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dc.contributor.authorYap, Min
dc.contributor.authorFeehily, Conor
dc.contributor.authorWalsh, Calum J.
dc.contributor.authorFenelon, Mark
dc.contributor.authorMurphy, Eileen F.
dc.contributor.authorMcAuliffe, Fionnuala M.
dc.contributor.authorvan Sinderen, Douwe
dc.contributor.authorO’Toole, Paul W.
dc.contributor.authorO’Sullivan, Orla
dc.contributor.authorCotter, Paul D.
dc.date.accessioned2021-11-11T16:56:47Z
dc.date.available2021-11-11T16:56:47Z
dc.date.issued2020-12-10
dc.identifier.citationYap M, Feehily C, Walsh CJ, et al. Evaluation of methods for the reduction of contaminating host reads when performing shotgun metagenomic sequencing of the milk microbiome. Scientific Reports 2020;10:21665. doi:10.1038/s41598-020-78773-6en_US
dc.identifier.urihttp://hdl.handle.net/11019/2605
dc.descriptionpeer revieweden_US
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_US
dc.description.sponsorshipIrish Dairy Levy
dc.language.isoenen_US
dc.publisherSpringeren_US
dc.relation.ispartofseriesScientific Reports;Vol. 10
dc.rightsAttribution-NonCommercial-ShareAlike 4.0 International*
dc.rights.urihttp://creativecommons.org/licenses/by-nc-sa/4.0/*
dc.subjectMetagenomicsen_US
dc.subjectNext-generation sequencingen_US
dc.titleEvaluation of methods for the reduction of contaminating host reads when performing shotgun metagenomic sequencing of the milk microbiomeen_US
dc.typeArticleen_US
dc.identifier.doihttps://doi.org/10.1038/s41598-020-78773-6
dc.identifier.pii78773
dc.contributor.sponsorIrish Dairy Levyen_US
dc.contributor.sponsorScience Foundation Irelanden_US
dc.contributor.sponsorPrecisionBiotics Ltd.en_US
dc.contributor.sponsorGrantNumberSFI/12/RC/2273en_US
dc.contributor.sponsorGrantNumber16/SP/3827en_US
dc.source.volume10
dc.source.issue1
refterms.dateFOA2021-11-11T16:56:47Z
dc.source.journaltitleScientific Reports
dc.identifier.eissn2045-2322


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