Metagenomic studies about cocoa fermentation have mainly reported on the analysis of short reads for determination of Operational Taxonomic Units. However, it is also important to determine MAGs, which are genomes deriving from the assembly of metagenomics. For this research, all the cocoa metagenomes from public databases were downloaded, resulting in five datasets: one from Ghana and four from Brazil. Besides,
in silico
approaches were used to describe putative phenotypes and metabolic potential of MAGs. A total of 17 high-quality MAGs were recovered from these microbiomes, as follows: (i) fungi -
Yamadazyma tenuis
(n=1); (ii) lactic acid bacteria -
Limosilactobacillus fermentum
(n=5),
Liquorilactobacillus cacaonum
(n=1)
, Liquorilactobacillus nagelli
(n=1),
Leuconostoc pseudomesenteroides
(n=1) and
Lactiplantibacillus plantarum
subsp.
plantarum
(n=1); (iii) acetic acid bacteria -
Acetobacter senegalensis
(n=2) and
Kozakia baliensis
(n=1) and (iv)
Bacillus subtilis
(n=1)
Brevundimonas
sp. (n=2) and
Pseudomonas
sp. (n=1). Medium-quality MAGs were also recovered from cocoa microbiomes, including some detected for the first time in this environment (
Liquorilactobacillus vini
,
Komagataeibacter saccharivorans
and
Komagataeibacter maltaceti
) and other previously described (
Fructobacillus pseudoficulneus
and
Acetobacter pasteurianus
). Taken all together, the MAGs were useful to provide an additional description of the microbiome of cocoa fermentation, revealing previously overlooked microorganisms, with prediction of key phenotypes and biochemical pathways.
Importance
The production of chocolate starts with the harvesting of cocoa fruits and the spontaneous fermentation of the seeds, in a microbial succession that depends on yeasts, lactic acid bacteria and acetic acid bacteria in order to eliminate bitter and astringent compounds present in the raw material, which will be further roasted and grinded to originate the cocoa powder that will enter the food processing industry. The microbiota of cocoa fermentation is not completely know, and yet it advanced from culture-based studies to the advent of Next Generation DNA sequencing, with the generation of a myriad of data, that need bioinformatic approaches to be properly analysed. Although the majority metagenomic of studies have been based on short reads (OTUs), it is also important to analyse entire genomes to determine more precisely possible ecological roles of different species. Metagenome-assembled genomes (MAGs) are very useful for this purpose, and in this paper, MAGs from cocoa fermentation microbiomes were described, as well the possible implications of their phenotypic and metabolic potentials are discussed.
Isolation and selection of microorganisms in cocoa fermentation