Revised taxonomic classification of the genomes, providing new insights into the genus .

BACKGROUND

strains are important opportunistic pathogens with great potential applications in industry and agriculture. Their significant genetic and phenotypic diversity has led to several changes in their taxonomic localization and was prone to inaccurate species classification based on traditional identification methods.

METHODS

All 2,615 genomes of the genus were obtained from the NCBI genome database. Genomic methods, including average nucleotide identity (ANI), were used to evaluate the 31 defined species. After evaluating the ANI thresholds applicable to , the species classification of all submitted genomes was revised.

RESULTS

Compared to the reference genomes of each species, 41.17% of the submitted genomes had ANI values below 95, and 8.58% of the genomes were even below 90%. Moreover, 45.3% (705/1555) of the strains actually belonged to other species within the complex (Smc), or even to distant relatives outside the Smc. Based on the ANI threshold values of 95 and 90% for species and complexes confirmed to be applicable to , 2,213 submitted genomes were re-divided into 116 ANI genome species.

CONCLUSION

The results confirmed that 16S rRNA gene sequencing has low discriminability for the closely related species. The annotated species of a considerable strain were indeed incorrect, especially since many strains did not belong to this representative pathogenic species of . This makes it necessary to reconsider the evolutionary relationship, pathogenicity, and clinical significance of .