November 10, 2021, by Lexi Earl

Improving farmer livelihoods through better cocoa bean fermentation

We can support small farmers by using science to understand cocoa bean fermentation, ensuring more consistent beans, and better incomes, write David Salt, David Gopaulchan, and Gabriel Castrillo

Cocoa is a significant global commodity, generating income, export revenues, and employment for producing countries. Cocoa is grown across the equatorial belt, by some six million smallholder farmers worldwide, who in turn support between 40 and 50 million people. Cocoa farmers grow and then harvest the cocoa pods from cocoa trees, splitting them open to reveal oval-shaped beans encased in creamy white pulp. The beans are then placed into wooden fermentation boxes and left to ferment for five to seven days. Cocoa bean fermentation is a spontaneous process that reduces bitterness and astringency in the beans while stimulating desirable aroma and flavour production. The flavours of the beans continue to develop as they undergo a drying process before sorting and packing.

Beans in their fermentation box

Fermenting beans covered with palm leaves to prevent heat escaping.

The fermentation and drying processes typically occur on the cacao farm, and are crucial to the flavour and aroma of the beans, and ultimately the final chocolate products. However, there has not been an in-depth, systematic analysis to understand what happens at the molecular, biochemical, and environmental levels during these processes. Why do some fermentations result in complex chocolate flavours with rich aromas and secondary notes, and others not? The genetics of the cocoa tree (the Cocoa Research Centre (CRC) at the University of the West Indies has over 2400 varieties in their gene bank) and other environmental factors play a role, but what else contributes to flavour development during cocoa bean fermentation? With the growth of bean-to-bar, single origin chocolates, there is increasing interest in unlocking the mysteries of fermentation. If cocoa beans can produce various flavours, how might we tease these out to produce desirable flavours during the fermentation process?

A box filled with fermenting cocoa beans that are creamy white in colour. Cocoa bean fermentation is crucial to developing chocolate flavours.

Sampling the fermentation

But understanding how to ferment beans to produce high quality cocoa is also important for farmers and their livelihoods. Historically, we have understood fermentations to be either good or bad. If a farmer has a bad fermentation, they may have to settle for significantly reduced prices offered by buyers, or may even be unable to sell their beans at market. This financial loss would have huge impacts on the farmer’s livelihood. But there is the potential to understand fermentations along a much wider spectrum than the good/bad binary.

Colombia produces what is known as fine or flavour cocoa – this is cocoa that provides more complexity of flavour (including nutty, citrus, and floral aromas) that artisan chocolate makers desire. Since 2019 we have been working with three smallholder female farmers in Colombia to better understand the environmental factors and microorganisms that participate in the cocoa fermentation process and that are linked to the final chocolate flavour. Our researchers travelled to Colombia to take microbial samples from farms in Huila, Santander, and Antioquia, three cocoa growing regions well-known for their uniquely flavoured beans. Using hand-held Oxford Nanopore DNA sequencers, and working with the farmers, researchers sampled the trees (leaves and pods), soils, worker’s hands, the fermentation boxes, and the fermenting beans. They also took daily pH and temperature measurements.

Sampling the fermentation box in search of microbes

The harvested beans were shipped to Luisa’s Vegan Chocolates here in Nottingham, where they have been made into single origin bars. The flavour profile of both the beans and the chocolate they produced were tested by both researchers at the Cocoa Research Centre, and by customers at Luisa’s Vegan Chocolates. Sensory analysis of liquors made from the fermented beans conducted by a trained expert panel at the CRC demonstrated that the beans from each region produced distinct flavour profiles, ranging from spicy, nutty and fresh fruit flavours (Santander region) to brown fruits and floral notes (Huila region). Antioquia beans had predominately ‘cocoa’ notes with some auxiliary flavours. These differences in flavour were echoed by customers in Nottingham who reported soft citrus and red fruit flavours for one farm, and sweeter caramel notes with nutty overtones for another.

Finished chocolate bars, their beans and the cocoa nibs

Our researchers have been working to understand which microbes are present in the cocoa bean fermentation, how the environment affects their growth dynamics, and the role they play in flavour development. Using metagenomic analysis of the microbial communities during the fermentation, they have found high amounts of yeast, lactic acid bacteria, and enterobacteria at the start of fermentations. These then transition to mainly acetic acid producing microbes over time. The potential sources of these microbes from the surrounding environment have also been identified. Most interestingly, researchers found marked differences in the types and abundance of microbes between the three regions, which appeared to contribute to different flavours of the beans.

Understanding the fermentation process becomes even more important when we consider the challenges of climate change. Cocoa farmers are susceptible to changing weather patterns and unpredictable weather events that can affect the harvest, and then the fermentation and drying processes. If we can provide more information for the farmers on the fermentation, this gives them more potential control over the crop, and ultimately their livelihoods.

Further reading

(2020) Researching fermentation in cocoa. Future Food blog:

(2020) Doing science in the field: Stories from our Colombian cocoa project. Future Food blog:

(2019) Eating chocolate in the name of science. Future Food blog:

(2019) Hot chocolate! Making artisan chocolate taste even better. University of Nottingham News:

(2019) Science adds flavour to unique chocolate made in Nottingham. University of Nottingham News:


David E Salt is the Director of the University of Nottingham’s multi-million pound Future Food Beacon of Excellence and a Professor of Genome-Enabled Biology. He spent more than twenty years as an academic in the US, before returning to the UK to establish and lead the Centre for Genome Enabled Biology at the University of Aberdeen (2011 – 2016). In 2016 he started at the University of Nottingham. He has long term research interests to understand the function of the genes and gene networks that regulate the plant ionome [defined as the elemental composition of an organism, tissue or cell], along with the evolutionary forces that shape this regulation. Over his career he has obtained 38 competitive research awards totalling £17.8 million (equivalent from US, UK and EU funding), and published 176 peer-reviewed papers in journals such as NatureScience and PNAS that have been cited ~35,000 times (h-index = 88).

David Gopaulchan has a PhD in Biochemistry with expertise in genetics, genomics, molecular and cellular biology, and is a postdoctoral researcher with the Future Food Beacon. His research is focused on studying genetic diversity of cacao populations towards conservation, understanding sequestration of cadmium in cacao towards mitigation, and controlling microbial communities involved in cocoa fermentation to improve quality and flavour. His interest also spans exploiting natural cacao variation to improve cacao yields, developing resilience varieties, and using more sustainable agriculture production systems. Follow David Gopaulchan on Twitter: @DavidGopaulchan

Gabriel Castrillo is an Associate Professor in Plant Microbiome. Prior to this he was a Nottingham Research Fellow with the Future Food Beacon. He studied biochemistry (1995-2000) at Havana University, Cuba and completed his PhD (2004-2009) as a MAE-AECI fellow in the lab of Prof Javier Paz-Ares at the Spanish National Centre for Biotechnology. From 2009-2013, he was a Postdoctoral Fellow in the same institute, in the lab of Prof Antonio Leyva. He left Spain to undertake a second postdoc (2014-2018) at the University of North Carolina, Chapel Hill, USA, in the lab of Prof Jeff L. Dangl. He has published in Nature and Science.

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