Minor taxa in human skin microbiome contribute to the personal identification.

Hikaru Watanabe,Ken Kurokawa,Hiroshi Mori,Takuji Yamada,Issei Nakamura,Yumiko Kurokawa,Sayaka Mizutani,Kazuhiro Takemoto

doi:10.1371/journal.pone.0199947

Abstract

The human skin microbiome can vary over time, and inter-individual variability of the microbiome is greater than the temporal variability within an individual. The skin microbiome has become a useful tool to identify individuals, and one type of personal identification using the skin microbiome has been reported in a community of less than 20 individuals. However, identification of individuals based on the skin microbiome has shown low accuracy in communities larger than 80 individuals. Here, we developed a new approach for personal identification, which considers that minor taxa are one of the important factors for distinguishing between individuals. We originally established a human skin microbiome for 66 samples from 11 individuals over two years (33 samples each year). Our method could classify individuals with 85% accuracy beyond a one-year sampling period. Moreover, we applied our method to 837 publicly available skin microbiome samples from 89 individuals and succeeded in identifying individuals with 78% accuracy. In short, our results investigate that (i) our new personal identification method worked well with two different communities (our data: 11 individuals; public data: 89 individuals) using the skin microbiome, (ii) defining the personal skin microbiome requires samples from several time points, (iii) inclusion of minor skin taxa strongly contributes to the effectiveness of personal identification.

Highlights

Distinct microbial communities exist all over and within the human body, and recent studies have revealed a strong correlation between the status of the bacterial composition of the gut microbiome and human disease [1,2]
Personal identification using human skin microbiome the query sample was the closest to the true owner’s and the Canberra distance was less than the threshold, we considered it as true positive (TP), whereas other cases were judged as false negatives (FN) or FP
To reveal the taxonomic composition of the skin microbiome at the species level, we computed 97% identity operational taxonomic unit (OTU) after sequencing the 16S rDNA amplicon that could be clustered into 4,155 OTUs (S2 Table), of which 659 OTUs could be classified into type strains, 492 OTUs were multiple hits to type strains, and 3,004 OTUs were unclassified at any type strain

Summary

Introduction

Distinct microbial communities exist all over and within the human body, and recent studies have revealed a strong correlation between the status of the bacterial composition of the gut microbiome and human disease [1,2]. The health of the human skin microbiome has been reported to be an important factor in the development of skin diseases [3,4,5,6]. The skin microbiome of an individual varies over time [7], but such a temporal variability is less than interindividual variability for more than 2.5 years [8,9]. The human skin microbiome has the potential to identify individuals. Samples of residual human-skin microbes from computer keyboards facilitated the identification of three individuals [10]. Particular microbes in the human skin have often been considered for use in forensic

Objectives

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Results

Conclusion