Fuzzy species among recombinogenic bacteria

Abstract

Background: It is a matter of ongoing debate whether a universal species concept is possible for bacteria. Indeed, it is not clear whether closely related isolates of bacteria typically form discrete genotypic clusters that can be assigned as species. The most challenging test of whether species can be clearly delineated is provided by analysis of large populations of closely-related, highly recombinogenic, bacteria that colonise the same body site. We have used concatenated sequences of seven house-keeping loci from 770 strains of 11 named Neisseria species, and phylogenetic trees, to investigate whether genotypic clusters can be resolved among these recombinogenic bacteria and, if so, the extent to which they correspond to named species.

Results: Alleles at individual loci were widely distributed among the named species but this distorting effect of recombination was largely buffered by using concatenated sequences, which resolved clusters corresponding to the three species most numerous in the sample, N. meningitidis, N. lactamica and N. gonorrhoeae. A few isolates arose from the branch that separated N. meningitidis from N. lactamica leading us to describe these species as 'fuzzy'.

Conclusion: A multilocus approach using large samples of closely related isolates delineates species even in the highly recombinogenic human Neisseria where individual loci are inadequate for the task. This approach should be applied by taxonomists to large samples of other groups of closely-related bacteria, and especially to those where species delineation has historically been difficult, to determine whether genotypic clusters can be delineated, and to guide the definition of species.

Figure 1

A tree constructed from concatenated MLST data resolves species clusters in Neisseria. The 50% majority rule consensus tree shown was produced in Mr Bayes using third position sites within the concatenated sequences of Neisserial species as described in methods. Assigned species names are indicated by the symbols. Two subtrees, A and B, are shown. These both contain strains identified as N. mucosa, N. sicca and N. subflava, showing that these named species do not form single clusters by this method. In these subtrees, the clades containing exclusively N. lactamica or N. gonorrhoeae have been collapsed.

Figure 2

Single locus trees fail to resolve species clusters. Individual minimum evolution trees constructed in Mega 2.1 for a) abcZ, b) adk, c) aroE, d) fumC, e) gdh, f) pdhC and g) pgm. The assigned species names of the strains in which these alleles occur are shown.