Schmedes Sarah E, Woerner August E, Novroski Nicole M M, Wendt Frank R, King Jonathan L, Stephens Kathryn M, Budowle Bruce
Graduate School of Biomedical Sciences, University of North Texas Health Science Center,3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA; Center for Human Identification, University of North Texas Health Science Center,3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA.
Center for Human Identification, University of North Texas Health Science Center,3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA.
Forensic Sci Int Genet. 2018 Jan;32:50-61. doi: 10.1016/j.fsigen.2017.10.004. Epub 2017 Oct 18.
The human skin microbiome is comprised of diverse communities of bacterial, eukaryotic, and viral taxa and contributes millions of additional genes to the repertoire of human genes, affecting human metabolism and immune response. Numerous genetic and environmental factors influence the microbiome composition and as such contribute to individual-specific microbial signatures which may be exploited for forensic applications. Previous studies have demonstrated the potential to associate skin microbial profiles collected from touched items to their individual owner, mainly using unsupervised methods from samples collected over short time intervals. Those studies utilize either targeted 16S rRNA or shotgun metagenomic sequencing to characterize skin microbiomes; however, these approaches have limited species and strain resolution and susceptibility to stochastic effects, respectively. Clade-specific markers from the skin microbiome, using supervised learning, can predict individual identity using skin microbiomes from their respective donors with high accuracy. In this study the hidSkinPlex is presented, a novel targeted sequencing method using skin microbiome markers developed for human identification. The hidSkinPlex (comprised of 286 bacterial (and phage) family-, genus-, species-, and subspecies-level markers), initially was evaluated on three bacterial control samples represented in the panel (i.e., Propionibacterium acnes, Propionibacterium granulosum, and Rothia dentocariosa) to assess the performance of the multiplex. The hidSkinPlex was further evaluated for prediction purposes. The hidSkinPlex markers were used to attribute skin microbiomes collected from eight individuals from three body sites (i.e., foot (Fb), hand (Hp) and manubrium (Mb)) to their host donor. Supervised learning, specifically regularized multinomial logistic regression and 1-nearest-neighbor classification were used to classify skin microbiomes to their hosts with up to 92% (Fb), 96% (Mb), and 100% (Hp) accuracy. All samples (n=72) regardless of body site origin were correctly classified with up to 94% accuracy, and body site origin could be predicted with up to 86% accuracy. Finally, human short tandem repeat and single-nucleotide polymorphism profiles were generated from skin swab extracts from a single subject to highlight the potential to use microbiome profiling in conjunction with low-biomass samples. The hidSkinPlex is a novel targeted enrichment approach to profile skin microbiomes for human forensic identification purposes and provides a method to further characterize the utility of skin microflora for human identification in future studies, such as the stability and diversity of the personal skin microbiome.
人类皮肤微生物群由细菌、真核生物和病毒类群的不同群落组成，为人类基因库贡献了数百万个额外的基因，影响人类新陈代谢和免疫反应。众多遗传和环境因素影响微生物群组成，因此促成了个体特异性的微生物特征，这些特征可用于法医应用。先前的研究已经证明，从接触物品上收集的皮肤微生物特征与其个体所有者之间存在关联的潜力，主要使用从短时间间隔收集的样本中采用的无监督方法。这些研究利用靶向16S rRNA或鸟枪法宏基因组测序来表征皮肤微生物群；然而，这些方法分别具有有限的物种和菌株分辨率以及对随机效应的敏感性。利用监督学习，来自皮肤微生物群的进化枝特异性标记可以使用来自各自供体的皮肤微生物群高精度地预测个体身份。在本研究中，展示了hidSkinPlex，这是一种使用为人类识别而开发的皮肤微生物群标记的新型靶向测序方法。hidSkinPlex（由286个细菌（和噬菌体）科、属、种和亚种水平的标记组成）最初在面板中代表的三个细菌对照样本（即痤疮丙酸杆菌、颗粒丙酸杆菌和龋齿罗氏菌）上进行评估，以评估多重检测的性能。hidSkinPlex进一步用于预测目的评估。hidSkinPlex标记用于将从三个身体部位（即足部（Fb）、手部（Hp）和胸骨柄（Mb））的八名个体收集的皮肤微生物群归属于其宿主供体。使用监督学习，特别是正则化多项逻辑回归和1-最近邻分类，将皮肤微生物群分类到其宿主，准确率高达92%（Fb）、96%（Mb）和100%（Hp）。所有样本（n = 72），无论身体部位来源如何，分类准确率高达94%，身体部位来源预测准确率高达86%。最后，从一名受试者的皮肤拭子提取物中生成了人类短串联重复序列和单核苷酸多态性图谱，以突出将微生物群分析与低生物量样本结合使用的潜力。hidSkinPlex是一种用于人类法医鉴定目的的新型靶向富集方法，可对皮肤微生物群进行分析，并为未来研究中进一步表征皮肤微生物群在人类识别中的效用提供了一种方法，例如个人皮肤微生物群的稳定性和多样性。
