Dual effects of complex fermentation on wild tomato products: Flavor diversification and functional enrichment

• Spontaneous and complex fermentation of wild-type tomatoes improved nutritional composition, polyphenol transformation, and lycopene stability. • Integration of physicochemical, microbial, and metabolomic analyses elucidated fermentation-driven metabolic remodeling and microbial succession. • Complex fermentation incorporating ginger, garlic, and chili promoted higher antioxidant and anti-inflammatory capacities through phytochemical–microbe interactions. • The study establishes an ingredient-driven, sustainable fermentation strategy for developing additive-free, plant-based functional foods with enhanced flavor and functionality. This study investigates the impact of spontaneous complex fermentation on the nutritional, sensory, and microbial characteristics of wild-type tomato (WT) products. Two fermentation strategies were compared: single spontaneous fermentation (WT) and spontaneous complex fermentation (WTC) involving ginger, garlic, and chili. The WTC samples demonstrated a more consistent elevation in polyphenol and flavonoid contents, as well as enhanced lycopene stability throughout the fermentation process. These changes corresponded with increased antioxidant and anti-inflammatory activities, particularly during the late fermentation stages. Untargeted metabolomic analysis revealed that spontaneous complex fermentation activated diverse pathways, including those related to amino acid metabolism, organic acid biosynthesis, and phenylpropanoid metabolism, supporting polyphenol biotransformation. Microbial community analysis further indicated that WTC fermentation led to greater microbial community modulation, characterized by increased diversity and the stable establishment of lactic acid bacteria. These findings underscore the potential of spontaneous fermentation as a sustainable strategy for developing plant-based functional foods by enhancing bioactive compound profiles, promoting microbial stability, and enriching flavor complexity without the use of synthetic additives.