Adopting omics-based approaches to facilitate the establishment of microbial consortia to generate reproducible fermented foods with desirable properties

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dc.contributor.authorZhang, Erkang
dc.contributor.authorClaesson, Marcus J
dc.contributor.authorCotter, Paul D
dc.contributor.funderEuropean Commission, EU
dc.contributor.funderEnterprise Ireland
dc.contributor.funderHORIZON EUROPE Framework Programme, 101084642-101060218
dc.date.accessioned2026-04-08T14:50:04Z
dc.date.available2026-04-08T14:50:04Z
dc.date.issued2026-02-06
dc.description.abstractThe quality of fermented foods is governed by the composition, function, and interactions of their microbial communities. However, fermentations carried out using traditional approaches are often variable with respect to their composition and are difficult to control, thereby limiting industrial reproducibility. Recent advances in omics technologies-including metagenomics, metatranscriptomics, metaproteomics, metabolomics, and culturomics-have greatly enhanced our ability to analyze and reconstruct the microbial ecosystems in fermented foods. This review first highlights the importance of omics analyses for characterizing microbial composition, metabolic potential, and functional interactions. It then discusses the bipartite structure of defined microbial consortia (DMCs), distinguishing between the core microbiome, comprising taxa consistently associated with fermentation performance, and the supplementary microbiome, consisting of variable species that influence flavor diversity and system stability. Finally, we describe a multi-omics-guided strategy for the design and refinement of DMCs, framed within the Assembly-Assessment-Redesign (A-A-R) workflow, which enables iterative optimization of microbial consortia for reproducible and desirable fermentation outcomes. Integrating omics insights with DMC engineering provides a systematic approach for precision fermentation, paving the way for next-generation fermented food production.en
dc.description.sponsorshipResearch Ireland (RI) under grant numbers 23/FFP-A/11857 (InFer), SFI/12/RC/2273 (APC Microbiome Ireland), and RI together with the Irish Department of Agriculture, Food and the Marine, SFI/16/RC/3835 (VistaMilk), by the Enterprise Ireland funded Food Health Ireland project and by the European Commission under the Horizon Europe program under grant numbers 101060218 (DOMINO) and 101084642 (Co-Diet)
dc.description.versionPublished Version
dc.format.extent13
dc.format.mimetypeapplication/pdfen
dc.identifier.articleid90
dc.identifier.authororcidZhang, Erkang
dc.identifier.authororcidClaesson, Marcus J§0000-0002-5712-0623
dc.identifier.authororcidCotter, Paul D
dc.identifier.citationZhang, E, Claesson, M J & Cotter, P D 2026, 'Adopting omics-based approaches to facilitate the establishment of microbial consortia to generate reproducible fermented foods with desirable properties', npj Science of Food, vol. 10, no. 1, 90. https://doi.org/10.1038/s41538-026-00740-8
dc.identifier.doi10.1038/s41538-026-00740-8
dc.identifier.issn2396-8370
dc.identifier.issued1
dc.identifier.otherPubMedCentral: PMC12987955
dc.identifier.otherORCID: /0000-0002-5712-0623/work/211143103
dc.identifier.urihttps://hdl.handle.net/10468/18686
dc.identifier.volume10
dc.language.isoen
dc.publisherNature Publishing Group
dc.relation.urihttps://www.scopus.com/pages/publications/105033498044
dc.rights© 2026. The Author(s).
dc.rights.accessrightsopen access
dc.rights.licensenameAttribution-NonCommercial-NoDerivatives 4.0 International
dc.rights.urihttps://creativecommons.org/licenses/by-nc-nd/4.0/
dc.statusPeer reviewed
dc.subjectIndustrial reproducibility
dc.subjectQuality of fermented foods
dc.subject[APCMicrobiome]
dc.subject[Microbiology]
dc.titleAdopting omics-based approaches to facilitate the establishment of microbial consortia to generate reproducible fermented foods with desirable propertiesen
dc.typeReview
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