Determination of the microbial community in Amazonian cocoa bean fermentation by Illumina-based metagenomic sequencing

High-throughput DNA sequencing (HTS) was used to investigate the microbial community of cocoa bean spontaneous fermentation in the Amazon biome. The characterization was described in three localities from Para state (Amazon biome) and one locality from Bahia state, the top Brazilian state for cocoa production, for comparison of the microbial community structure. The microbial community profile was determined through a metagenomics approach using the Illumina HiSeq platform. Our data showed that the microbial community is composed of a consortium consisting of yeast (i.e., Pichia and Candida), filamentous fungi (i.e., Aspergillus, Penicillium and Fusarium), lactic acid bacteria (i.e., Leuconostoc, Lactococcus, and Lactobacillus), acetic acid bacteria (i.e., Acetobacter and Gluconobacter), enterobacteria and bacilli. Interestingly, Acetobacter pasteurianus was found in higher relative abundance than expected, and three acetic acid bacteria species were identified for the first time in cocoa fermentation (i.e., Komagataeibacter hansenii, Roseomonas sp. and Acidisphaera sp.). Some microorganisms were only detected in Amazonian cocoa and not detected in Bahia cocoa, including six yeast species (i.e., Starmerella bacillaris, Candida temnochilae, Zygosaccharomyces bailii, Candida glabrata, Saccharomycopsis crataegensis and Saccharomycopsis amapae) and seven lactic acid bacteria (i.e., Lactococcus lactis, Fructobacillus pseudoficulneus, Weissella confusa, Pediococcus pentosaceus, Lactobacillus reuteri, Lactobacillus murinus and Lactobacillus pontis). This study provides the first description of the microbiome in cocoa fermentation from the Amazon region, and these data open new perspectives for exploring these microorganisms in biotechnology applications, as well as their use as a starter culture to obtain high-quality cocoa beans.