High-Sensitive Detection and Dynamic of Microbiome during Cocoa Bean Fermentation

Monitoring of the fermentation microbiome was carried out on selected farms in three agroecological zones from Colombia. Valles-Interandinos-Secos (VISe), Montaña-Santandereana (MoSa) and Cafetera-Marginal-Baja (CaMab), during two periods of 2016. Cocoa beans were collected from the upper and intermediate zones of wooden boxes for 4-6 days. The microbial community composition at the 97% OTU-level was similar in all fermentation systems, and the dynamics and interactions of the OTUs of bacteria and fungi follow a predictable microbial succession.