Assessing saliva microbiome collection and processing methods

Abstract The oral microbiome has been connected with lung health and may be of significance in the progression of SARS-CoV-2 infection. Saliva-based SARS-CoV-2 tests provide the opportunity to leverage stored samples for assessing the oral microbiome. However, these collection kits have not been tes...

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Autores principales:	Abigail J. S. Armstrong, Veenat Parmar, Martin J. Blaser
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Microbial ecology QR100-130
Acceso en línea:	https://doaj.org/article/820ccae3f377459fa14b3a0c2c4d7084
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spelling	oai:doaj.org-article:820ccae3f377459fa14b3a0c2c4d70842021-11-21T12:26:18ZAssessing saliva microbiome collection and processing methods10.1038/s41522-021-00254-z2055-5008https://doaj.org/article/820ccae3f377459fa14b3a0c2c4d70842021-11-01T00:00:00Zhttps://doi.org/10.1038/s41522-021-00254-zhttps://doaj.org/toc/2055-5008Abstract The oral microbiome has been connected with lung health and may be of significance in the progression of SARS-CoV-2 infection. Saliva-based SARS-CoV-2 tests provide the opportunity to leverage stored samples for assessing the oral microbiome. However, these collection kits have not been tested for their accuracy in measuring the oral microbiome. Saliva is highly enriched with human DNA and reducing it prior to shotgun sequencing may increase the depth of bacterial reads. We examined both the effect of saliva collection method and sequence processing on measurement of microbiome depth and diversity by 16 S rRNA gene amplicon and shotgun metagenomics. We collected 56 samples from 22 subjects. Each subject provided saliva samples with and without preservative, and a subset provided a second set of samples the following day. 16 S rRNA gene (V4) sequencing was performed on all samples, and shotgun metagenomics was performed on a subset of samples collected with preservative with and without human DNA depletion before sequencing. We observed that the beta diversity distances within subjects over time was smaller than between unrelated subjects, and distances within subjects were smaller in samples collected with preservative. Samples collected with preservative had higher alpha diversity measuring both richness and evenness. Human DNA depletion before extraction and shotgun sequencing yielded higher total and relative reads mapping to bacterial sequences. We conclude that collecting saliva with preservative may provide more consistent measures of the oral microbiome and depleting human DNA increases yield of bacterial sequences.Abigail J. S. ArmstrongVeenat ParmarMartin J. BlaserNature PortfolioarticleMicrobial ecologyQR100-130ENnpj Biofilms and Microbiomes, Vol 7, Iss 1, Pp 1-8 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Microbial ecology QR100-130
spellingShingle	Microbial ecology QR100-130 Abigail J. S. Armstrong Veenat Parmar Martin J. Blaser Assessing saliva microbiome collection and processing methods
description	Abstract The oral microbiome has been connected with lung health and may be of significance in the progression of SARS-CoV-2 infection. Saliva-based SARS-CoV-2 tests provide the opportunity to leverage stored samples for assessing the oral microbiome. However, these collection kits have not been tested for their accuracy in measuring the oral microbiome. Saliva is highly enriched with human DNA and reducing it prior to shotgun sequencing may increase the depth of bacterial reads. We examined both the effect of saliva collection method and sequence processing on measurement of microbiome depth and diversity by 16 S rRNA gene amplicon and shotgun metagenomics. We collected 56 samples from 22 subjects. Each subject provided saliva samples with and without preservative, and a subset provided a second set of samples the following day. 16 S rRNA gene (V4) sequencing was performed on all samples, and shotgun metagenomics was performed on a subset of samples collected with preservative with and without human DNA depletion before sequencing. We observed that the beta diversity distances within subjects over time was smaller than between unrelated subjects, and distances within subjects were smaller in samples collected with preservative. Samples collected with preservative had higher alpha diversity measuring both richness and evenness. Human DNA depletion before extraction and shotgun sequencing yielded higher total and relative reads mapping to bacterial sequences. We conclude that collecting saliva with preservative may provide more consistent measures of the oral microbiome and depleting human DNA increases yield of bacterial sequences.
format	article
author	Abigail J. S. Armstrong Veenat Parmar Martin J. Blaser
author_facet	Abigail J. S. Armstrong Veenat Parmar Martin J. Blaser
author_sort	Abigail J. S. Armstrong
title	Assessing saliva microbiome collection and processing methods
title_short	Assessing saliva microbiome collection and processing methods
title_full	Assessing saliva microbiome collection and processing methods
title_fullStr	Assessing saliva microbiome collection and processing methods
title_full_unstemmed	Assessing saliva microbiome collection and processing methods
title_sort	assessing saliva microbiome collection and processing methods
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/820ccae3f377459fa14b3a0c2c4d7084
work_keys_str_mv	AT abigailjsarmstrong assessingsalivamicrobiomecollectionandprocessingmethods AT veenatparmar assessingsalivamicrobiomecollectionandprocessingmethods AT martinjblaser assessingsalivamicrobiomecollectionandprocessingmethods
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Assessing saliva microbiome collection and processing methods

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