<named-content content-type="genus-species">Cutibacterium acnes</named-content> (<named-content content-type="genus-species">Propionibacterium acnes</named-content>) 16S rRNA Genotyping of Microbial Samples from Possessions Contributes to Owner Identification

ABSTRACT The human skin surface harbors huge numbers of microbes. The skin microbiota interacts with its host and forms a skin microbiome profile that is specific for each individual. It has been reported that the skin microbiota that is left on an individual’s possessions can act as a sort of “fing...

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Autores principales:	Jiayue Yang, Tomoya Tsukimi, Mia Yoshikawa, Kenta Suzuki, Tomoki Takeda, Masaru Tomita, Shinji Fukuda
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2019
Materias:	Cutibacterium acnes 16S rRNA genotype skin microbiome next-generation sequencing owner identification Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/55dd611d98824392a22df2b6f93209c1
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spelling	oai:doaj.org-article:55dd611d98824392a22df2b6f93209c12021-12-02T18:15:44Z<named-content content-type="genus-species">Cutibacterium acnes</named-content> (<named-content content-type="genus-species">Propionibacterium acnes</named-content>) 16S rRNA Genotyping of Microbial Samples from Possessions Contributes to Owner Identification10.1128/mSystems.00594-192379-5077https://doaj.org/article/55dd611d98824392a22df2b6f93209c12019-12-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSystems.00594-19https://doaj.org/toc/2379-5077ABSTRACT The human skin surface harbors huge numbers of microbes. The skin microbiota interacts with its host and forms a skin microbiome profile that is specific for each individual. It has been reported that the skin microbiota that is left on an individual’s possessions can act as a sort of “fingerprint” and be used for owner identification. However, this approach needs to be improved to take into account any long-term instability of skin microbiota and contamination from nonspecific bacteria. Here, we took advantage of single-nucleotide polymorphisms (SNPs) in the 16S-encoding rRNA gene of Cutibacterium acnes, the most common and abundant bacterium on human skin, to perform owner identification. We first developed a high-throughput genotyping method based on next-generation sequencing to characterize the SNPs of the C. acnes 16S rRNA gene and found that the genotype composition of C. acnes 16S rRNA is individual specific. Owner identification accuracy of around 90% based on random forest machine learning was achieved by using a combination of C. acnes 16S rRNA genotype and skin microbiome profile data. Furthermore, our study showed that the C. acnes 16S rRNA genotype remained more stable over time than the skin microbiome profile. This characteristic of C. acnes was further confirmed by the analysis of publicly available human skin metagenome data. Our approach, with its high precision, good reproducibility, and low costs, thus provides new possibilities in the field of microbiome-based owner identification and forensics in general. IMPORTANCE Cutibacterium acnes is the most common and abundant bacterial species on human skin, and the gene that encodes its 16S rRNA has multiple single-nucleotide polymorphisms. In this study, we developed a method to efficiently determine the C. acnes 16S rRNA genotype composition from microbial samples taken from the hands of participants and from their possessions. Using the C. acnes 16S rRNA genotype composition, we could predict the owner of a possession with around 90% accuracy when the 16S rRNA gene-based microbiome profile was included. We also showed that the C. acnes 16S rRNA genotype composition was more stable over time than the skin microbiome profile and thus is more suitable for owner identification.Jiayue YangTomoya TsukimiMia YoshikawaKenta SuzukiTomoki TakedaMasaru TomitaShinji FukudaAmerican Society for MicrobiologyarticleCutibacterium acnes16S rRNA genotypeskin microbiomenext-generation sequencingowner identificationMicrobiologyQR1-502ENmSystems, Vol 4, Iss 6 (2019)
institution	DOAJ
collection	DOAJ
language	EN
topic	Cutibacterium acnes 16S rRNA genotype skin microbiome next-generation sequencing owner identification Microbiology QR1-502
spellingShingle	Cutibacterium acnes 16S rRNA genotype skin microbiome next-generation sequencing owner identification Microbiology QR1-502 Jiayue Yang Tomoya Tsukimi Mia Yoshikawa Kenta Suzuki Tomoki Takeda Masaru Tomita Shinji Fukuda <named-content content-type="genus-species">Cutibacterium acnes</named-content> (<named-content content-type="genus-species">Propionibacterium acnes</named-content>) 16S rRNA Genotyping of Microbial Samples from Possessions Contributes to Owner Identification
