Phylogenomic analysis of the understudied Neisseriaceae species reveals a poly- and paraphyletic Kingella genus

Abstract

Taxonomic classification and phylogenetic analysis of the Neisseriaceae family has focused on the pathogens Neisseria meningitidis and Neisseria gonorrhoeae. Less is known about the relationships of commensal Neisseria species and other Neisseriaceae genera, raising the possibility that the phylogeny of this family may not agree with taxonomy. In this study we used available nucleotide sequences and a phylogenetic approach to assess the Kingella genus and its relatives. We found that this genus is both paraphyletic and polyphyletic. Kingella potus is more closely related to Neisseria bacilliformis than other Kingella species. The Alysiella and Simonsiella genera form a distinct clade within the Kingella genus that is closely related to the pathogens K. kingae and K. negevensis. We find a phylogenetic relationship between Conchiformibius, Alysiella, Simonsiella, and Kingella, which we name the CASK clade. Finally, we define the gene sets that differentiate each genus of the CASK clade from one another and from the rest of the Neisseriaceae family. ImportanceUnderstanding the evolutionary relationships between the species in the Neisseriaceae has been a persistent challenge in bacterial systematics due to high recombination rates in these species. Previous studies of this family have focused on N. meningitidis and N. gonorrhoeae. However, previously understudied Neisseriaceae species are gaining new attention, with K. kingae now recognized as a common human pathogen and with Alysiella and Simonsiella being unique in the bacterial world as multicellular organisms. A better understanding of the genomic evolution of the Neisseriaceae can lead to identification of the specific genes and traits that characterize the remarkable diversity of this family.