Microbial drivers of coffee flavor formation: linking fermentation ecology with roasting conversion

The fermentation of coffee has long been regarded principally as a practical step for mucilage removal, and microorganisms have frequently been described as auxiliary participants rather than central drivers of flavor development. This standpoint is increasingly difficult to maintain. Evidence from multi-omics studies and research on microbial interactions indicates that fermenting microbial communities are involved not only in substrate decomposition and basic metabolic conversion but also in the formation of flavor-active compounds and their precursors through cross-feeding, metabolic division of labor, and other cooperative processes. Hence, the fermentation process in coffee should be regarded as an active stage in flavor production instead of a passive post-harvest treatment. The present review compiles recent advances on coffee fermentation and roasting, with special emphasis on how flavor is formed in both stages. We focus on the cooperative roles played by yeasts, lactic acid bacteria, and Bacillus species, which can form relatively stable metabolic networks and thus affect the accumulation of esters, ketones, organic acids, and related precursor molecules. The transformation of fermentation-derived metabolites during roasting is also examined, especially their conversion via the Maillard reaction, Strecker degradation, and caramelization. From this perspective, a conceptual framework linking microorganisms, flavor precursors, and roasting-derived products is proposed to describe the major pathways of flavor formation during fermentation and roasting. In this context, three types of regulatory modes are discussed: positive regulation, suppression of undesirable metabolites, and precursor enhancement. This review also considers future opportunities for more precise flavor control through the rational design of cooperative microbial consortia, synthetic biology-assisted strategies, and intelligent process management, while noting the practical difficulties that still exist for industrial application. Taken together, these advances support a more integrated understanding of coffee flavor formation and thus provide a useful foundation for the directed modulation of flavor in coffee processing.