Coffee is an important crop that assures a sustainable economy to farmers in tropical regions. A dramatic concern for coffee production is currently represented by climate change, which threatens the survival of Coffea arabica
cultivation worldwide and imposes modifications of the agronomic practices to prevent this risk. The quality of coffee beans depends on optimized protocols of cultivation, ripe berries collection, and removal of the outer fruit layers by dry or wet processes and moisture reduction. Storage and shipment represent two steps where bean quality needs to be preserved by preventing fungal contamination that may impact the final product and form mycotoxins, mainly ochratoxin A. In this review, we describe the challenges faced by the coffee industry to guarantee quality from production to roasting and brewing. An overview of novel technologies, such as the application of starter cultures in fermentation and the exploitation of industrial enzymes in accelerating the process of flavour development in coffee beans, is given. Moreover, the results of studies on microbial populations on coffee and the differences found in fungi, yeasts and bacteria composition among the investigations, are summarized. In particular, this review describes new attempts to contain the development of mycotoxigenic fungi, through the application of antagonistic microorganisms such as S. cerevisiae
. The new wave of specialty coffees, i.e., those with a cupping score higher than 85/100, is also presented. It is shown how, through careful coffee production methods and controlled fermentation processes, coffee producers may increase their income by assuring high standards of quality and high added value for the coffee experience sector.
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