Burnett School of Biomedical Science, College of Medicine, University of Central Florida, Orlando, Florida, United States of America.
Department of Computer Science, University of Central Florida, Orlando, Florida, United States of America.
PLoS One. 2023 Oct 13;18(10):e0291964. doi: 10.1371/journal.pone.0291964. eCollection 2023.
With mutations constantly accumulating in bacterial genomes, it is unclear whether the previously identified bacterial strains are really present in an extant sample. To address this question, we did a case study on the known strains of the bacterial species S. aureus and S. epidermis in 68 atopic dermatitis shotgun metagenomic samples. We evaluated the likelihood of the presence of all sixteen known strains predicted in the original study and by two popular tools in this study. We found that even with the same tool, only two known strains were predicted by the original study and this study. Moreover, none of the sixteen known strains was likely present in these 68 samples. Our study thus indicates the limitation of the known-strain-based studies, especially those on rapidly evolving bacterial species. It implies the unlikely presence of the previously identified known strains in a current environmental sample. It also called for de novo bacterial strain identification directly from shotgun metagenomic reads.
随着细菌基因组中不断积累突变，以前鉴定的细菌菌株是否真的存在于现存样本中尚不清楚。为了解决这个问题，我们对 68 个特应性皮炎鸟枪法宏基因组样本中的已知细菌物种金黄色葡萄球菌和表皮葡萄球菌菌株进行了案例研究。我们评估了在原始研究和本研究中两种流行工具中预测的所有 16 种已知菌株存在的可能性。我们发现，即使使用相同的工具，原始研究和本研究也仅预测了两种已知菌株。此外，这 68 个样本中都不太可能存在这 16 种已知菌株。因此，我们的研究表明了基于已知菌株的研究的局限性，尤其是对于快速进化的细菌物种。这意味着以前鉴定的已知菌株不太可能存在于当前的环境样本中。这也呼吁直接从鸟枪法宏基因组reads 中进行新的细菌菌株鉴定。
