The highly personalized human skin microbiome may serve as a viable marker in personal identification. Amplicon sequencing resolution using 16S rRNA cannot identify bacterial communities sufficiently to discriminate between individuals. Thus, novel higher-resolution genetic markers are required for forensic purposes. The clustered regularly interspaced short palindromic repeats (CRISPRs) are prokaryotic genetic elements that can provide a history of infections encountered by the bacteria. The sequencing of CRISPR spacers may provide phylogenetic information with higher resolution than other markers. However, using spacer sequencing for discrimination of personal skin microbiome is difficult due to limited information on CRISPRs in human skin microbiomes. It remains unclear whether personal microbiome discrimination can be achieved using spacer diversity or which CRISPRs will be forensically relevant. We identified common CRISPRs in the human skin microbiome via metagenomic reconstruction and used amplicon sequencing for deep sequencing of spacers. We successfully reconstructed 24 putative CRISPR arrays using metagenomic data sets. A total of 1,223,462 reads from three CRISPR arrays revealed that spacers in the skin microbiome were highly personalized, and conserved repeats were commonly shared between individuals. These individual specificities observed using CRISPR typing were confirmed by comparing the CRISPR diversity to microbiome diversity assessed using 16S rRNA amplicon sequencing. CRISPR typing achieved 95.2% accuracy in personal classification, whereas 16S rRNA sequencing only achieved 52.6%. These results suggest that sequencing CRISPRs in the skin microbiome may be a more powerful approach for personal identification and ecological studies compared to conventional 16S rRNA sequencing.

中文翻译：

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评价人类皮肤微生物组中的CRISPR多样性以进行个人鉴定

高度个性化的人类皮肤微生物组可作为个人识别的可行标记。使用16S rRNA进行扩增子测序解析无法充分鉴定细菌群落以区分个体。因此，为了法医目的需要新颖的高分辨率遗传标记。簇状规则间隔的短回文重复序列（CRISPR）是原核遗传元件，可提供细菌遇到的感染史。CRISPR间隔区的测序可以提供比其他标记更高的分辨率的系统信息。然而，由于人皮肤微生物组中关于CRISPR的信息有限，因此使用间隔测序来区分个人皮肤微生物组是困难的。尚不清楚是否可以使用间隔子多样性来实现对个人微生物组的区分，或者哪些CRISPRs将具有法医意义。我们通过宏基因组重建技术鉴定了人类皮肤微生物组中常见的CRISPR，并使用扩增子测序对间隔子进行了深度测序。我们使用宏基因组数据集成功地重建了24个推定的CRISPR阵列。从三个CRISPR阵列中读取的总共1,223,462个结果显示，皮肤微生物组中的间隔区高度个性化，并且保守的重复序列通常在个体之间共享。通过将CRISPR多样性与使用16S rRNA扩增子测序评估的微生物组多样性进行比较，证实了使用CRISPR类型观察到的这些个体特异性。CRISPR分类在个人分类中达到95.2％的准确性，而16S rRNA测序仅达到52.6％。这些结果表明，与传统的16S rRNA测序相比，在皮肤微生物组中对CRISPRs进行测序可能是用于个人识别和生态研究的更有效方法。