Phylogenomic analysis of the understudiedNeisseriaceaespecies reveals a poly- and paraphyleticKingellagenus

Abstract

AbstractTaxonomic classification and phylogenetic analysis of theNeisseriaceaefamily has focused on the pathogensNeisseria meningitidisandNeisseria gonorrhoeae. Less is known about the relationships of commensalNeisseriaspecies and otherNeisseriaceaegenera, 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 theKingellagenus and its relatives. We found that this genus is both paraphyletic and polyphyletic.Kingella potusis more closely related toNeisseria bacilliformisthan otherKingellaspecies. TheAlysiellaandSimonsiellagenera form a distinct clade within theKingellagenus that is closely related to the pathogensK. kingaeandK. negevensis. We find a phylogenetic relationship betweenConchiformibius,Alysiella,Simonsiella, andKingella, 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 theNeisseriaceaefamily.ImportanceUnderstanding the evolutionary relationships between the species in theNeisseriaceaehas been a persistent challenge in bacterial systematics due to high recombination rates in these species. Previous studies of this family have focused onN. meningitidisandN. gonorrhoeae. However, previously understudiedNeisseriaceaespecies are gaining new attention, withK. kingaenow recognized as a common human pathogen and withAlysiellaandSimonsiellabeing unique in the bacterial world as multicellular organisms. A better understanding of the genomic evolution of theNeisseriaceaecan lead to identification of the specific genes and traits that characterize the remarkable diversity of this family.