Cacao fermentation microbiome

Cacao fermentation is a spontaneous process in which microorganisms play a key role in the development of distinctive chocolate flavors. The microbiota acting during cacao fermentation has been routinely characterized by cultured based techniques and next generation sequencing (NGS) using the Illumina platform. However, the potential of in situ sequencing technologies to monitor the microbial dynamics during cacao fermentation has not been assessed. Samples of cacao beans were taken at 0, 24, 48, 72, and 96 hours after the start of the fermentation. Total DNA was extracted, and sequencing libraries were prepared for further sequencing using Illumina and Nanopore MinION sequencing platforms. This is the first study assessing the applicability of MinION sequencing for the characterization of microbial populations during cacao fermentation.