Fermentation
Novel biosynthetic pathway discovery for fermentation-derived functional molecule production
Many of the desirable properties of food derive from specific functional molecules (e.g., specific lipids, enzymes, and volatile compounds). These molecules include proteins and small molecules with defined structures that allow them to interact with other food matrix components or directly with a consumer’s senses to generate particular flavors, aromas, and textures.
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Fermentation
- Host strain development
- Ingredient optimization
- Target molecule discovery
Resources:
- Role of Lipids in Food Flavor Generation
- Flavor and Metabolite Profiles of Meat, Meat Substitutes, and Traditional Plant-Based High-Protein Food Products
- https://gfi.org/solutions/biosynthetic-pathway-discovery-fermentation/
- Current perspectives in food-based studies exploiting multi-omics approaches
Current challenges
Many of the desirable properties of food derive from specific functional molecules (e.g., specific lipids, enzymes, and volatile compounds). These molecules include proteins and small molecules with defined structures that allow them to interact with other food matrix components or directly with a consumer’s senses to generate particular flavours, aromas, and textures. After identifying specific target molecules or desired functionalities in animal-derived foods, scientists can work backward, mining microbial sequences for candidate molecules in the microbial realm that might provide similar functionality. This process can also elucidate the pathways that produce these molecules and inform strategies for designing microbial strains that produce these molecules at scale.
The totality of microbial genomic information comprises an overwhelmingly vast, diverse sequence space, much of which remains unexplored. Only relatively recently have powerful “omics” and bioinformatics tools allowed researchers to catalogue microbial nucleic acids and proteins and organise them into metabolic pathways and functions. However, most current research on microbial metabolic pathways is not focused on food applications.
Proposed solutions
- Strategies for genome mining and molecular manipulation developed by scientists investigating natural products for pharmaceutical candidates could be adapted directly to identify microbial sequences that could produce molecules that mimic key animal molecules.
- In addition to finding animal-free analogues, mining microbial sequence space also promises to discover entirely new food ingredients. Mining microbial sequences for novel biosynthetic capabilities is part of bioprospecting, a mature field of computational biology that has demonstrated success in various biotechnological applications, such as drug discovery and the development of industrial enzymes.
- For alternative proteins, if the desired functionality is known but not a molecular name or structure, computational strategies established by natural product bioprospectors can help identify candidate molecules that achieve that functionality. A similar approach is currently being used by food ingredient companies Shiru and Motif.
- One particularly rich potential sequence space with untapped potential is metagenomic information: sequences containing unidentified or perhaps uncultivable organisms from microbial consortia. Computational mining of metagenomes will allow for the discovery of entirely new catalytic molecules and pathways for target synthesis.
- Creating open access microbial sequence information repositories: Most current research on microbial metabolic pathways is not focused on food applications, though interest in this area is growing.
- Comprehensive repositories of genomic, proteomic, and metabolomic information for microorganisms are available, including databases for microbial natural products and omics tools for food applications built with databases such as KEGG and ATLAS (which are general metabolic repositories that describe biochemical reaction steps for reconstructing microbial metabolic pathways). To improve depth of exploration of microbial sequence space and identification of potential candidate molecules, as well as biosynthetic pathways suitable for commercial-scale production, increased availability of publicly-accessible computational resources specifically tailored to food molecule applications is imperative.