Multiomics analysis reveals microbial diversity and activity through spontaneous fermentation of Theobroma cacao
Ynara da Costa Fonseca,
Celina Eugenio Bahule,
Hector Herrera,
Luiza Helena da Silva Martins,
Alessandra Santos Lopes,
Juliana Silva Cassoli,
Felipe Costa Trindade,
Isa Rebecca Chagas da Costa,
Paulo Henrique de Oliveira Costa,
Guilherme Oliveira,
Rafael Borges da Silva Valadares
Affiliations
Ynara da Costa Fonseca
Graduate Program in Agricultural Applied Biotechnology, Federal Rural University of Amazonia, President Tancredo Neves Ave, 2501, Belém, CEP 66.077-830, Brazil; Vale Institute of Technology, Boaventura da Silva Street 955, Belém, CEP 66050-090, Brazil
Celina Eugenio Bahule
Center of Studies in Science and Technology (NECET), Rovuma University, Niassa Branch, Lichinga, Mozambique
Hector Herrera
Departamento de Ciencias Forestales, Facultad de Ciencias Agropecuarias y Medioambiente, Universidad de La Frontera, Temuco, 4811230, Chile; Center for Biodiversity and Ecological Sustainability (C-BEST), Facultad de Ciencias Agropecuarias y Medioambiente, Universidad de La Frontera, Chile
Luiza Helena da Silva Martins
Institute of Animal Health and Production, Federal Rural University of Amazonia, President Tancredo Neves Ave., 2501, Belém, CEP 66077-830, Brazil
Alessandra Santos Lopes
Faculty of Food Engineering, Institute of Technology, Federal University of Pará, Belém, CEP 66075-110, Brazil
Juliana Silva Cassoli
Laboratory of Omics Sciences, Institute of Biological Sciences, Guamá Campus, Federal University of Pará, 66075-110, Belém, Brazil
Felipe Costa Trindade
Vale Institute of Technology, Boaventura da Silva Street 955, Belém, CEP 66050-090, Brazil
Isa Rebecca Chagas da Costa
Vale Institute of Technology, Boaventura da Silva Street 955, Belém, CEP 66050-090, Brazil
Paulo Henrique de Oliveira Costa
Vale Institute of Technology, Boaventura da Silva Street 955, Belém, CEP 66050-090, Brazil
Guilherme Oliveira
Vale Institute of Technology, Boaventura da Silva Street 955, Belém, CEP 66050-090, Brazil
Rafael Borges da Silva Valadares
Vale Institute of Technology, Boaventura da Silva Street 955, Belém, CEP 66050-090, Brazil; Corresponding author. Vale Institute of Technology Sustainable Development, Rua Boaventura da Silva 955, Umarizal, CEP 66055-090, Belém, PA, Brazil.
To gain insight into the active microbiota during spontaneous fermentation of Theobroma cacao 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 T. cacao 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 Saccharomyces, Lactobacillus and Acetobacter, novel genera were also metabolically active, including Microvirga, Inquilinus, Candolleomyces and Lasiodiplodia.. The results showed a consistency in the main genera detected by both techniques, but the identification of unexplored genera such as Inquilinus, Microvirga, Cyphellophora and Ashbya gossypii, 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.
