Evaluation of DNA extraction protocols from liquid-based cytology specimens for studying cervical microbiota.

Cervical microbiota (CM) are considered an important factor affecting the progression of cervical intraepithelial neoplasia (CIN) and are implicated in the persistence of human papillomavirus (HPV). Collection of liquid-based cytology (LBC) samples is routine for cervical cancer screening and HPV ge...

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Autores principales:	Takeo Shibata, Mayumi Nakagawa, Hannah N Coleman, Sarah M Owens, William W Greenfield, Toshiyuki Sasagawa, Michael S Robeson
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/8da7e7d4cc0c43eeae15c1d015d198d7
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spelling	oai:doaj.org-article:8da7e7d4cc0c43eeae15c1d015d198d72021-12-02T20:14:53ZEvaluation of DNA extraction protocols from liquid-based cytology specimens for studying cervical microbiota.1932-620310.1371/journal.pone.0237556https://doaj.org/article/8da7e7d4cc0c43eeae15c1d015d198d72021-01-01T00:00:00Zhttps://doi.org/10.1371/journal.pone.0237556https://doaj.org/toc/1932-6203Cervical microbiota (CM) are considered an important factor affecting the progression of cervical intraepithelial neoplasia (CIN) and are implicated in the persistence of human papillomavirus (HPV). Collection of liquid-based cytology (LBC) samples is routine for cervical cancer screening and HPV genotyping and can be used for long-term cytological biobanking. We sought to determine whether it is possible to access microbial DNA from LBC specimens, and compared the performance of four different extraction protocols: (ZymoBIOMICS DNA Miniprep Kit; QIAamp PowerFecal Pro DNA Kit; QIAamp DNA Mini Kit; and IndiSpin Pathogen Kit) and their ability to capture the diversity of CM from LBC specimens. LBC specimens from 20 patients (stored for 716 ± 105 days) with CIN values of 2 or 3 were each aliquoted for each of the four kits. Loss of microbial diversity due to long-term LBC storage could not be assessed due to lack of fresh LBC samples. Comparisons with other types of cervical sampling were not performed. We observed that all DNA extraction kits provided equivalent accessibility to the cervical microbial DNA within stored LBC samples. Approximately 80% microbial genera were shared among all DNA extraction protocols. Potential kit contaminants were observed as well. Variation between individuals was a significantly greater influence on the observed microbial composition than was the method of DNA extraction. We also observed that HPV16 was significantly associated with community types that were not dominated by Lactobacillus iners.Takeo ShibataMayumi NakagawaHannah N ColemanSarah M OwensWilliam W GreenfieldToshiyuki SasagawaMichael S RobesonPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 16, Iss 8, p e0237556 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Takeo Shibata Mayumi Nakagawa Hannah N Coleman Sarah M Owens William W Greenfield Toshiyuki Sasagawa Michael S Robeson Evaluation of DNA extraction protocols from liquid-based cytology specimens for studying cervical microbiota.
description	Cervical microbiota (CM) are considered an important factor affecting the progression of cervical intraepithelial neoplasia (CIN) and are implicated in the persistence of human papillomavirus (HPV). Collection of liquid-based cytology (LBC) samples is routine for cervical cancer screening and HPV genotyping and can be used for long-term cytological biobanking. We sought to determine whether it is possible to access microbial DNA from LBC specimens, and compared the performance of four different extraction protocols: (ZymoBIOMICS DNA Miniprep Kit; QIAamp PowerFecal Pro DNA Kit; QIAamp DNA Mini Kit; and IndiSpin Pathogen Kit) and their ability to capture the diversity of CM from LBC specimens. LBC specimens from 20 patients (stored for 716 ± 105 days) with CIN values of 2 or 3 were each aliquoted for each of the four kits. Loss of microbial diversity due to long-term LBC storage could not be assessed due to lack of fresh LBC samples. Comparisons with other types of cervical sampling were not performed. We observed that all DNA extraction kits provided equivalent accessibility to the cervical microbial DNA within stored LBC samples. Approximately 80% microbial genera were shared among all DNA extraction protocols. Potential kit contaminants were observed as well. Variation between individuals was a significantly greater influence on the observed microbial composition than was the method of DNA extraction. We also observed that HPV16 was significantly associated with community types that were not dominated by Lactobacillus iners.
format	article
author	Takeo Shibata Mayumi Nakagawa Hannah N Coleman Sarah M Owens William W Greenfield Toshiyuki Sasagawa Michael S Robeson
author_facet	Takeo Shibata Mayumi Nakagawa Hannah N Coleman Sarah M Owens William W Greenfield Toshiyuki Sasagawa Michael S Robeson
author_sort	Takeo Shibata
title	Evaluation of DNA extraction protocols from liquid-based cytology specimens for studying cervical microbiota.
title_short	Evaluation of DNA extraction protocols from liquid-based cytology specimens for studying cervical microbiota.
title_full	Evaluation of DNA extraction protocols from liquid-based cytology specimens for studying cervical microbiota.
title_fullStr	Evaluation of DNA extraction protocols from liquid-based cytology specimens for studying cervical microbiota.
title_full_unstemmed	Evaluation of DNA extraction protocols from liquid-based cytology specimens for studying cervical microbiota.
title_sort	evaluation of dna extraction protocols from liquid-based cytology specimens for studying cervical microbiota.
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/8da7e7d4cc0c43eeae15c1d015d198d7
work_keys_str_mv	AT takeoshibata evaluationofdnaextractionprotocolsfromliquidbasedcytologyspecimensforstudyingcervicalmicrobiota AT mayuminakagawa evaluationofdnaextractionprotocolsfromliquidbasedcytologyspecimensforstudyingcervicalmicrobiota AT hannahncoleman evaluationofdnaextractionprotocolsfromliquidbasedcytologyspecimensforstudyingcervicalmicrobiota AT sarahmowens evaluationofdnaextractionprotocolsfromliquidbasedcytologyspecimensforstudyingcervicalmicrobiota AT williamwgreenfield evaluationofdnaextractionprotocolsfromliquidbasedcytologyspecimensforstudyingcervicalmicrobiota AT toshiyukisasagawa evaluationofdnaextractionprotocolsfromliquidbasedcytologyspecimensforstudyingcervicalmicrobiota AT michaelsrobeson evaluationofdnaextractionprotocolsfromliquidbasedcytologyspecimensforstudyingcervicalmicrobiota
_version_	1718374658746613760

Evaluation of DNA extraction protocols from liquid-based cytology specimens for studying cervical microbiota.

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