Comparative genome analysis of human pathogen Parvimonas micra revealed strain JM503A as potential novel species in the genus Parvimonas and high intra-species functional diversity

Parvimonas micra is a Gram-positive, anaerobic bacterium commonly found in the oral cavity, skin and gastrointestinal tract. While typically a harmless organism, it can cause infections in individuals with weakened immune systems, leading to conditions like periodontitis and deep-tissue abscesses. This study focuses on the comparative genomic analysis of P. micra to explore its evolutionary relationships, antimicrobial resistance profiles and functional diversity by assessing phylogenetic analyses, resistance genes, virulence factors, mobile genetic elements, carbohydrate-active enzymes and pan-genome analysis. Comparative genomic analysis of 11 P. micra strains reveals significant functional variations among the strains, indicating notable interspecies diversity. Phylogenetic and comparative genome analysis revealed that strain JM503A is taxonomically distinct from the P. micra species, with genome similarity ranging from 54% to 61%. The 16S rRNA sequence similarity of strain JM503A is 98.28%, indicating a distinct phylogenetic position. The average nucleotide identity value ranging from 91.32% to 91.7% and digital DNA–DNA hybridization values ranging from 43.00% to 44.00% of JM503A with other strains are below the cutoff values <95% and <70%, respectively, which confirms JM503A as a novel species. Based on its evolutionary relationships, strain JM503A is identified as a potential new species of Parvimonas , providing important evidence for its reclassification as a new species within the genus Parvimonas .