What a new Nature Microbiology study means for cocoa and how Computomics technology helps turn microbiomes into reproducible flavor.

Cocoa bean fermentation has always been variable. Cocoa growers and chocolate makers rely on spontaneous microbial activity, which can produce unique but inconsistent flavors. A new open-access study in Nature Microbiology demonstrates that a defined 9-member microbial community can reproduce fine-flavor chocolate attributes under controlled conditions. This marks a shift from observing fermentation to steering standardized, flavor-targeted processes.

From “who is there?” to “what are they doing?”
Early cocoa fermentation metagenomics mapped community diversity and already used MEGAN for taxonomic profiling (Illeghems et al., PLOS ONE, 2012). That work established the utility of shotgun sequencing and software-assisted interpretation in cocoa fermentation. It showed the surprising variety of yeasts, lactic acid bacteria, and acetic acid bacteria that shape fermentation outcomes and flavors. Today, we build on that foundation with genome-resolved and function-aware analyses that connect microbes to flavor chemistry and sensory outcomes.

How Computomics Technology helps

At Computomics, we build on this scientific foundation. Standardizing metagenomics pipelines with MEGAN and our bioinformatics platform MORPHEUS, we analyze microbial communities in detail: which species are present, what metabolic functions they perform, and how they interact, even over time. This information can be linked to sensory data and chemical measurements to understand how microbes contribute to chocolate’s aroma and taste.

Our approach can be applied to:

• Fermentation monitoring: tracking microbial dynamics across batches.
• Starter culture design: identifying core microbes and their functional roles.
• Quality assurance: detecting deviations early and ensuring consistency.
• Innovation: exploring how microbial variation leads to new flavor profiles.

         

Looking ahead:

Controlled microbial communities won’t replace the richness of origin-specific fermentations overnight, but they open up new possibilities: reproducible flavor design, tailored fermentation processes, and reduced waste. With robust microbiome analytics, chocolate producers can combine tradition with precision science to create consistent, high-quality products - and even design new flavor experiences.

References:
Gopaulchan D. et al. Nature Microbiology (open access). https://www.nature.com/articles/s41564-025-02077-6
Illeghems K. et al. PLOS ONE 2012. https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0038040