Overview on the mechanisms of coffee germination and fermentation and their significance for coffee and coffee beverage quality.

Quality of coffee is a complex trait and is influenced by physical and sensory parameters. A complex succession of transformations during the processing of seeds to roasted coffee will inevitably influence the in-cup attributes of coffee. Germination and fermentation of the beans are two bioprocesses that take place during post-harvest treatment, and may lead to significant modifications of coffee attributes. The aim of this review is to address the current knowledge of dynamics of these two processes and their significance for bean modifications and coffee quality. The first part of this review gives an overview of coffee germination and its influence on coffee chemistry and quality. The germination process initiates while these non-orthodox seeds are still inside the cherry. This process is asynchronous and the evolution of germination depends on how the beans are processed. A range of metabolic reactions takes place during germination and can influence the carbohydrate, protein, and lipid composition of the beans. The second part of this review focuses on the microbiota associated with the beans during post-harvesting, exploring its effects on coffee quality and safety. The microbiota associated with the coffee cherries and beans comprise several bacterial, yeast, and fungal species and affects the processing from cherries to coffee beans. Indigenous bacteria and yeasts play a role in the degradation of pulp/mucilage, and their metabolism can affect the sensory attributes of coffee. On the other hand, the fungal population occurring during post-harvest and storage negatively affects coffee quality, especially regarding spoilage, off-tastes, and mycotoxin production.