Genomic-based taxonomic classification of the order Sphingomonadales

作者：Yuan Wang, Hao You, Yan-Hui Kong, Cong Sun, Linhuan Wu, Song‐Gun Kim, Jung-Sook Lee, Lin Xu, Xue‐Wei Xu · 发表于：INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · 年份：2025 · DOI：10.1099/ijsem.0.006769 · 被引用次数：11 · 研究领域：Genomics and Phylogenetic Studies、Microbial Community Ecology and Physiology、Enzyme Production and Characterization

The order Sphingomonadales strains are globally distributed in various biomes and are renowned for their biodegradable and biosynthesis capabilities. At present, it consists of 4 families and 49 genera making it the third largest order within the class Alphaproteobacteria . However, their taxonomy remains complex, especially due to polyphyly in the family Sphingomonadaceae . In this study, we collected 429 Sphingomonadales type strain genomes, reconstructed robust phylogenomic relationships, and proposed delineation thresholds at the genus and family levels based on average amino acid identities (AAI) and evolutionary distances (ED). Based on the maximum-likelihood and Bayesian phylogenomic trees reconstructed by two molecular sets determined by orthologous sequence identity and the Genome Taxonomy Database, the consensus degree values were all higher than 90%, revealing that those phylogenomic trees had similar topological structures. By confirming monophyletic taxa and determining stable nodes, we reclassified the order Sphingomonadales into thirteen families including nine novel ones. AAI calculations indicated that the average intra-family AAI values ranged from 0.62 to 0.84, while inter-family ones were 0.51 to 0.60. ED summaries demonstrated that the average and median intra-family ED values were 0.16 to 0.57, and inter-family ones ranged from 0.50 to 1.22. Comparisons of AAI and ED values calculated by using genomic and phylogenetic analyses supported that those 13 fam...