Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, People's Republic of China.
Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, People's Republic of China.
Syst Appl Microbiol. 2022 Nov;45(6):126352. doi: 10.1016/j.syapm.2022.126352. Epub 2022 Aug 27.
Many genera closest to the family Comamonadaceae have not been classified into any family; moreover, some of them are not monophyletic groups beyond the genus level. To resolve the taxonomic uncertainty of the closest-to-Comamonadaceae (CTC) group, we performed 16S rRNA gene- and genome-based phylogenetic analyses combined with genome relatedness indices and phenotypic traits comparison. Phylogenies based on the 16S rRNA gene and genome sequences demonstrated that the CTC group formed a coherent and robust monophyletic lineage and was sister to the family Comamonadaceae, thereby proposing the CTC group as a novel family, Sphaerotilaceae fam. nov. The resolved genus- and species-level taxonomic relationships of this new family were then validated by the phylogenomic reconstruction and comparisons of genome relatedness indices including digital DNA-DNA hybridization and average nucleotide identity (ANI) as well as comprehensive phenotypic analysis for type strains. Finally, we reclassified all misidentified genera and species, resulting in 19 new combinations, and proposed Sphaerotilaceae-specific thresholds of ANI and average amino acid identity for genus delineation. Collectively, this study has established a sound taxonomic framework of the novel family Sphaerotilaceae and will help guide future taxonomic efforts and prevent the propagation of taxonomic errors.
许多与贪噬菌科最为接近的属尚未被分类到任何科中；此外，其中一些属在属级水平以上不是单系群。为了解决最接近贪噬菌科（CTC）群的分类不确定性，我们进行了基于 16S rRNA 基因和基因组的系统发育分析，结合了基因组相关性指数和表型特征比较。基于 16S rRNA 基因和基因组序列的系统发育表明，CTC 群形成了一个连贯而强大的单系谱系，是贪噬菌科的姊妹群，从而提出将 CTC 群作为一个新的科，即 Sphaerotilaceae 科。通过对新科的属和种水平的分类关系进行基因组重建和基因组相关性指数（包括数字 DNA-DNA 杂交和平均核苷酸同一性（ANI）以及综合表型分析）的比较，以及对模式菌株的综合表型分析，验证了该新科的分类关系。最后，我们重新分类了所有错误鉴定的属和种，产生了 19 个新组合，并提出了用于属划分的 Sphaerotilaceae 特异性 ANI 和平均氨基酸同一性的阈值。总的来说，这项研究建立了一个健全的新型 Sphaerotilaceae 科的分类框架，将有助于指导未来的分类工作，并防止分类错误的传播。
