Evaluating the Information Content of Shallow Shotgun Metagenomics

ABSTRACT Although microbial communities are associated with human, environmental, plant, and animal health, there exists no cost-effective method for precisely characterizing species and genes in such communities. While deep whole-metagenome shotgun (WMS) sequencing provides high taxonomic and funct...

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Autores principales:	Benjamin Hillmann, Gabriel A. Al-Ghalith, Robin R. Shields-Cutler, Qiyun Zhu, Daryl M. Gohl, Kenneth B. Beckman, Rob Knight, Dan Knights
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2018
Materias:	human microbiome metagenomics microbiome shotgun metagenomics Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/73770f00f77e4992943016aa90b9f047
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spelling	oai:doaj.org-article:73770f00f77e4992943016aa90b9f0472021-12-02T18:15:43ZEvaluating the Information Content of Shallow Shotgun Metagenomics10.1128/mSystems.00069-182379-5077https://doaj.org/article/73770f00f77e4992943016aa90b9f0472018-10-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSystems.00069-18https://doaj.org/toc/2379-5077ABSTRACT Although microbial communities are associated with human, environmental, plant, and animal health, there exists no cost-effective method for precisely characterizing species and genes in such communities. While deep whole-metagenome shotgun (WMS) sequencing provides high taxonomic and functional resolution, it is often prohibitively expensive for large-scale studies. The prevailing alternative, 16S rRNA gene amplicon (16S) sequencing, often does not resolve taxonomy past the genus level and provides only moderately accurate predictions of the functional profile; thus, there is currently no widely accepted approach to affordable, high-resolution, taxonomic, and functional microbiome analysis. To address this technology gap, we evaluated the information content of shallow shotgun sequencing with as low as 0.5 million sequences per sample as an alternative to 16S sequencing for large human microbiome studies. We describe a library preparation protocol enabling shallow shotgun sequencing at approximately the same per-sample cost as 16S sequencing. We analyzed multiple real and simulated biological data sets, including two novel human stool samples with ultradeep sequencing of 2.5 billion sequences per sample, and found that shallow shotgun sequencing recovers more-accurate species-level taxonomic and functional profiles of the human microbiome than 16S sequencing. We discuss the inherent limitations of shallow shotgun sequencing and note that 16S sequencing remains a valuable and important method for taxonomic profiling of novel environments. Although deep WMS sequencing remains the gold standard for high-resolution microbiome analysis, we recommend that researchers consider shallow shotgun sequencing as a useful alternative to 16S sequencing for large-scale human microbiome research studies where WMS sequencing may be cost-prohibitive. IMPORTANCE A common refrain in recent microbiome-related academic meetings is that the field needs to move away from broad taxonomic surveys using 16S sequencing and toward more powerful longitudinal studies using shotgun sequencing. However, performing deep shotgun sequencing in large longitudinal studies remains prohibitively expensive for all but the most well-funded research labs and consortia, which leads many researchers to choose 16S sequencing for large studies, followed by deep shotgun sequencing on a subset of targeted samples. Here, we show that shallow- or moderate-depth shotgun sequencing may be used by researchers to obtain species-level taxonomic and functional data at approximately the same cost as amplicon sequencing. While shallow shotgun sequencing is not intended to replace deep shotgun sequencing for strain-level characterization, we recommend that microbiome scientists consider using shallow shotgun sequencing instead of 16S sequencing for large-scale human microbiome studies.Benjamin HillmannGabriel A. Al-GhalithRobin R. Shields-CutlerQiyun ZhuDaryl M. GohlKenneth B. BeckmanRob KnightDan KnightsAmerican Society for Microbiologyarticlehuman microbiomemetagenomicsmicrobiomeshotgun metagenomicsMicrobiologyQR1-502ENmSystems, Vol 3, Iss 6 (2018)
institution	DOAJ
collection	DOAJ
language	EN
topic	human microbiome metagenomics microbiome shotgun metagenomics Microbiology QR1-502
spellingShingle	human microbiome metagenomics microbiome shotgun metagenomics Microbiology QR1-502 Benjamin Hillmann Gabriel A. Al-Ghalith Robin R. Shields-Cutler Qiyun Zhu Daryl M. Gohl Kenneth B. Beckman Rob Knight Dan Knights Evaluating the Information Content of Shallow Shotgun Metagenomics
