The Use and Limitations of the 16S rRNA Sequence for Species Classification of Anaplasma Samples.
The Use and Limitations of the 16S rRNA Sequence for Species Classification of Anaplasma Samples.
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DOI：
10.3390/microorganisms10030605
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发表时间：
2022-03-12
期刊：
影响因子：
4.5
通讯作者：
Brayton KA
中科院分区：
文献类型：
--
作者：
Caudill MT;Brayton KA
随着更廉价、高通量测序技术的出现，在以前未探索的生态位和地理区域调查生物多样性的能力大幅提高。在无形体属（Anaplasma）中，该属包含几种具有医学和经济重要性的造血内病原体，自上次正式的分类整理以来，至少已提出了25个新物种。鉴于这些细菌的专性细胞内特性，根据《原核生物国际命名法规》的规则，这些提出的物种都未能在命名法中获得正式地位。许多新物种的提出仅使用从少数基因（最常见的是16S rRNA基因）的靶向或宏基因组PCR研究中获得的序列数据。我们研究了16S rRNA基因序列在将无形体样本区分到物种水平的效用。我们发现，虽然无形体属的遗传多样性似乎比上次该属分类时所认识到的更大，但仅试图从16S rRNA基因来确定物种描述时必须谨慎。具体而言，基因组不同的物种具有相似的16S rRNA基因序列，特别是当仅使用16S rRNA的部分扩增子时。此外，我们提供了可对无形体属正式命名的物种进行分类的关键依据。
With the advent of cheaper, high-throughput sequencing technologies, the ability to survey biodiversity in previously unexplored niches and geographies has expanded massively. Within Anaplasma, a genus containing several intra-hematopoietic pathogens of medical and economic importance, at least 25 new species have been proposed since the last formal taxonomic organization. Given the obligate intracellular nature of these bacteria, none of these proposed species have been able to attain formal standing in the nomenclature per the International Code of Nomenclature of Prokaryotes rules. Many novel species’ proposals use sequence data obtained from targeted or metagenomic PCR studies of only a few genes, most commonly the 16S rRNA gene. We examined the utility of the 16S rRNA gene sequence for discriminating Anaplasma samples to the species level. We find that while the genetic diversity of the genus Anaplasma appears greater than appreciated in the last organization of the genus, caution must be used when attempting to resolve to a species descriptor from the 16S rRNA gene alone. Specifically, genomically distinct species have similar 16S rRNA gene sequences, especially when only partial amplicons of the 16S rRNA are used. Furthermore, we provide key bases that allow classification of the formally named species of Anaplasma.
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