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Sequences, sequence clusters and bacterial species.

Hanage WP, Fraser C, Spratt BG - Philos. Trans. R. Soc. Lond., B, Biol. Sci. (2006)

Bottom Line: Single gene sequences (or rRNA gene sequences) have very few informative sites to resolve the strains of closely related species, and relationships among similar species may be confounded by interspecies recombination.The development of large MLSA Internet databases provides the ability to assign new strains to previously defined species clusters and an electronic taxonomy.The advantages and problems in using sequence clusters as the basis of species assignments are discussed.

View Article: PubMed Central - PubMed

Affiliation: Department of Infectious Disease Epidemiology, Imperial College London, St Mary's Hospital Campus, Norfolk Place, London W2 1PG, UK.

ABSTRACT
Whatever else they should share, strains of bacteria assigned to the same species should have house-keeping genes that are similar in sequence. Single gene sequences (or rRNA gene sequences) have very few informative sites to resolve the strains of closely related species, and relationships among similar species may be confounded by interspecies recombination. A more promising approach (multilocus sequence analysis, MLSA) is to concatenate the sequences of multiple house-keeping loci and to observe the patterns of clustering among large populations of strains of closely related named bacterial species. Recent studies have shown that large populations can be resolved into non-overlapping sequence clusters that agree well with species assigned by the standard microbiological methods. The use of clustering patterns to inform the division of closely related populations into species has many advantages for poorly studied bacteria (or to re-evaluate well-studied species), as it provides a way of recognizing natural discontinuities in the distribution of similar genotypes. Clustering patterns can be used by expert groups as the basis of a pragmatic approach to assigning species, taking into account whatever additional data are available (e.g. similarities in ecology, phenotype and gene content). The development of large MLSA Internet databases provides the ability to assign new strains to previously defined species clusters and an electronic taxonomy. The advantages and problems in using sequence clusters as the basis of species assignments are discussed.

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Interspecies recombination and its effect on species assignments based on a single gene sequence. The relatedness among isolates of three species is inferred from a tree constructed using the sequences of a single house-keeping gene. Isolates of species A are well resolved from those of species B, and from the strain of the more distantly related species C used an outgroup. Consider a homologous recombinational event that occurs in a strain of species B (arrow), replacing the single locus used to assign the species with the corresponding sequence from a strain of a relatively divergent species. Now, the strain will not be recognized as a strain of species B and will be incorrectly assigned (dotted line) as more distantly related to species B than the outgroup.
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fig1: Interspecies recombination and its effect on species assignments based on a single gene sequence. The relatedness among isolates of three species is inferred from a tree constructed using the sequences of a single house-keeping gene. Isolates of species A are well resolved from those of species B, and from the strain of the more distantly related species C used an outgroup. Consider a homologous recombinational event that occurs in a strain of species B (arrow), replacing the single locus used to assign the species with the corresponding sequence from a strain of a relatively divergent species. Now, the strain will not be recognized as a strain of species B and will be incorrectly assigned (dotted line) as more distantly related to species B than the outgroup.

Mentions: The sequences of a number of protein coding genes have also been used to assign bacteria to species. These have the advantage over 16S rRNA of evolving more rapidly and thus provide an increased ability to resolve species within a genus. However, the use of a single gene has major drawbacks as there may be too few informative nucleotide sites to resolve very similar species and homologous recombination (HR) among similar species may distort the true relationships between species (figure 1). HR is believed to be relatively common among many bacteria (Feil & Spratt 2001) and probably also among many archaea (Papke et al. 2004; Whitaker et al. 2005). It typically results in the replacement of a small fragment (a few kilobases) of the chromosome of a recipient bacterium with the corresponding region from a different strain of the species or from a closely related species. Laboratory studies indicate that the efficiency of recombination falls off in a log-linear fashion with increasing sequence divergence (Majewski & Cohan 1999; Majewski et al. 2000), but there is ample evidence that replacements occur in nature between species that differ at 5–25% in nucleotide sequence (Dowson et al. 1989; Spratt et al. 1989; Zhou et al. 1997; Kalia et al. 2001).


Sequences, sequence clusters and bacterial species.

