Evaluation of CRISPR Diversity in the Human Skin Microbiome for Personal Identification

ABSTRACT 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 requ...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Kochi Toyomane, Ryo Yokota, Ken Watanabe, Tomoko Akutsu, Ai Asahi, Satoshi Kubota
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2021
Materias:	human skin microbiome CRISPR metagenomics forensic science next-generation sequencing Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/be4d530af67b4d68a79f5fdb7265afd9
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:be4d530af67b4d68a79f5fdb7265afd9
record_format	dspace
spelling	oai:doaj.org-article:be4d530af67b4d68a79f5fdb7265afd92021-12-02T19:36:37ZEvaluation of CRISPR Diversity in the Human Skin Microbiome for Personal Identification10.1128/mSystems.01255-202379-5077https://doaj.org/article/be4d530af67b4d68a79f5fdb7265afd92021-02-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSystems.01255-20https://doaj.org/toc/2379-5077ABSTRACT 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. IMPORTANCE Microbial community diversity analysis can be utilized to characterize the personal microbiome that varies between individuals. CRISPR sequences, which reflect virome structure, in the human skin environment may be highly personalized similar to the structures of individual viromes. In this study, we identified 24 putative CRISPR arrays using a shotgun metagenome data set of the human skin microbiome. The findings of this study expand our understanding of the nature of CRISPRs by identifying novel CRISPR candidates. We developed a method to efficiently determine the diversity of three CRISPR arrays. Our analysis revealed that the CRISPR spacer diversity in the human skin microbiome is highly personalized compared with the microbiome diversity assessed by 16S rRNA sequencing, providing a new perspective on the study of the skin microbiome.Kochi ToyomaneRyo YokotaKen WatanabeTomoko AkutsuAi AsahiSatoshi KubotaAmerican Society for Microbiologyarticlehuman skin microbiomeCRISPRmetagenomicsforensic sciencenext-generation sequencingMicrobiologyQR1-502ENmSystems, Vol 6, Iss 1 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	human skin microbiome CRISPR metagenomics forensic science next-generation sequencing Microbiology QR1-502
spellingShingle	human skin microbiome CRISPR metagenomics forensic science next-generation sequencing Microbiology QR1-502 Kochi Toyomane Ryo Yokota Ken Watanabe Tomoko Akutsu Ai Asahi Satoshi Kubota Evaluation of CRISPR Diversity in the Human Skin Microbiome for Personal Identification
description	ABSTRACT 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. IMPORTANCE Microbial community diversity analysis can be utilized to characterize the personal microbiome that varies between individuals. CRISPR sequences, which reflect virome structure, in the human skin environment may be highly personalized similar to the structures of individual viromes. In this study, we identified 24 putative CRISPR arrays using a shotgun metagenome data set of the human skin microbiome. The findings of this study expand our understanding of the nature of CRISPRs by identifying novel CRISPR candidates. We developed a method to efficiently determine the diversity of three CRISPR arrays. Our analysis revealed that the CRISPR spacer diversity in the human skin microbiome is highly personalized compared with the microbiome diversity assessed by 16S rRNA sequencing, providing a new perspective on the study of the skin microbiome.
format	article
author	Kochi Toyomane Ryo Yokota Ken Watanabe Tomoko Akutsu Ai Asahi Satoshi Kubota
author_facet	Kochi Toyomane Ryo Yokota Ken Watanabe Tomoko Akutsu Ai Asahi Satoshi Kubota
author_sort	Kochi Toyomane
title	Evaluation of CRISPR Diversity in the Human Skin Microbiome for Personal Identification
title_short	Evaluation of CRISPR Diversity in the Human Skin Microbiome for Personal Identification
title_full	Evaluation of CRISPR Diversity in the Human Skin Microbiome for Personal Identification
title_fullStr	Evaluation of CRISPR Diversity in the Human Skin Microbiome for Personal Identification
title_full_unstemmed	Evaluation of CRISPR Diversity in the Human Skin Microbiome for Personal Identification
title_sort	evaluation of crispr diversity in the human skin microbiome for personal identification
publisher	American Society for Microbiology
publishDate	2021
url	https://doaj.org/article/be4d530af67b4d68a79f5fdb7265afd9
work_keys_str_mv	AT kochitoyomane evaluationofcrisprdiversityinthehumanskinmicrobiomeforpersonalidentification AT ryoyokota evaluationofcrisprdiversityinthehumanskinmicrobiomeforpersonalidentification AT kenwatanabe evaluationofcrisprdiversityinthehumanskinmicrobiomeforpersonalidentification AT tomokoakutsu evaluationofcrisprdiversityinthehumanskinmicrobiomeforpersonalidentification AT aiasahi evaluationofcrisprdiversityinthehumanskinmicrobiomeforpersonalidentification AT satoshikubota evaluationofcrisprdiversityinthehumanskinmicrobiomeforpersonalidentification
_version_	1718376348426174464

Evaluation of CRISPR Diversity in the Human Skin Microbiome for Personal Identification

Ejemplares similares