Description of Sediminicola litoralis sp. nov. isolated from tidal flat sediment and functional genomic analysis of the genus Sediminicola.

BACKGROUND: The genus Sediminicola represents one of the least characterized taxa within the well-studied family Flavobacteriaceae, with only two formally recognized species to date. The scarcity of cultivated isolates and the lack of genomic data for type strains have significantly hindered comprehensive insights into its phylogenetic diversity, metabolic capabilities, and potential biotechnological utility. In this study, a novel bacterial strain, designated 1XM1-17T, was isolated from tidal flat sediment. Through a polyphasic taxonomic approach combined with functional genomic analysis, we systematically investigated its taxonomic classification and conducted the first detailed metabolic profiling of the genus Sediminicola to bridge this knowledge gap. RESULTS: The phylogenetic inference based on the 16S rRNA gene and genome sequences revealed that strain 1XM1-17T formed a separate branch from the type strains S. luteus GDMCC 1.2596T and S. arcticus GDMCC 1.2805T. The digital DNA‒DNA hybridization (dDDH), average nucleotide identity (ANI), and amino acid identity (AAI) values between strain 1XM1-17T and two relatives above were 23.7 and 21.9%, 82.6 and 80.6%, 87.96 and 86.49%, significantly below the thresholds of 70% dDDH, 95‒96% ANI and AAI as threshold definitions. The morphological, physiological, and chemotaxonomic characteristics readily supported its affiliation within the genus Sediminicola while distinguishing it from its relatives. Phylogenomic analyses based on an expanded genomic dataset revealed an underestimation of the species diversity of the genus Sediminicola. Functional genome analysis revealed that this genus possesses conserved genetic determinants for nitrogen, sulfur, and phosphorus metabolism; gliding motility; and the T9SS, but fewer secondary metabolite biosynthetic gene clusters and CAZymes than other Flavobacteriaceae members. The genus Sediminicola was found to be widely distributed in marine environments, particularly in sediments. CONCLUSIONS: Based on the phenotypic and genotypic evidence, strain 1XM1-17T was determined to represent a novel species of the genus Sediminicola, with the proposed name Sediminicola litoralis sp. nov. (type strain, 1XM1-17T = GDMCC 1.2384T = KCTC 82665T). This study establishes the taxonomic status of strain 1XM1-17T and provides an insight into the metabolic function of the genus Sediminicola.