and biotin, and amino acids methonine, threonine and leucine.

For simplicity strain I can be designated as a – b – c – d + e + and strain II as a + b + c + d – e – . A mixture of the two auxotrophic strains was cultured together on a complete medium and samples taken and plated on minimal medium. Surprisingly prototrophic colonies in a frequency of 1 per 10 6 or 10 7 cells plated were found growing on the minimal medium.

Lederberg argued that the prototrophs would have a genotype of the wild type a + b + c + d + e + . The question arose on the origin of the prototroph colonies whether from mutation, transformation or recombination by some form of sexual union.

Mutation was ruled out because it is improbable for so many gene loci in each strain to undergo mutation simultaneously. Transformation was negated experimentally when broken DNA fragments from either strain failed to produce recombinants. It appeared therefore that some form of sexual union between living cells had produced the wild type genotype.

Further experiment by Hayes, a British geneticist, and by Jacob and Wollman, two French geneticists gave better insight of this process when they found that genetic recombination takes place in bacteria as a one-way transfer of genetic material from a male type donor to a female type receptor and the process was termed conjugation.

Biofilms and Disease

Biofilms, complex colonies of bacteria acting as a unit in their release of toxins, are highly resistant to antibiotics and host defense.

Learning Objectives

Give examples of the roles played by biofilms in human diseases

Key Takeaways

Key Points

  • Once a biofilm infection is established, it is very difficult to eradicate because biofilms exhibit great resistance to most methods used to control microbial growth, including antibiotics.
  • Biofilms are able to grow anywhere there is an optimal combination of moisture, nutrients, and a surface.
  • Biofilms are responsible for diseases such as infections in patients and readily settle within wounds and burns they can also easily colonize medical devices and other surfaces where sterility is vital for health.

Key Terms

  • biofilm: a thin film of mucus created by and containing a colony of bacteria and other microorganisms
  • nosocomial: contracted in a hospital, or arising from hospital treatment

Biofilms and Disease

Biofilms are complex colonies of bacteria (often containing several species) that exchange chemical signals to coordinate the release of toxins that will attack the host. Once established, they are very difficult to destroy as they are highly resistant to antimicrobial treatments and host defense. Biofilms form when microorganisms adhere to the surface of some object in a moist environment and begin to reproduce. They grow virtually everywhere in almost any environment where there is a combination of moisture, nutrients, and a surface. Biofilms are responsible for diseases such as infections in patients with cystic fibrosis, Legionnaires’ disease, and otitis media. They produce dental plaque and colonize catheters, prostheses, transcutaneous and orthopedic devices, contact lenses, and internal devices such as pacemakers. They also form in open wounds and burned tissue. In healthcare environments, biofilms grow on hemodialysis machines, mechanical ventilators, shunts, and other medical equipment. In fact, 65 percent of all infections acquired in the hospital (nosocomial infections) are attributed to biofilms. Biofilms are also related to diseases contracted from food because they colonize the surfaces of vegetable leaves and meat, as well as food-processing equipment that is not adequately cleaned.

The Five Stages of Biofilm Development: Stage 1: initial attachment stage 2: irreversible attachment stage 3: maturation I stage 4: maturation II stage 5: dispersion. Each stage of development in the diagram is paired with a photomicrograph of a developing Pseudomonas aeruginosa biofilm. All photomicrographs are shown at the same scale.

Biofilm infections develop gradually and often do not cause immediate symptoms. They are rarely resolved by host defense mechanisms. Once an infection by a biofilm is established, it is very difficult to eradicate because biofilms tend to be resistant to most of the methods used to control microbial growth, including antibiotics. Biofilms respond poorly or only temporarily to antibiotics. It has been said that they can resist up to 1,000 times the antibiotic concentrations used to kill the same bacteria when they are free-living or planktonic. An antibiotic dose that large would harm the patient therefore, scientists are working on new ways to eradicate biofilms.

Enzyme Nanoarchitectures: Enzymes Armored with Graphene

Nalok Dutta , Malay K. Saha , in Methods in Enzymology , 2018

2.2.1 Isolation of Enzyme Secreting Bacterial Strains

The bacterial strain was isolated from Himalayan hot spring soil near Manikaran (Himachal Pradesh, India). Approximately 5 g of soil sample was added to sterile 0.9% saline water. The sample saline mix was incubated overnight at 37°C and the saline supernatant was used as the bacterial source. Lipolytic bacterial strains were isolated from the soil by using serial dilution technique on tributyrin agar containing (0.5% (w/v) peptone, 0.3% (w/v) yeast, 1% (v/v) tributyrin and 2% agar, pH 7.0). Pure cultures of the isolates were maintained on minimal media agar slants containing (1.5% yeast extract, 0.5% NaCl, 1% peptone and 2% agar, pH 7.0). Culture plates were incubated at 37°C. Colonies showing clear zones (due to hydrolysis of tributyrin) around them were picked out, purified on tributyrin agar plates, and transferred to agar slants. The isolate with higher lipolytic activity was used for further processes.

