A defined microbial community reproduces attributes of fine flavour chocolate fermentation

Cocoa (Theobroma cacao L.) bean fermentation is a spontaneous process involving interactions between abiotic and biotic factors that contribute to the final flavours of chocolate. Understanding these underlying interactions could enable desired flavour profiles to be reproduced under controlled conditions. Here, using bean fermentation samples from Colombian farms, we established that pH, temperature and microbiota composition, including both bacteria and fungi, influence key flavour attributes of premium chocolate. Genome-resolved metagenomics revealed that metabolic traits necessary for the development of the flavour profile of chocolate are redundantly present in the fermentation microbial community. Using a defined and metabolically competent microbial consortium, the feasibility of replicating fine flavour attributes of chocolate under controlled conditions was confirmed via omics, metabolic networks and a trained tasting panel. Our results provide the basis for the design of fermentation starters to robustly reproduce fine chocolate characteristics. An in-depth microbiological and metagenomic analysis of Colombian farm and fermentation facilities resulted in the design of a defined microbial community that can reproduce the flavour of fine chocolate.

• Publication year

  2025

• Venue

  Nature Microbiology

• Publication date

  2025-08-18

• Fields of study

  Biology, Medicine, Environmental Science

• Identifiers
  DOI 10.1038/s41564-025-02077-6PMID 40825855PMCID 12408344
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

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