Kislichkina Angelina A, Sizova Angelika A, Skryabin Yury P, Dentovskaya Svetlana V, Anisimov Andrey P
Department of Culture Collection, State Research Center for Applied Microbiology and Biotechnology, Obolensk, Russia.
Department of Molecular Microbiology, State Research Center for Applied Microbiology and Biotechnology, Obolensk, Russia.
Front Microbiol. 2025 Jan 7;15:1519733. doi: 10.3389/fmicb.2024.1519733. eCollection 2024.
16S rRNA genes sequencing has been used for routine species identification and phylogenetic studies of bacteria. However, the high sequence similarity between some species and heterogeneity within copies at the intragenomic level could be a limiting factor of discriminatory ability. In this study, we aimed to compare 16S rRNA genes sequences and genome-based analysis (core SNPs and ANI) for identification of non-pathogenic . We used complete and draft genomes of 373 strains from the NCBI Genome database. The taxonomic affiliations of 34 genomes based on core SNPs and the ANI results did not match those specified in the GenBank database (NCBI). The intragenic homology of the 16S rRNA gene copies exceeded 99.5% in complete genomes, but above 50% of genomes have four or more variants of the 16S rRNA gene. Among 327 draft genomes of non-pathogenic , 11% did not have a full-length 16S rRNA gene. Most of draft genomes has one copy of gene and it is not possible to define the intragenomic heterogenicity. The average homology of 16S rRNA gene was 98.76%, and the maximum variability was 2.85%. The low degree of genetic heterogenicity of the gene (0.36%) was determined in group /////. The identical gene sequences were found in the genomes of the and strains identified using ANI and core SNPs analyses. The phylogenetic tree based on 16S rRNA genes differed from the tree based on core SNPs of the genomes and did not represent phylogenetic relationship between the species. These findings will help to fill the data gaps in genome characteristics of deficiently studied non-pathogenic .
16S rRNA基因测序已用于细菌的常规物种鉴定和系统发育研究。然而，一些物种之间的高序列相似性以及基因组内拷贝的异质性可能是鉴别能力的限制因素。在本研究中，我们旨在比较16S rRNA基因序列和基于基因组的分析（核心单核苷酸多态性和平均核苷酸一致性）以鉴定非致病性[具体物种未提及]。我们使用了来自NCBI基因组数据库的373株菌株的完整基因组和草图基因组。基于核心单核苷酸多态性和平均核苷酸一致性结果的34个基因组的分类归属与GenBank数据库（NCBI）中指定的不匹配。完整基因组中16S rRNA基因拷贝的基因内同源性超过99.5%，但超过50%的基因组有四个或更多16S rRNA基因变体。在327个非致病性[具体物种未提及]的草图基因组中，11%没有全长16S rRNA基因。大多数草图基因组有一个基因拷贝，无法确定基因组内的异质性。16S rRNA基因的平均同源性为98.76%，最大变异性为2.85%。在[具体分组未提及]组中确定了该基因的低遗传异质性程度（0.36%）。在使用平均核苷酸一致性和核心单核苷酸多态性分析鉴定的[具体物种未提及]和[具体物种未提及]菌株的基因组中发现了相同的基因序列。基于16S rRNA基因的系统发育树与基于基因组核心单核苷酸多态性的树不同，并且没有代表[具体物种未提及]物种之间的系统发育关系。这些发现将有助于填补研究不足的非致病性[具体物种未提及]基因组特征的数据空白。
