Genome-based reclassification of Virgibacillus kapii Daroonpunt et al. 2016 and Virgibacillus massiliensis Khelaifia et al. 2023 as later heterotypic synonyms of Virgibacillus salexigens (Garabito et al. 1997) Heyrman et al. 2003

Abstract

In the present study, genome-based metrics, phylogenetic and pangenomic analyses were used to investigate the relationship between three closely related species within the genus Virgibacillus ( Virgibacillus salexigens , Virgibacillus kapii and Virgibacillus massiliensis ). While 16S rRNA gene comparison revealed high similarity, overall genomic relatedness indices, including digital DNA–DNA hybridization (dDDH) and average nucleotide identity (ANI), exceeded the species delineation thresholds (ANI: 95–96 %, dDDH: 70%), indicating an even closer genetic relationship. Additionally, the phylogenomic analysis, along with pan-genome analysis, further supported the close relationship, placing the three species in a well-supported branch with a significant proportion of 3,809 shared core genes. Based on the combined evidence from genomic and phenotypic comparison, we propose reclassifying V. kapii Daroonpunt et al. 2016 and V. massiliensis Khelaifia et al. 2023 as later heterotypic synonyms of V. salexigens (Garabito et al. 1997) Heyrman et al. 2003. This study underscores the effectiveness of genome-based methods for accurate and reliable bacterial classification.