SynBioFooDB: a comprehensive resource for synthetic biology-driven food biomanufacturing

Abstract

Enabled by synthetic biology and metabolic engineering, microbial biomanufacturing is reshaping the production of food-related compounds by offering sustainable alternatives to resource-intensive extraction and conventional chemical synthesis. However, information linking food-related compounds to biosynthetic pathways and microbial biomanufacturing evidence remains fragmented across the literature and poorly represented in existing food-oriented resources, hindering cross-study comparison, evidence synthesis, and rational design of microbial production systems. Here, we present SynBioFooDB (https://synbiofoodb.biodesign.ac.cn/), a knowledgebase dedicated to synthetic biology-driven food biomanufacturing. SynBioFooDB integrates 74 237 food-related compounds with standardized chemical identities and annotations covering food occurrence, bioactivity, toxicity, and regulatory information. It further provides expert-curated biomanufacturing evidence for 1054 compounds from 5592 publications, linking microbial hosts, substrates, genetic modifications, and quantitative production metrics through structured and traceable records. The database also contains 2002 literature-reported biosynthetic pathways for 971 compounds, enabling comparison of alternative precursors, enzyme combinations, and pathway architectures. For compounds without literature-reported pathways, SynBioFooDB provides computationally predicted candidate pathways to facilitate pathway prioritization and experimental evaluation. By integrating compound-level context, biomanufacturing evidence, and biosynthetic pathway information, SynBioFooDB supports systematic exploration, comparison, and rational design of microbial production strategies for food-related compounds.