Whole genome phylogeny of Neisseriaceae species

Bacteria in the family Neisseriaceae are common inhabitants of animals. Prominent examples include the disease-causing agents of meningitis (Neisseria meningitidis) and gonorrhea (Neisseria gonorrhoeae), but most species do no harm or are even beneficial. Everyone carries bacteria in this family somewhere on their body.

While working on a recent paper (click here for full-text), I needed a robust phylogenetic tree of all documented Neisseriaceae species. Apparently, this has not been done before, at least at the whole-genome level. So I made one myself. Hopefully it will also be of use to someone else.


The tree was built using a maximum-likelihood PROTCATLG model, with 363 orthologous genes (108,434 amino acid residues). Circles indicate nodes with 100% bootstrap support (1,000 replicates). Bar, substitutions per site. Please ignore the coloring (or read the paper for relevant details!)

A couple of (obvious) observations from this data: (A) the genus Neisseria is polyphyletic. Taxonomic revisions will be needed to sort this mess out. (B) The Neisseria-containing clade is quite distinct from the other Neisseriaceae genera (e.g., Chromobacterium, Chitinibacter, etc.). The latter are typically environmental (e.g., lives in soil, water), while the former are mostly animal-associated. However, previous suggestions to divide the Neisseriaceae family into two based on such differences will also be difficult to implement, as this tree shows that the Chromobacterium/Chitinibacter/etc. species are not monophyletic.

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