Reclassification of Massilia and related species

The genera Massilia, Duganella, Pseudoduganella and Rugamonas of the family Oxalobacteraceae are highly intermingled since 16S rRNA gene sequence analysis offers poor resolution for this group. In this study a number of methods were assessed to determine the reliability of individual methods for species assignation to genera that is both robust and useful for future expansion of the genera with new data. Both 16S rRNA gene and MLST (16S rRNA, gyrB, lepA genes) analysis still has significant resolution issues. BionNJ clustered average nucleotide and amino acid identity (ANI, AAI) data and GTDB-based conserved concatenated protein sequence data provided consistent outcomes, successfully resolving species into the same coherent groups. To determine whether the observed genera are meaningful from a functional point of view constrained ordination was also performed using annotated gene data obtained via PANNZER2 and for carbohydrate degradative genes searched using information from the CaZY database. The results show the descriptive annotation obtained from PANNZER2 could allow clear cut classification at the genus level when assessed within a constrained ordination. CaZY-based data had much less resolving power by comparison. The results from the combined approaches were used to redefine the names and species membership of Oxalobacteraceae genera. Massilia was renamed Telluria with Telluria mixta as type species. Duganella, Pseudoduganella, Rugamonas, Mokoshia gen. nov. (type species Mokoshia rubra comb. nov.) and Zemynaea gen. nov. (type species Zemynaea arenosa comb. nov.) received Massilia species not reclassified as Telluria . Rugamonas is now restricted to the type species Rugamonas rubra. Pseudoduganella danionis is transferred back to the genus Duganella as Duganella danionis comb. nov, while Telluria chitinolytica is renamed Pseudoduganella chitinolytica comb. nov. The combined results firstly clarify the taxonomy of several genera of family Oxalobacteraceae and bolsters the GTDB as a means that improves the quality and clarity of prokaryote systematic taxonomy. This study also suggests constrained ordination of descriptive genome annotation information derived represents another potential means for objective taxonomic decision making as well as for testing assumptions.