Coffee is one of the most popular non-alcoholic beverages across cultures and traditions. Packed with antioxidants and caffeine, coffee fights off oxidative stress and inflammation in the body, reduces the risk of type 2 diabetes, liver disease, and depression, and improves focus and alertness. While coffee is being relished globally, the role of microbes in producing this black drink is often overlooked, as explained by Arindam Mitra in this #FEMSmicroBlog. #MicrobiologyIsEverwhere
Coffee beans as the source for a bitter hot drink
The coffee plant Coffea is a tropical evergreen shrub that belongs to the Rubiaceae family. It thrives in warm climates, primarily in regions around the equator, such as Central and South America, Africa, and Asia.
The plant produces fruits, whose seeds are commonly known as coffee beans. The fruit, or so-called coffee cherry, usually contains two seeds, which are extracted, processed, and roasted to make the beverage we enjoy. Hence, only the seed of the coffee cherry is used to produce coffee, not the surrounding fruit.
The microbes involved in the coffee fermentation process
To make coffee, microbial communities and their metabolic activities play important roles in shaping its taste and aroma. Various microorganisms, including yeasts, bacteria, and fungi, secrete enzymes to break down the sticky mucilage layer surrounding the coffee beans.
Yeasts, such as Hanseniaspora uvarum and Pichia kudriavzevii, dominate the early to mid-stages, break down sugars, and produce compounds such as ethanol, lactic acid, and glycerol. They contribute significantly to mucilage degradation and start the fermentation process.
Lactic acid bacteria, such as Leuconostoc mesenteroides and Lactobacillus plantarum, appear in the mid-to-late stages of fermentation. The produced lactic acid lowers the pH which aids in the degradation process. These bacteria also make other metabolites like mannitol and glycerol.
Pectinolytic bacteria, such as Erwinia soli and Klebsiella pneumoniae, are less prevalent but still contribute to breaking down the pectin in the mucilage by producing pectate lyase. However, their activity is weaker compared to that of the yeasts.

Bacterial metabolites give coffee its final flavour
Together, microbes produce more than 700 volatile compounds which are responsible for coffee’s complex flavours. Hence, microbial diversity is essential for the quality of fermentation, as each species contributes a unique flavour and aroma to the final coffee product.
Ethanol and lactic acid give coffee its acidity and shape its overall sensory profile. Ethyl acetate and isoamyl acetate are esters produced by the yeasts Saccharomyces cerevisiae and Pichia kudriavzevii. These impart fruity and floral notes to the coffee, which even survive the roasting process. Isoamyl alcohol and benzyl alcohol contribute to the coffee’s complexity by adding winey and fruity aromas.
Different fermentation methods further unlock unique flavours. For example, during anaerobic fermentation, coffee cherries are fermented in sealed, oxygen-free tanks. This slows down microbial activity and allows the development of higher acidity and complex flavours through distinct fruity, floral, and wine-like notes.
In comparison, carbonic maceration involves fermenting coffee cherries in sealed CO₂-filled tanks. It promotes fermentation within the cherries, enhancing fruity and wine-like flavours. This technique produces a brighter, more complex flavour profile with enhanced acidity and floral notes.
Controlling coffee fermentation
When well-controlled, coffee fermentation produces the pleasant fruity, floral, or even caramel-like flavours that we enjoy so much. Yet, poor control can result in undesirable off-flavours like onion or stinky cheese.
To improve coffee quality, many coffee producers rely on starter cultures—selected strains of microbes with optimized fermentation activities. By introducing specific strains that perform well under various conditions and enhance flavour and aroma, they better control the fermentation process and ensure a consistently high-quality product.
This concept is similar to the ones used in other industries like wine, beer, and cheese production. As coffee science advances, using selected microbial strains, such as Lactobacillus plantarum, Saccharomyces cerevisiae, and Pichia fermentans, in the fermentation process only improves the quality and consistency of coffee at a global scale.
Coffee – another delicious microbial fermentation product
Coffee gives us another reason to be grateful to microbes as they play crucial roles in making this delicious and rejuvenating beverage. Much like when producing wine, cheese, or chocolate, microbes produce the unique flavours and aromas that make coffee so enjoyable.
- If you enjoyed the topic of this blog, find more research on microbes and coffee in the FEMS Journals.
About the author of this blog
Arindam Mitra is a Professor and the Dean of the School of Allied and Healthcare Professions at RV University in Bengaluru, India. He is an elected member of the Advisory Council of the Microbiology Society and holds additional roles as Society Champion, editorial board member for Microbiology Today, and member of the Sustainability and Impact and Influence Committees. His research focuses on infectious diseases, microbial biofilms, antimicrobial resistance (AMR), and vaccine development. He serves as an editor for PLOS One, the Canadian Journal of Infectious Diseases and Medical Microbiology, PeerJ Life and Environment, and Frontiers in Microbiology. Passionate about fostering collaborative learning, he strives to enhance education, research, and the societal impact of microbiology. In his leisure time, he enjoys a good cup of coffee.
About this blog section
The section #MicrobiologyIsEverywhere highlights the global relevance of microbiology. The section acknowledges that microbiology knows no borders, as well as the fact that microbiologists are everywhere and our FEMS network extends well beyond Europe. This blog entry type accepts contributions from excellent blogs translated into English. Regional stories with global relevance are welcomed. National or international events sponsored, organised or connected to FEMS are also covered.
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