Evaluation of methods for the reduction of contaminating host reads when performing shotgun metagenomic sequencing of the milk microbiome

Abstract Shotgun metagenomic sequencing is a valuable tool for the taxonomic and functional profiling of microbial communities. However, this approach is challenging in samples, such as milk, where a low microbial abundance, combined with high levels of host DNA, result in inefficient and uneconomic...

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Autores principales:	Min Yap, Conor Feehily, Calum J. Walsh, Mark Fenelon, Eileen F. Murphy, Fionnuala M. McAuliffe, Douwe van Sinderen, Paul W. O’Toole, Orla O’Sullivan, Paul D. Cotter
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2020
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/ebd35d15f2fe424d9aae078bc49b7de4
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spelling	oai:doaj.org-article:ebd35d15f2fe424d9aae078bc49b7de42021-12-02T11:43:36ZEvaluation of methods for the reduction of contaminating host reads when performing shotgun metagenomic sequencing of the milk microbiome10.1038/s41598-020-78773-62045-2322https://doaj.org/article/ebd35d15f2fe424d9aae078bc49b7de42020-12-01T00:00:00Zhttps://doi.org/10.1038/s41598-020-78773-6https://doaj.org/toc/2045-2322Abstract Shotgun metagenomic sequencing is a valuable tool for the taxonomic and functional profiling of microbial communities. However, this approach is challenging in samples, such as milk, where a low microbial abundance, combined with high levels of host DNA, result in inefficient and uneconomical sequencing. Here we evaluate approaches to deplete host DNA or enrich microbial DNA prior to sequencing using three commercially available kits. We compared the percentage of microbial reads obtained from each kit after shotgun metagenomic sequencing. Using bovine and human milk samples, we determined that host depletion with the MolYsis complete5 kit significantly improved microbial sequencing depth compared to other approaches tested. Importantly, no biases were introduced. Additionally, the increased microbial sequencing depth allowed for further characterization of the microbiome through the generation of metagenome-assembled genomes (MAGs). Furthermore, with the use of a mock community, we compared three common classifiers and determined that Kraken2 was the optimal classifier for these samples. This evaluation shows that microbiome analysis can be performed on both bovine and human milk samples at a much greater resolution without the need for more expensive deep-sequencing approaches.Min YapConor FeehilyCalum J. WalshMark FenelonEileen F. MurphyFionnuala M. McAuliffeDouwe van SinderenPaul W. O’TooleOrla O’SullivanPaul D. CotterNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 10, Iss 1, Pp 1-11 (2020)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Min Yap Conor Feehily Calum J. Walsh Mark Fenelon Eileen F. Murphy Fionnuala M. McAuliffe Douwe van Sinderen Paul W. O’Toole Orla O’Sullivan Paul D. Cotter Evaluation of methods for the reduction of contaminating host reads when performing shotgun metagenomic sequencing of the milk microbiome
description	Abstract Shotgun metagenomic sequencing is a valuable tool for the taxonomic and functional profiling of microbial communities. However, this approach is challenging in samples, such as milk, where a low microbial abundance, combined with high levels of host DNA, result in inefficient and uneconomical sequencing. Here we evaluate approaches to deplete host DNA or enrich microbial DNA prior to sequencing using three commercially available kits. We compared the percentage of microbial reads obtained from each kit after shotgun metagenomic sequencing. Using bovine and human milk samples, we determined that host depletion with the MolYsis complete5 kit significantly improved microbial sequencing depth compared to other approaches tested. Importantly, no biases were introduced. Additionally, the increased microbial sequencing depth allowed for further characterization of the microbiome through the generation of metagenome-assembled genomes (MAGs). Furthermore, with the use of a mock community, we compared three common classifiers and determined that Kraken2 was the optimal classifier for these samples. This evaluation shows that microbiome analysis can be performed on both bovine and human milk samples at a much greater resolution without the need for more expensive deep-sequencing approaches.
format	article
author	Min Yap Conor Feehily Calum J. Walsh Mark Fenelon Eileen F. Murphy Fionnuala M. McAuliffe Douwe van Sinderen Paul W. O’Toole Orla O’Sullivan Paul D. Cotter
author_facet	Min Yap Conor Feehily Calum J. Walsh Mark Fenelon Eileen F. Murphy Fionnuala M. McAuliffe Douwe van Sinderen Paul W. O’Toole Orla O’Sullivan Paul D. Cotter
author_sort	Min Yap
title	Evaluation of methods for the reduction of contaminating host reads when performing shotgun metagenomic sequencing of the milk microbiome
title_short	Evaluation of methods for the reduction of contaminating host reads when performing shotgun metagenomic sequencing of the milk microbiome
title_full	Evaluation of methods for the reduction of contaminating host reads when performing shotgun metagenomic sequencing of the milk microbiome
title_fullStr	Evaluation of methods for the reduction of contaminating host reads when performing shotgun metagenomic sequencing of the milk microbiome
title_full_unstemmed	Evaluation of methods for the reduction of contaminating host reads when performing shotgun metagenomic sequencing of the milk microbiome
title_sort	evaluation of methods for the reduction of contaminating host reads when performing shotgun metagenomic sequencing of the milk microbiome
publisher	Nature Portfolio
publishDate	2020
url	https://doaj.org/article/ebd35d15f2fe424d9aae078bc49b7de4
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Evaluation of methods for the reduction of contaminating host reads when performing shotgun metagenomic sequencing of the milk microbiome

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