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

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dc.contributor.authorYap, Minen
dc.contributor.authorFeehily, Conoren
dc.contributor.authorWalsh, Calum J.en
dc.contributor.authorFenelon, Mark A.en
dc.contributor.authorMurphy, Eileen F.en
dc.contributor.authorMcAuliffe, Fionnuala M.en
dc.contributor.authorvan Sinderen, Douween
dc.contributor.authorO’Toole, Paul W.en
dc.contributor.authorO’Sullivan, Orlaen
dc.contributor.authorCotter, Paul D.en
dc.contributor.funderIrish Dairy Levyen
dc.contributor.funderScience Foundation Irelanden
dc.date.accessioned2023-11-16T12:28:41Z
dc.date.available2023-11-16T12:28:41Z
dc.date.issued2020en
dc.description.abstractShotgun 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.en
dc.description.statusPeer revieweden
dc.description.versionPublished Versionen
dc.format.mimetypeapplication/pdfen
dc.identifier.articleid21665en
dc.identifier.citationYap, M., Feehily, C., Walsh, C.J., Fenelon, M., Murphy, E.F., McAuliffe, F.M., Van Sinderen, D., O’Toole, P.W., O’Sullivan, O. and Cotter, P.D. (2020) ‘Evaluation of methods for the reduction of contaminating host reads when performing shotgun metagenomic sequencing of the milk microbiome’, Scientific Reports, 10(1), 21665 (11pp). doi: 10.1038/s41598-020-78773-6en
dc.identifier.doi10.1038/s41598-020-78773-6en
dc.identifier.endpage11en
dc.identifier.issn2045-2322en
dc.identifier.issued1en
dc.identifier.journaltitleScientific Reportsen
dc.identifier.startpage1en
dc.identifier.urihttps://hdl.handle.net/10468/15236
dc.identifier.volume10en
dc.language.isoenen
dc.publisherNature Researchen
dc.relation.ispartofScientific Reportsen
dc.relation.projectinfo:eu-repo/grantAgreement/SFI/SFI Research Centres/12/RC/2273/IE/Alimentary Pharmabiotic Centre (APC) - Interfacing Food & Medicine/en
dc.relation.projectinfo:eu-repo/grantAgreement/SFI/SFI Spokes Programme::Fixed Call/16/SP/3827/IE/Determinants of Mother-to-Infant Transfer of Microbiota/en
dc.rights© The Author(s) 2020. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creat iveco mmons .org/licen ses/by/4.0/.en
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/en
dc.subjectShotgun metagenomic sequencingen
dc.subjectMilk microbiomeen
dc.subjectBovine and human milk samplesen
dc.subjectMicrobial DNAen
dc.subjectMetagenome-assembled genomesen
dc.subjectMAGsen
dc.subjectKraken2en
dc.titleEvaluation of methods for the reduction of contaminating host reads when performing shotgun metagenomic sequencing of the milk microbiomeen
dc.typeArticle (peer-reviewed)en
dc.typejournal-articleen
oaire.citation.issue1en
oaire.citation.volume10en
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