Coffee is the major export product of some countries such as Uganda, Burundi, Rwanda, and Ethiopia and is the second beverage widely consumed in the world. The international coffee trade involves about 500 million people in its management, from cultivation to the final consumption. Among some 100 species of the Coffea genus, only C . arabica and C . canephora are economically important worldwide. The basis of the coffee activity success relies on the adoption of good agricultural and processing practices. Harvesting is one of the most important steps that influences coffee quality. Harvesting coffee is particularly challenging because coffee fruit typically does not ripen uniformly. Almost all fine coffee is still picked selectively by hand. Coffee beans must be removed from the fruit and dried before they can be roasted; this can be done in two ways: natural (dry) and wet (washed) methods. Drying operation is the most important stage of the process affecting the final quality of the green coffee. In some regions or in certain years, coffee quality is inferior due to environmental conditions, mainly related to temperatures and relative humidity favoring the development of spoiled microorganisms (bacteria, fungi, and yeast) that had a negative impact on the quality of the coffee. However, some microorganisms like the genus Cladosporium and yeasts are associated with good quality beverages. In all processing methods (dry, wet, and semidry), the objectives of fermentation are to remove the mucilaginous layer rich in polysaccharides (pectin) and to reduce the water content present in the fruits. The fermentation process when well controlled ensures the development of microorganisms that give a high-quality beverage with good coffee aroma. In agricultural products, such as coffee, could have the development of the filamentous fungi and possible mycotoxin production. Coffee bean contamination with ochratoxin A (OTA) may occur throughout the entire production chain and is directly related to the care and quality of the crop management, harvest, postharvest storage, and type of roasting. The types of roasting and particle size interfere with the residual content of OTA in the beverage.
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