Fatahi-Bafghi Mehdi
Research Center for Health Technology Assessment and Medical Informatics, School of Public Health, Shahid Sadoughi University of Medical Sciences, Yazd, Iran.
Department of Microbiology, Faculty of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran.
Int J Syst Evol Microbiol. 2025 Aug;75(8). doi: 10.1099/ijsem.0.006865.
In the present study, we conducted the whole-genome sequence analysis of JCM 13306 and DSM 1083 from the genus for assigning taxonomic placement. Sequence analysis of the 16S rRNA gene revealed that JCM 13306 had the highest sequence similarity to species, with sequence similarities ranging from 97.24% to 97.92% nucleotide identity. Likewise, sequence analysis of the 16S rRNA gene exhibited DSM 1083 with 99.36%, 99.00% and 98.93% similarity to ATCC 53690, ATCC 49405 and ATCC 49720, respectively. JCM 13306 and DSM 1083 have indicated a distinct position in the phylogenetic (based on concatenated sequences of 81 core proteins and 16S rRNA gene) and phylogenomic trees from some type strains of the family; however, JCM 13306 and DSM 1083 were strongly clustered with species of the (family ) and (family ), respectively. Besides, the amino acid identity values between JCM 13306 and the members of the family were 53.95-57.98%, as well as between DSM 1083 and this family which were 50.43-51.41%. These values were below the cut-off level for genus demarcation (60-85%). The scores of digital DNA-DNA hybridization (70%), average nucleotide identity by blast (95-96%) and average nucleotide identity using MUMmer (96%) between JCM 13306 and DSM 1083, with the members of the family, were below the threshold value for bacterial species delineation. Therefore, based on genomic and phylogenomic analysis, we propose reclassifying JCM 13306 and DSM 1083 as comb. nov. in the family and comb. nov. in the family, respectively.
在本研究中,我们对该属的JCM 13306和DSM 1083进行了全基因组序列分析以确定其分类地位。16S rRNA基因序列分析表明,JCM 13306与某物种具有最高的序列相似性,核苷酸同一性序列相似性范围为97.24%至97.92%。同样,16S rRNA基因序列分析显示DSM 1083与ATCC 53690、ATCC 49405和ATCC 49720的相似性分别为99.36%、99.00%和98.93%。JCM 13306和DSM 1083在基于81个核心蛋白和16S rRNA基因串联序列的系统发育树和系统基因组树中与该科的一些模式菌株相比处于不同位置;然而,JCM 13306和DSM 1083分别与(科)的某属和(科)的某属物种紧密聚类。此外,JCM 13306与该科成员之间的氨基酸同一性值为53.95 - 57.98%,DSM 1083与该科成员之间的氨基酸同一性值为50.43 - 51.41%。这些值低于属划分的截止水平(60 - 85%)。JCM 13306和DSM 1083与该科成员之间的数字DNA - DNA杂交得分(70%)、通过blast的平均核苷酸同一性(95 - 96%)以及使用MUMmer的平均核苷酸同一性(96%)均低于细菌物种划分的阈值。因此,基于基因组和系统基因组分析,我们建议将JCM 13306重新分类为科的新组合,将DSM 1083重新分类为科的新组合。