The saliva microbiome profiles are minimally affected by collection method or DNA extraction protocols

Abstract Saliva has attracted attention as a diagnostic fluid due to the association of oral microbiota with systemic diseases. However, the lack of standardised methods for saliva collection has led to the slow uptake of saliva in microbiome research. The aim of this study was to systematically eva...

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Autores principales:	Yenkai Lim, Makrina Totsika, Mark Morrison, Chamindie Punyadeera
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/372c016923814e2ea9c164611470ea3e
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spelling	oai:doaj.org-article:372c016923814e2ea9c164611470ea3e2021-12-02T12:32:59ZThe saliva microbiome profiles are minimally affected by collection method or DNA extraction protocols10.1038/s41598-017-07885-32045-2322https://doaj.org/article/372c016923814e2ea9c164611470ea3e2017-08-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-07885-3https://doaj.org/toc/2045-2322Abstract Saliva has attracted attention as a diagnostic fluid due to the association of oral microbiota with systemic diseases. However, the lack of standardised methods for saliva collection has led to the slow uptake of saliva in microbiome research. The aim of this study was to systematically evaluate the potential effects on salivary microbiome profiles using different methods of saliva collection, storage and gDNA extraction. Three types of saliva fractions were collected from healthy individuals with or without the gDNA stabilising buffer. Subsequently, three types of gDNA extraction methods were evaluated to determine the gDNA extraction efficiencies from saliva samples. The purity of total bacterial gDNA was evaluated using the ratio of human β-globin to bacterial 16S rRNA PCR while 16S rRNA gene amplicon sequencing was carried out to identify the bacterial profiles present in these samples. The quantity and quality of extracted gDNA were similar among all three gDNA extraction methods and there were no statistically significant differences in the bacterial profiles among different saliva fractions at the genus-level of taxonomic classification. In conclusion, saliva sampling, processing and gDNA preparation do not have major influence on microbiome profiles.Yenkai LimMakrina TotsikaMark MorrisonChamindie PunyadeeraNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-10 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Yenkai Lim Makrina Totsika Mark Morrison Chamindie Punyadeera The saliva microbiome profiles are minimally affected by collection method or DNA extraction protocols
description	Abstract Saliva has attracted attention as a diagnostic fluid due to the association of oral microbiota with systemic diseases. However, the lack of standardised methods for saliva collection has led to the slow uptake of saliva in microbiome research. The aim of this study was to systematically evaluate the potential effects on salivary microbiome profiles using different methods of saliva collection, storage and gDNA extraction. Three types of saliva fractions were collected from healthy individuals with or without the gDNA stabilising buffer. Subsequently, three types of gDNA extraction methods were evaluated to determine the gDNA extraction efficiencies from saliva samples. The purity of total bacterial gDNA was evaluated using the ratio of human β-globin to bacterial 16S rRNA PCR while 16S rRNA gene amplicon sequencing was carried out to identify the bacterial profiles present in these samples. The quantity and quality of extracted gDNA were similar among all three gDNA extraction methods and there were no statistically significant differences in the bacterial profiles among different saliva fractions at the genus-level of taxonomic classification. In conclusion, saliva sampling, processing and gDNA preparation do not have major influence on microbiome profiles.
format	article
author	Yenkai Lim Makrina Totsika Mark Morrison Chamindie Punyadeera
author_facet	Yenkai Lim Makrina Totsika Mark Morrison Chamindie Punyadeera
author_sort	Yenkai Lim
title	The saliva microbiome profiles are minimally affected by collection method or DNA extraction protocols
title_short	The saliva microbiome profiles are minimally affected by collection method or DNA extraction protocols
title_full	The saliva microbiome profiles are minimally affected by collection method or DNA extraction protocols
title_fullStr	The saliva microbiome profiles are minimally affected by collection method or DNA extraction protocols
title_full_unstemmed	The saliva microbiome profiles are minimally affected by collection method or DNA extraction protocols
title_sort	saliva microbiome profiles are minimally affected by collection method or dna extraction protocols
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/372c016923814e2ea9c164611470ea3e
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_version_	1718393911046569984

The saliva microbiome profiles are minimally affected by collection method or DNA extraction protocols

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