description	ABSTRACT The human skin surface harbors huge numbers of microbes. The skin microbiota interacts with its host and forms a skin microbiome profile that is specific for each individual. It has been reported that the skin microbiota that is left on an individual’s possessions can act as a sort of “fingerprint” and be used for owner identification. However, this approach needs to be improved to take into account any long-term instability of skin microbiota and contamination from nonspecific bacteria. Here, we took advantage of single-nucleotide polymorphisms (SNPs) in the 16S-encoding rRNA gene of Cutibacterium acnes, the most common and abundant bacterium on human skin, to perform owner identification. We first developed a high-throughput genotyping method based on next-generation sequencing to characterize the SNPs of the C. acnes 16S rRNA gene and found that the genotype composition of C. acnes 16S rRNA is individual specific. Owner identification accuracy of around 90% based on random forest machine learning was achieved by using a combination of C. acnes 16S rRNA genotype and skin microbiome profile data. Furthermore, our study showed that the C. acnes 16S rRNA genotype remained more stable over time than the skin microbiome profile. This characteristic of C. acnes was further confirmed by the analysis of publicly available human skin metagenome data. Our approach, with its high precision, good reproducibility, and low costs, thus provides new possibilities in the field of microbiome-based owner identification and forensics in general. IMPORTANCE Cutibacterium acnes is the most common and abundant bacterial species on human skin, and the gene that encodes its 16S rRNA has multiple single-nucleotide polymorphisms. In this study, we developed a method to efficiently determine the C. acnes 16S rRNA genotype composition from microbial samples taken from the hands of participants and from their possessions. Using the C. acnes 16S rRNA genotype composition, we could predict the owner of a possession with around 90% accuracy when the 16S rRNA gene-based microbiome profile was included. We also showed that the C. acnes 16S rRNA genotype composition was more stable over time than the skin microbiome profile and thus is more suitable for owner identification.
format	article
author	Jiayue Yang Tomoya Tsukimi Mia Yoshikawa Kenta Suzuki Tomoki Takeda Masaru Tomita Shinji Fukuda
author_facet	Jiayue Yang Tomoya Tsukimi Mia Yoshikawa Kenta Suzuki Tomoki Takeda Masaru Tomita Shinji Fukuda
author_sort	Jiayue Yang
title	<named-content content-type="genus-species">Cutibacterium acnes</named-content> (<named-content content-type="genus-species">Propionibacterium acnes</named-content>) 16S rRNA Genotyping of Microbial Samples from Possessions Contributes to Owner Identification
title_short	<named-content content-type="genus-species">Cutibacterium acnes</named-content> (<named-content content-type="genus-species">Propionibacterium acnes</named-content>) 16S rRNA Genotyping of Microbial Samples from Possessions Contributes to Owner Identification
title_full	<named-content content-type="genus-species">Cutibacterium acnes</named-content> (<named-content content-type="genus-species">Propionibacterium acnes</named-content>) 16S rRNA Genotyping of Microbial Samples from Possessions Contributes to Owner Identification
title_fullStr	<named-content content-type="genus-species">Cutibacterium acnes</named-content> (<named-content content-type="genus-species">Propionibacterium acnes</named-content>) 16S rRNA Genotyping of Microbial Samples from Possessions Contributes to Owner Identification
title_full_unstemmed	<named-content content-type="genus-species">Cutibacterium acnes</named-content> (<named-content content-type="genus-species">Propionibacterium acnes</named-content>) 16S rRNA Genotyping of Microbial Samples from Possessions Contributes to Owner Identification
title_sort	<named-content content-type="genus-species">cutibacterium acnes</named-content> (<named-content content-type="genus-species">propionibacterium acnes</named-content>) 16s rrna genotyping of microbial samples from possessions contributes to owner identification
publisher	American Society for Microbiology
publishDate	2019
url	https://doaj.org/article/55dd611d98824392a22df2b6f93209c1
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<named-content content-type="genus-species">Cutibacterium acnes</named-content> (<named-content content-type="genus-species">Propionibacterium acnes</named-content>) 16S rRNA Genotyping of Microbial Samples from Possessions Contributes to Owner Identification

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