The solution to the bacterial species problem

To return to our original quotation, Hey [1] is right in the case of bacteria too: the species problem is very much in our heads. Sometimes the many contingent genetic and ecological forces driving bacterial genome evolution will have produced clusters of genomes so much like each other and so much unlike any others in the world that even the tightest species definition will be satisfied. Sometimes this will merely appear to be so, because we have selected as medically interesting, or have been able to culture, certain organisms only by virtue of their possession of a single gene, while a spectrum of otherwise genomically similar relatives lacking it have gone unnoticed. Sometimes it will not be so, the contingent genetic and ecological forces working against each other and producing 'clusters' so fuzzy and with gene content versus genome sequence incongruities so striking that even the loosest criteria for genomic coherence cannot be met. We might, in an effort to match definition and concept, choose to think of genuine 'species' as those evolutionary groups that both satisfy an accepted species definition based on genomic coherence and whose coherence can be understood as the product of a biological process, as in the ecotype or BSC model. But many bacteria will not belong to such groups - and it is not a given that any such 'genuine' species exist.

There will, of course, always be a need to have some agreed-upon way of naming organisms, some species definition. Konstantinidis and Tiedje [7] suggest, primarily because of variability in gene content among closely related strains, that "standards could be as stringent as including only strains that show a greater than 99% ANI, or are less identical at the nucleotide level but share an overlapping ecological niche." But they do not endorse such a tightening up, because this "would instantaneously increase the number of existing species probably by a factor of 10, and cause considerable confusion in the diagnostic and regulatory (legal) fields". Without a magic bullet that makes our species definition and our species concept (or concepts) "one and the same", such expediency considerations will always - and legitimately - play a role in defining species.

It will often also be expedient to think in terms of lineages of strains within species and of phylogenetic relationships between species. There seems to be no other sensible way of doing this than to use concatenated shared (core) genes, and to represent the results as trees [18, 30, 31]. Useful as such trees may be, we must realize that they will not represent the true intergenomic relationships in recombinogenic groups, which will be reticulate, not tree-like - nor will they describe the evolutionary behavior of the non-core part of the pangenome of any species, which may be much larger than the core [32].

In understanding genome evolution, the 'species concept' does limited work. The ecotype and BSC models (see Figure 2) are useful heuristics, but calling them models for speciation does not make them more useful. In biogeography and biodiversity studies, the word 'species' may actually work some mischief. Questions such as 'How many species of bacteria are there?' or 'Are bacterial species cosmopolitan?' are invaluable in stimulating research into the diversity and distribution of microbial genotypes and phenotypes. But without a species definition coupled to a magic bullet concept that guarantees that defined species are natural biological entities, these questions would be better reformulated in terms of genotypes and phenotypes. There will never be such a magic bullet. In using species concepts, we microbiologists would do well to follow the advice of a philosopher, William James, who wrote: "Since it is only the conceptual form which forces the dialectic contradictions upon the innocent sensible reality, the remedy would seem to be simple. Use concepts when they help, and drop them when they hinder, understanding."

Methods of Conjugation

Bacterial conjugation occurs via three methods:

F + -F – Conjugation

This kind of conjugation occurs between the donor cell having fertility factor or F + and the recipient cell that lacks such factor or indicated as F – . F-plasmid refers to the fertility factor that functions in the expression of pilus, synthesis and exchange of plasmid DNA during mating. The role of fertility factor is controlled by the cluster of 25 tra genes, which is broadly classified into two types:

  1. Mpf: It is an acronym of the term Mating pair formation. Mpf genes hold the mating cells together and provide a passage for the DNA and protein transfer through pilus and some channels, respectively.
  2. Dtr: It is an acronym of the term DNA transfer and replication. Dtr is a gene product engaged in the processing and transferring of plasmid DNA.

The F-pili of the donor cell initiates the process of mating by first binding with the outer membrane protein of the recipient cell. Eventually, a cytoplasmic bridge appears between the F + and F – cell, which commonly refers to the conjugation tube or pilus.

Through this cytoplasmic bridge, a relaxase enzyme creates a nick in one strand of the F-plasmid at the oriT site. The nicked strand moves to the recipient cell from 5’-3’ prime.
OriT refers to the site where the transfer of plasmid DNA occurs. Thus, a pilus formed between the F + and F – cell facilitates the transfer of F-plasmid DNA.

The single stranded DNA moves into the recipient cell, which later transform into the circular F-plasmid ds-DNA. After the completion of conjugation, both the partners would carry F-plasmid DNA.

Hfr-F – Conjugation

It merely refers to the mating between the high-frequency recombination and F – strains. Hfr strains possess F-plasmid integrated with the bacterial chromosome. An Hfr strain will function as a donor cell, which can pass on the chromosomal genes to the F – strain.
One strand of the chromosomal DNA from the Hfr strain will move to the recipient cell from the origin of the transfer site. Unlike conjugation between F + -F – strain, it involves the transfer of full bacterial chromosome and a part of F-plasmid from the Hfr donor to the F – strain.

In contrast to F + -F – strain conjugation, only a part of F-plasmid is transferred that would not cause the transformation of F – strain into F + strain. The replicated donor DNA enters the recipient cell and may degrade into fragments.

The fragmented DNA incorporates with the recipient’s nucleoid via recombination. Hfr-F – Conjugation is a relatively important process that helps in studying the mechanism of gene mapping and the relative positions of the genes in a bacterial chromosome can be also identified.

F ’ -F – Conjugation

Here, mating occurs between the F ’ and F – strains. F ’ – strain contains excised F-plasmid integrated with the chromosomal DNA of the Hfr strain. F – Strain only contains the bacterial nucleoid and functions as a recipient cell.
This kind of conjugation is virtually identical, where the F ’ plasmid enters the F – strain without being incorporated into the recipient’s nucleoid. Therefore, a recipient cell becomes F ’ – strain and functions as partially diploid merozygote, by carrying F ’ – plasmid or possessing two sets of genes.

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