Multiomics analysis reveals microbial diversity and activity through spontaneous fermentation of Theobroma cacao

To gain insight into the active microbiota during spontaneous fermentation of <i>Theobroma cacao</i> L., this study assessed protein diversity during 120 h using a combined metabarconding and metaproteomics approach. During the first days of fermentation, most of the peptides were associated with <i>T. cacao</i> and yeast (0-72 h). Peptides associated with bacteria became more abundant after 72 h of fermentation, coinciding with a decrease in peptides associated with cocoa (96-120 h). In addition to the known microorganisms involved in fermentation, such as <i>Saccharomyces</i>, <i>Lactobacillus</i> and <i>Acetobacter</i>, novel genera were also metabolically active, including <i>Microvirga</i>, <i>Inquilinus</i>, <i>Candolleomyces</i> and <i>Lasiodiplodia</i>.. The results showed a consistency in the main genera detected by both techniques, but the identification of unexplored genera such as <i>Inquilinus</i>, <i>Microvirga</i>, <i>Cyphellophora</i> and <i>Ashbya gossypii</i>, among others, suggests that this omics approach needs to be used together for more comprehensive results on spontaneous fermentation. In conclusion, studies combining techniques such as metabarcoding and metaproteomics should be considered in fermentation studies, as a single technique would result in omissions regarding the activity of certain microorganisms that may be important for the course of spontaneous fermentation.