Coffee has a microbiome that alters flavor

Contributed by Bart Weimer:

A fuel that keeps people and science moving is coffee. Humans have had a fascination with coffee for over 9000 years! We have long recognized that coffee flavor is extremely different among regions f the world, but also by brewing method. The exact same coffee variety can have different flavors depending on the soil, cultivation elevation, region of the world, roasting method, extraction temperature, and contact with metal during the brewing process. The popularity of coffee has boomed in recent years. Until recently, the microbiome of coffee was not widely characterized. Most knew that it was a fermentation process that altered the flavor, but a recent study by Ludlow et al. (2016) demonstrated that the flavor can be manipulated and tracked based on the fungal microbiome. This is a great step forward in the coffee world since the industry largely depends on the native biota to ferment the beans right after harvest. This could enable use of starter cultures to alter the microbiome so that it can direct the community diversity. Ludlow et al. demonstrated that the microbiome of coffee (oh and by the way, cocao) is directed by Saccharomyces cerevisiae – the common bread yeast!! They also demonstrated the the genomic variation was distinct between regions of the world and aligned with human migration around the world as we trekked out of Africa. Since coffee is native to Ethiopia they postulated that humans distributed coffee and variations in the microbiome around the world and that the microbiome adapted to the new locals. As a coffee snob, this work is fascinating because it starts to describe a microevolution for a commodity that humans have persisted with for thousands of years.

Ludlow, Catherine L., Gareth A. Cromie, Cecilia Garmendia-Torres, Amy Sirr, Michelle Hays, Colburn Field, Eric W. Jeffery, Justin C. Fay, Aimée M. Dudley. 2016. Independent Origins of Yeast Associated with Coffee and Cacao Fermentation. Current Biology (

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