Networks and groups within the genus Neisseria: Analysis of argF, recA, rho, and 16S rRNA sequences from human Neisseria species

To understand the pattern of nucleotide sequence variation among bacteria t hat frequently exchange chromosomal genes, we analyzed sequences of the rec A, argF, and rho genes, as well as part of the small-subunit (16S) rRNA gen e, from about 50 isolates of human commensal Neisseria species and the path ogenic N. meningitidis and N. gonorrhoeae. Almost all isolates of these spe cies could be assigned to five phylogenetic groups that are found for all g enes examined and generally are supported by high bootstrap values. In cont rast, the phylogenetic relationships among groups varied according to the g ene analyzed with notable incongruences involving N. cinerea and N. lactami ca. Further analysis using split decomposition showed that for each gene, i ncluding 16S rRNA, the patterns of sequence divergence within N. meningitid is and closely related species were inconsistent with a bifurcating treelik e phylogeny and better represented by an interconnected network. These data indicate that the human commensal Neisseria species can be separated into discrete groups of related species but that the relationships both within a nd among these groups, including those reconstructed using 16S rRNA, have b een distorted by interspecies recombination events.