Quantitative intra- and intergeneric taxonomic relationships among Micrococcaceae strains reveal contradictions in the historical assignments of the strains and indicate the need for species reclassification

Abstract

We report phylogenetic studies of a bacterial isolate (Isolate SG) recovered from a suspension culture of Arabidopsis thaliana (L.) Heynh. In doing this, we use the known results acquired by whole genome sequencing of the DNA of Micrococcaceae strains closely related to Isolate SG in the 16S rRNA gene test and we evaluate the intra-and intergeneric taxonomic relationships between them using a set of five whole genome tests (ANI, AAI, MiGA, GTDB-Tk, and AAIprofiler). Quantitative analysis of the clustering of the proteomes of these strains by the average amino acid identity (AAI)-based test showed the need to clarify (with possible renaming) the generic assignment of the strains both within and between the identified monophyletic groups. The need for such reclassification was also shown by the AAI-profiler test (Medlar et al., 2018) against the UniProt database (250 million records) with the proteome of Rothia sp. ND6WE1A -a strain most evolutionarily similar to Isolate SG. The contradictions in the historically given names of strains and metagenomic objects at the genus and family levels, which were identified by using sets of the genomes and proteomes of the strains related to Isolate SG, can be eliminated with appropriate reclassification of the objects by using quantitative criteria in the AAI-based tests.