Phylogenomic and genome-relatedness analyses resolve genus and family boundaries within the family Verrucomicrobiaceae

The family Verrucomicrobiaceae comprises diverse Gram-negative bacteria inhabiting environmental and host-associated niches, whose genus-level taxonomy is in need of revision. A genome-scale revision of 46 type strains was performed using phylogenomics based on 120 conserved proteins, together with average amino acid identity (AAI), percentage of conserved proteins (POCP) and 16S rRNA gene analyses. Phylogenomic reconstruction resolved Verrucomicrobiaceae into well-supported clades corresponding to established genera but also revealed marked taxonomic inconsistencies. Luteolibacter was consistently recovered as polyphyletic, separating into two deeply divergent clades (AAI 62.8–84.0%; POCP 41.0–70.9%), supporting the emended genus Luteolibacter (Clade I) and the establishment of Neoluteolibacter gen. nov. (Clade II). Akkermansia formed a monophyletic lineage but also exhibited strong internal structuring into three ecologically distinct clades associated with mammalian, avian and reptilian hosts. Inter-clade AAI (60.8–63.7%) and 16S rRNA gene similarities (92.4–93.3%) were below accepted genus thresholds, supporting its division into Akkermansia sensu stricto , Neoakkermansia gen. nov. and Parakkermansia gen. nov. The genus Prosthecobacter formed a robust clade incorporating Brevifollis gellanilyticus , which exhibited genomic similarity consistent with genus inclusion (AAI 68.9–71.2%; POCP 61.4–64.2%), supporting its transfer as Prosthecobacter gellanilyticus comb. nov. At the species level, high genomic relatedness supported the synonymy of Rubritalea halochordaticola with Rubritalea squalenifaciens (AAI 97.0%; ANI 96.37%; dDDH 69.3%) and of ‘ Candidatus Akkermansia timonensis’ with Akkermansia biwaensis (AAI 100%; ANI 99.92%; dDDH 99.6%). At higher taxonomic ranks, phylogenomic evidence indicates that Rubritaleaceae and Akkermansiaceae fall within Verrucomicrobiaceae , supporting their synonymization.