Institut für Systembiotechnologie

Microbial systems biology of natural cocoa fermentation – the key to the beloved chocolate aroma

Good chocolate is among the world’s most beloved foods, which is why scientists are seeking worldwide to improve the product, and enhance the world’s pleasure. In a team of researchers from Germany and Switzerland —the heartland of fine chocolate— we have embarked upon a quest to better understand natural cocoa fermentation, the key process for the development of chocolate aroma. Particularly, we focus on the microbial communities during the fermentation of cocoa beans, and we use 13C metabolic flux analysis to unravel their metabolic role and contribution during the complex process. For this purpose, we simulate cocoa pulp fermentation in the laboratory and map metabolic pathway fluxes of the microorganisms involved: lactic acid bacteria, acetic acid bacteria and yeasts, feeding them specific isotopes that can easily be tracked. In the future the enhanced understanding of natural cocoa fermentation should enable more efficient fermentations. The project is a collaboration with the Nestlé Research Center, the heart of scientific research within Nestlé, the world’s leading nutrition, health and wellness company.


  • Novel approaches for the analysis of metabolites and fluxes in complex fermentation processes
  • Metabolic fluxes in lactic acid bacteria, acetic acid bacteria and yeasts
  • Understanding of carbon cross talk and further interactions within the microbial consortia


Schwechheimer, SK, Becker, J, Wittmann, C (2018) Towards better understanding of industrial cell factories: novel approaches for 13C metabolic flux analysis in complex nutrient environments. Curr. Opin. Biotechnol. 54:128-137. Link.

Adler P, Bolten CJ, Dohnt K, Hansen CE, Wittmann C (2013) Core fluxome and metafluxome of lactic acid bacteria under simulated cocoa pulp fermentation conditions. Appl Environ Microbiol. 79: 5670-5681. Link.

Adler P, Frey LJ, Berger A, Bolten C J, Hansen C E, Wittmann C (2014) The key to acetate: Metabolic fluxes of acetic acid bacteria under cocoa pulp fermentation simulating conditions. Appl. Environ. Microbiol. In press. Link.