Colombian cocoa is recognized as fine and aromatic cocoa by the ICCO, a category that represents only 5% of global production. Its organoleptic characteristics depend on genetics, the agroecological niche, and post-harvest processes such as fermentation, where microbial activity generates flavor precursors. Although significant progress has been made in understanding these processes, gaps remain in how to optimize them for the reproducible production of fine cocoa. This research explores the interaction between gene expression in the cocoa seed and its microbiome during fermentation, as well as the contribution of microbial metabolic pathways to the sensory profile of chocolate. Controlled fermentations were conducted using fruits from local hybrids and regional varieties from four agroecological regions of Arauca, Colombia. Samples were collected at 0, 24, and 48 hours from both the seeds and the pulp microbiome, and RNA was extracted for gene expression analysis through metatranscriptomics. Using rRNA, active microorganisms in the seed and pulp of the cocoa bean were identified. The most abundant genera in the seeds were Cutibacterium, Pseudomonas, Periweisella, and Limosilactobacillus, while in the pulp, Enterobacter, Erwinia, Pantoea, Limosilactobacillus, Leuconostoc, Granulibacter, and Acetobacter were predominant. Additionally, overexpressed genes in Theobroma cacao were identified, related to vicilin degradation, terpene and flavonoid biosynthesis, germination, and senescence-processes crucial to flavor development. Furthermore, key metabolic pathways were found in the pulp microbiome, including the Ehrlich pathway, phenylalanine metabolism, sugar fermentation, amino acid and protein biosynthesis, butanoate metabolism, and ester biosynthesis. These pathways are involved in the production of metabolites associated with fine flavor and aroma notes, such as 3-methylbutanal, phenylacetaldehyde, acetaldehyde, ethanol, acetate, pyrazine precursors, furanones, pyrroles, lactate, ethyl acetate, butyl acetate, hexyl acetate, acetoin, 2,3-butanediol, and benzaldehyde. In conclusion, our results provide key insights into microbial dynamics and their impact on cocoa’s sensory quality. This study contributes to the development of strategies to optimize fermentation and standardize fine cocoa production, ultimately benefiting producers.

Funding: This research is developed within the framework of the project led by AGROSAVIA and financed with resources from the Colombia’s General Royalties System (SGR).Acknowledgements: We express our sincere gratitude to Dr. Sebastián Escobar for his leadership in the framework of the General Royalties System-funded project, whose support was essential for the development of this research.