New publication linking fermented-food, microbiomes & innovation

Recent advances in genome-scale metabolic modeling (GSMM) are transforming our understanding of how the microbiomes of fermented foods operate, but there is still a crucial gap: while GSMM is well-established in microbial ecology, its application to food systems innovation remains under-leveraged. The review paper, “Microbiome Metabolic Modeling as a Tool for Innovation in Fermented Food Science” (Karimi et al., 2025), provides an overview of current research utilizing GSMM in fermented food science. An integrated and unified strategy for designing food microbiomes using both bottom-up and top-down GSMM strategies is proposed. Challenges, bottlenecks and perspective of GSMM in fermented food science is discussed.

Short summary:

• The paper synthesizes state-of-the-art GSMM approaches, showing how they can be used to predict metabolic interactions within food microbiomes.
• It highlights opportunities for designing novel fermented foods with optimized metabolic traits (e.g., enhanced production of beneficial metabolites, reduction of undesirable by-products).
• It also underscores the importance of integrative “omics” (genomics, transcriptomics, metabolomics) to refine and validate models — bridging computational biology and real-world food innovation.

If you’re interested, you can read the full paper here: Microbiome Metabolic Modeling as a tool for innovation in fermented foods – ScienceDirect.