Fermentation-induced molecular remodeling in African indigenous tubers: cassava and cocoyam

Cassava and cocoyam are major dietary staples in sub-Saharan Africa, commonly processed by natural fermentation before consumption. Although fermentation reduces antinutritional compounds and improves food quality, its molecular effects remain poorly characterized. We used untargeted mass spectrometry-based metabolomics with a computational annotation pipeline to compare fermentation-induced molecular remodeling in the two tubers, which showed distinct responses. In cassava, 718 of 773 significant features (92.9%) were decreased, indicating a predominantly catabolic process. In cocoyam, the response was more balanced, with 385 of 1013 features (38.0%) enriched, including di- and tripeptides consistent with proteolytic processing. Class analysis, molecular networking, and pathway enrichment against reference microbial models revealed tuber-specific signatures: in cassava, purine metabolism was the most enriched pathway and fatty acids were the chemical class that decreased the most relative to its overall metabolome, whereas cocoyam showed stronger enrichment of amino acid pathways. Cyanogenic glycoside-related features were decreased, consistent with detoxification. Biotransformation prediction also suggested putative fermentation products absent from current databases, highlighting the under-characterized chemistry of these tubers.