description	ABSTRACT Although microbial communities are associated with human, environmental, plant, and animal health, there exists no cost-effective method for precisely characterizing species and genes in such communities. While deep whole-metagenome shotgun (WMS) sequencing provides high taxonomic and functional resolution, it is often prohibitively expensive for large-scale studies. The prevailing alternative, 16S rRNA gene amplicon (16S) sequencing, often does not resolve taxonomy past the genus level and provides only moderately accurate predictions of the functional profile; thus, there is currently no widely accepted approach to affordable, high-resolution, taxonomic, and functional microbiome analysis. To address this technology gap, we evaluated the information content of shallow shotgun sequencing with as low as 0.5 million sequences per sample as an alternative to 16S sequencing for large human microbiome studies. We describe a library preparation protocol enabling shallow shotgun sequencing at approximately the same per-sample cost as 16S sequencing. We analyzed multiple real and simulated biological data sets, including two novel human stool samples with ultradeep sequencing of 2.5 billion sequences per sample, and found that shallow shotgun sequencing recovers more-accurate species-level taxonomic and functional profiles of the human microbiome than 16S sequencing. We discuss the inherent limitations of shallow shotgun sequencing and note that 16S sequencing remains a valuable and important method for taxonomic profiling of novel environments. Although deep WMS sequencing remains the gold standard for high-resolution microbiome analysis, we recommend that researchers consider shallow shotgun sequencing as a useful alternative to 16S sequencing for large-scale human microbiome research studies where WMS sequencing may be cost-prohibitive. IMPORTANCE A common refrain in recent microbiome-related academic meetings is that the field needs to move away from broad taxonomic surveys using 16S sequencing and toward more powerful longitudinal studies using shotgun sequencing. However, performing deep shotgun sequencing in large longitudinal studies remains prohibitively expensive for all but the most well-funded research labs and consortia, which leads many researchers to choose 16S sequencing for large studies, followed by deep shotgun sequencing on a subset of targeted samples. Here, we show that shallow- or moderate-depth shotgun sequencing may be used by researchers to obtain species-level taxonomic and functional data at approximately the same cost as amplicon sequencing. While shallow shotgun sequencing is not intended to replace deep shotgun sequencing for strain-level characterization, we recommend that microbiome scientists consider using shallow shotgun sequencing instead of 16S sequencing for large-scale human microbiome studies.
format	article
author	Benjamin Hillmann Gabriel A. Al-Ghalith Robin R. Shields-Cutler Qiyun Zhu Daryl M. Gohl Kenneth B. Beckman Rob Knight Dan Knights
author_facet	Benjamin Hillmann Gabriel A. Al-Ghalith Robin R. Shields-Cutler Qiyun Zhu Daryl M. Gohl Kenneth B. Beckman Rob Knight Dan Knights
author_sort	Benjamin Hillmann
title	Evaluating the Information Content of Shallow Shotgun Metagenomics
title_short	Evaluating the Information Content of Shallow Shotgun Metagenomics
title_full	Evaluating the Information Content of Shallow Shotgun Metagenomics
title_fullStr	Evaluating the Information Content of Shallow Shotgun Metagenomics
title_full_unstemmed	Evaluating the Information Content of Shallow Shotgun Metagenomics
title_sort	evaluating the information content of shallow shotgun metagenomics
publisher	American Society for Microbiology
publishDate	2018
url	https://doaj.org/article/73770f00f77e4992943016aa90b9f047
work_keys_str_mv	AT benjaminhillmann evaluatingtheinformationcontentofshallowshotgunmetagenomics AT gabrielaalghalith evaluatingtheinformationcontentofshallowshotgunmetagenomics AT robinrshieldscutler evaluatingtheinformationcontentofshallowshotgunmetagenomics AT qiyunzhu evaluatingtheinformationcontentofshallowshotgunmetagenomics AT darylmgohl evaluatingtheinformationcontentofshallowshotgunmetagenomics AT kennethbbeckman evaluatingtheinformationcontentofshallowshotgunmetagenomics AT robknight evaluatingtheinformationcontentofshallowshotgunmetagenomics AT danknights evaluatingtheinformationcontentofshallowshotgunmetagenomics
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Evaluating the Information Content of Shallow Shotgun Metagenomics

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