Genomic and phylogenetic re-assessment of the genus Stenotrophomonas: Description of Stenotrophomonas thermophila sp. nov., and the proposal of Parastenotrophomonas gen. Nov., Pseudostenotrophomonas gen. Nov., Pedostenotrophomonas gen. Nov., and Allo

The Stenotrophomonas maltophilia species complex (Smc) currently comprises 19 genomospecies, known for their ecological versatility and role as opportunistic human pathogens. However, significant genomic variability among strains has complicated their classification, and only a few species within the Smc have been validly described. Despite successive taxonomic revisions, there remains no consensus on the naming of many genomospecies, largely due to the phenotypic heterogeneity across the complex. In this study, we performed a comprehensive genomic and phylogenetic re-assessment to clarify the boundaries of the Stenotrophomonas genus and its species complex. Using whole-genome phylogeny and Overall Genome-Related Indices (OGRIs) such as digital DNA-DNA hybridization (dDDH), Average Nucleotide Identity (ANIb and ANIm), and Average Amino Acid Identity (AAI), we established precise cutoffs for defining the genus and the Smc. Our analysis led to the formal revision of the Stenotrophomonas genus, resulting in the delineation of four novel bacterial genera: Allostenotrophomonas gen. Nov., Pedostenotrophomonas gen. Nov., Parastenotrophomonas gen. Nov., and Pseudostenotrophomonas gen. Nov. Additionally, we standardized the nomenclature within the Smc by identifying reference strains for each genomospecies. Among these, we describe a novel species, Stenotrophomonas thermophila sp. nov. (type strain BurA1^T = LMG 33562^T = EML 1882^T). This study provides a robust framework for future taxonomic and ecological studies within the Stenotrophomonas genus.