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dc.contributor.authorWalsh, Liam H.
dc.contributor.authorCoakley, Mairéad
dc.contributor.authorWalsh, Aaron M.
dc.contributor.authorO’Toole, Paul W.
dc.contributor.authorCotter, Paul
dc.date.accessioned2023-01-09T12:11:28Z
dc.date.available2023-01-09T12:11:28Z
dc.date.issued2022-10-26
dc.identifier.citationLiam H. Walsh, Mairéad Coakley, Aaron M. Walsh, Paul W. O’Toole & Paul D. Cotter (2022) Bioinformatic approaches for studying the microbiome of fermented food, Critical Reviews in Microbiology, DOI: 10.1080/1040841X.2022.2132850en_US
dc.identifier.issn1040-841X
dc.identifier.urihttp://hdl.handle.net/11019/2885
dc.descriptionpeer-revieweden_US
dc.description.abstractHigh-throughput DNA sequencing-based approaches continue to revolutionise our understanding of microbial ecosystems, including those associated with fermented foods. Metagenomic and metatranscriptomic approaches are state-of-the-art biological profiling methods and are employed to investigate a wide variety of characteristics of microbial communities, such as taxonomic membership, gene content and the range and level at which these genes are expressed. Individual groups and consortia of researchers are utilising these approaches to produce increasingly large and complex datasets, representing vast populations of microorganisms. There is a corresponding requirement for the development and application of appropriate bioinformatic tools and pipelines to interpret this data. This review critically analyses the tools and pipelines that have been used or that could be applied to the analysis of metagenomic and metatranscriptomic data from fermented foods. In addition, we critically analyse a number of studies of fermented foods in which these tools have previously been applied, to highlight the insights that these approaches can provide.en_US
dc.description.sponsorshipEuropean Union’s Horizon 2020 research and innovation programme
dc.language.isoenen_US
dc.publisherInforma UK Limiteden_US
dc.relation.ispartofseriesCritical Reviews in Microbiology;
dc.rightsAttribution-NonCommercial-ShareAlike 4.0 International*
dc.rights.urihttp://creativecommons.org/licenses/by-nc-sa/4.0/*
dc.subjecthigh-throughput sequencingen_US
dc.subjectMetagenomicsen_US
dc.subjectmetatranscriptomicsen_US
dc.subjectbioinformaticsen_US
dc.subjectfermented foodsen_US
dc.titleBioinformatic approaches for studying the microbiome of fermented fooden_US
dc.typeArticleen_US
dc.identifier.doihttps://doi.org/10.1080/1040841X.2022.2132850
dc.identifier.pii10.1080/1040841X.2022.2132850
dc.contributor.sponsorEuropean Unionen_US
dc.contributor.sponsorScience Foundation Irelanden_US
dc.contributor.sponsorDepartment of Agriculture, Food and the Marineen_US
dc.contributor.sponsorEnterprise Irelanden_US
dc.contributor.sponsorGrantNumber818368en_US
dc.contributor.sponsorGrantNumberFI/12/RC/2273_P2en_US
dc.contributor.sponsorGrantNumberFI/16/RC/3835en_US
dc.contributor.sponsorGrantNumberC/2018/0025en_US
dc.source.beginpage1
dc.source.endpage33
refterms.dateFOA2023-01-09T12:11:29Z
dc.source.journaltitleCritical Reviews in Microbiology
dc.identifier.eissn1549-7828


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