Comparative genomics of oral isolates of Streptococcus mutans by in silico genome subtraction does not reveal accessory DNA associated with severe early childhood caries.
Comparative genomics of oral isolates of Streptococcus mutans by in silico genome subtraction does not reveal accessory DNA associated with severe early childhood caries.
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通过计算机基因组消减对变形链球菌口腔分离株进行的比较基因组学并未揭示与严重儿童早期龋齿相关的辅助 DNA。
DOI：
10.1016/j.meegid.2013.11.003
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发表时间：
2014
期刊：
影响因子：
--
通讯作者：
Caufield,PageW
中科院分区：
文献类型：
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作者：
Argimón,Silvia;Konganti,Kranti;Chen,Hao;Alekseyenko,AlexanderV;Brown,Stuart;Caufield,PageW
比较基因组学是一种流行的鉴定微生物毒力决定因素的方法，特别是因为从致病和非致病菌株中对大量完整的细菌基因组进行测序已经变得相对便宜。比较基因组学的生物信息学管道通常包括基因预测和注释，可能需要强大的计算机能力。为了解决这一问题，我们开发了一种基于blastn的、独立于特征识别和注释的基因组规模的电子吸收杂交快速方法。采用全基因组比较的方法，以儿童早期重度龋病相关变形链球菌(S)菌株为研究对象，与儿童无龋者(CF)菌株进行全基因组比较。通过Simrank-mer Share计算，本研究中包含的突变株的范围在79.5%到90.9%之间，证实这是一个遗传异质性的菌株群。我们在19个菌株中发现了特定于菌株的遗传元件，大小从200到39kb不等。这些元件含有蛋白质编码区，其功能主要与移动DNA有关。然而，我们没有发现任何与龋病一致相关的遗传位点，即所有S-ECC品系都共有，而在CF品系中不存在。相反，我们没有发现任何与健康组相关的基因位点。将以前发表的脑膜炎奈瑟氏菌致病株和携带株的基因组与Ourin硅胶基因组相比较，得到了相同的致病株特异性基因，从而验证了我们的方法。我们的结果表明。不能根据特定遗传因素的存在或不存在来区分来自龋齿活跃或无龋牙列的突变株。Ourin硅基因组消减方法可作为微生物基因组比较(MGC)工具，具有用户友好的Java图形界面。
Comparative genomics is a popular method for the identification of microbial virulence determinants, especially since the sequencing of a large number of whole bacterial genomes from pathogenic and non-pathogenic strains has become relatively inexpensive. The bioinformatics pipelines for comparative genomics usually include gene prediction and annotation and can require significant computer power. To circumvent this, we developed a rapid method for genome-scalein silicosubtractive hybridization, based on blastn and independent of feature identification and annotation. Whole genome comparisons byin silicogenome subtraction were performed to identify genetic loci specific toStreptococcus mutansstrains associated with severe early childhood caries (S-ECC), compared to strains isolated from caries-free (CF) children.The genome similarity of the 20S. mutansstrains included in this study, calculated by Simrank k-mer sharing, ranged from 79.5% to 90.9%, confirming this is a genetically heterogeneous group of strains. We identified strain-specific genetic elements in 19 strains, with sizes ranging from 200 to 39 kb. These elements contained protein-coding regions with functions mostly associated with mobile DNA. We did not, however, identify any genetic loci consistently associated with dental caries, i.e., shared by all the S-ECC strains and absent in the CF strains. Conversely, we did not identify any genetic loci specific with the healthy group. Comparison of previously published genomes from pathogenic and carriage strains ofNeisseria meningitidiswith ourin silicogenome subtraction yielded the same set of genes specific to the pathogenic strains, thus validating our method.Our results suggest thatS. mutansstrains derived from caries active or caries free dentitions cannot be differentiated based on the presence or absence of specific genetic elements. Ourin silicogenome subtraction method is available as the Microbial Genome Comparison (MGC) tool, with a user-friendly JAVA graphical interface.