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

<i>Parvimonas micra</i> 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 <i>P. micra</i> 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 <i>P. micra</i> 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 <i>P. micra</i> 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 <i>Parvimonas</i>, providing important evidence for its reclassification as a new species within the genus <i>Parvimonas</i>.