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

Zhang, Erkang; Claesson, Marcus J.; Cotter, Paul D.

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

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Files

s41538-026-00740-8.pdf(1.43 MB)

Published Version

Date

2026-02-06

Authors

Zhang, Erkang

Claesson, Marcus J.

Cotter, Paul D.

Publisher

Nature Research

Published Version

10.1038/s41538-026-00740-8

Abstract

The 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.

Keywords

Quality of fermented foods , Industrial reproducibility , [Microbiology] , [APCMicrobiome]

Citation

Zhang, E., Claesson, M. J. and 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, 10(1), pp. . https://doi.org/10.1038/s41538-026-00740-8