Hanage WP, Fraser C, Spratt BG - Philos. Trans. R. Soc. Lond., B, Biol. Sci. (2006)

Interspecies recombination and its effect on species assignments based on a single gene sequence. The relatedness among isolates of three species is inferred from a tree constructed using the sequences of a single house-keeping gene. Isolates of species A are well resolved from those of species B, and from the strain of the more distantly related species C used an outgroup. Consider a homologous recombinational event that occurs in a strain of species B (arrow), replacing the single locus used to assign the species with the corresponding sequence from a strain of a relatively divergent species. Now, the strain will not be recognized as a strain of species B and will be incorrectly assigned (dotted line) as more distantly related to species B than the outgroup.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC1764932&req=5

fig1: Interspecies recombination and its effect on species assignments based on a single gene sequence. The relatedness among isolates of three species is inferred from a tree constructed using the sequences of a single house-keeping gene. Isolates of species A are well resolved from those of species B, and from the strain of the more distantly related species C used an outgroup. Consider a homologous recombinational event that occurs in a strain of species B (arrow), replacing the single locus used to assign the species with the corresponding sequence from a strain of a relatively divergent species. Now, the strain will not be recognized as a strain of species B and will be incorrectly assigned (dotted line) as more distantly related to species B than the outgroup.
Mentions: The sequences of a number of protein coding genes have also been used to assign bacteria to species. These have the advantage over 16S rRNA of evolving more rapidly and thus provide an increased ability to resolve species within a genus. However, the use of a single gene has major drawbacks as there may be too few informative nucleotide sites to resolve very similar species and homologous recombination (HR) among similar species may distort the true relationships between species (figure 1). HR is believed to be relatively common among many bacteria (Feil & Spratt 2001) and probably also among many archaea (Papke et al. 2004; Whitaker et al. 2005). It typically results in the replacement of a small fragment (a few kilobases) of the chromosome of a recipient bacterium with the corresponding region from a different strain of the species or from a closely related species. Laboratory studies indicate that the efficiency of recombination falls off in a log-linear fashion with increasing sequence divergence (Majewski & Cohan 1999; Majewski et al. 2000), but there is ample evidence that replacements occur in nature between species that differ at 5–25% in nucleotide sequence (Dowson et al. 1989; Spratt et al. 1989; Zhou et al. 1997; Kalia et al. 2001).

Bottom Line: Single gene sequences (or rRNA gene sequences) have very few informative sites to resolve the strains of closely related species, and relationships among similar species may be confounded by interspecies recombination.The development of large MLSA Internet databases provides the ability to assign new strains to previously defined species clusters and an electronic taxonomy.The advantages and problems in using sequence clusters as the basis of species assignments are discussed.

View Article: PubMed Central - PubMed

Affiliation: Department of Infectious Disease Epidemiology, Imperial College London, St Mary's Hospital Campus, Norfolk Place, London W2 1PG, UK.

ABSTRACT
Whatever else they should share, strains of bacteria assigned to the same species should have house-keeping genes that are similar in sequence. Single gene sequences (or rRNA gene sequences) have very few informative sites to resolve the strains of closely related species, and relationships among similar species may be confounded by interspecies recombination. A more promising approach (multilocus sequence analysis, MLSA) is to concatenate the sequences of multiple house-keeping loci and to observe the patterns of clustering among large populations of strains of closely related named bacterial species. Recent studies have shown that large populations can be resolved into non-overlapping sequence clusters that agree well with species assigned by the standard microbiological methods. The use of clustering patterns to inform the division of closely related populations into species has many advantages for poorly studied bacteria (or to re-evaluate well-studied species), as it provides a way of recognizing natural discontinuities in the distribution of similar genotypes. Clustering patterns can be used by expert groups as the basis of a pragmatic approach to assigning species, taking into account whatever additional data are available (e.g. similarities in ecology, phenotype and gene content). The development of large MLSA Internet databases provides the ability to assign new strains to previously defined species clusters and an electronic taxonomy. The advantages and problems in using sequence clusters as the basis of species assignments are discussed.

Show MeSH
Related in: MedlinePlus