Dissecting industrial fermentations of fine flavour cocoa through metagenomic analysis

Abstract

The global demand for fine-flavour cocoa has increased worldwide during the last years. Fine-flavour cocoa offers exceptional quality and unique fruity and floral flavour attributes of high demand by the world's elite chocolatiers. Several studies have highlighted the relevance of cocoa fermentation to produce such attributes. Nevertheless, little is known regarding the microbial interactions and biochemistry that lead to the production of these attributes on farms of industrial relevance, where traditional fermentation methods have been pre-standardized and scaled up. In this study, we have used metagenomic approaches to dissect on-farm industrial fermentations of fine-flavour cocoa. Our results revealed the presence of a shared core of nine dominant microorganisms (i.e. Limosilactobacillus fermentum, Saccharomyces cerevisiae, Pestalotiopsis rhododendri, Acetobacter aceti group, Bacillus subtilis group, Weissella ghanensis group, Lactobacillus_uc, Malassezia restricta and Malassezia globosa) between two farms located at completely different agro-ecological zones. Moreover, a community metabolic model was reconstructed and proposed as a tool to further elucidate the interactions among microorganisms and flavour biochemistry. Our work is the first to reveal a core of microorganisms shared among industrial farms, which is an essential step to process engineering aimed to design starter cultures, reducing fermentation times, and controlling the expression of undesirable phenotypes.

Functional yeast starter cultures for cocoa fermentation

“…Always considered as a single microbial group because of their many common activities during food fermentation processes, yeasts appear in a relatively high species diversity during cocoa fermentation (Agyirifo et al, 2019; Almeida et al, 2019; Arana‐Sánchez et al, 2015; Ardhana & Fleet, 2003; Crafack et al, 2013; Daniel et al, 2009; Delgado‐Ospina et al, 2020; Díaz‐Muñoz et al, 2021; Fernández‐Niño et al, 2021; Hamdouche et al, 2015, 2019; Ho et al, 2014, 2015; Illeghems et al, 2012; Jespersen et al, 2005; Koné et al, 2016; Lagunes Gálvez et al, 2007; Lima et al, 2021; Maura et al, 2016; Meersman et al, 2013; Miguel et al, 2017; Moreira et al, 2013, 2017; Mota‐Gutierrez et al, 2018; Nielsen et al, 2005, 2007; Ouattara & Niamké, 2021; Pacheco‐Montealegre et al, 2020; Papalexandratou & De Vuyst, 2011; Papalexandratou, Falony, et al, 2011; Papalexandratou et al, 2019; Papalexandratou et al, 2013; Pereira et al, 2012; Ramos et al, 2020; Samagaci et al, 2016; Serra et al, 2019; Verce et al, 2021; Visintin et al, 2016). In decreasing order of relative abundance, Pichia , Hanseniaspora , Saccharomyces and Candida are the most commonly found genera involved in cocoa fermentation, representing an even greater species diversity.…”

Unraveling potential enzymes and their functional role in fine cocoa beans fermentation using temporal shotgun metagenomics

“…168, Limosilactobacillus fermentum IFO 3956 and Acetobacter aceti were used to build a metabolic pathway for L-leucine, L-phenylalanine, L-tyrosine. L-tryptophan, valine, and L-threonine showing that these amino acids are crucial as flavor and odor precursors and bioactive compounds in fine cocoa ( Fernández-Niño et al, 2021 ).…”

Microbes of traditional fermentation processes as synthetic biology chassis to tackle future food challenges

“…by metabolomics), and their ecology (Lavefve et al, 2019). With Next Generation Sequencing techniques being available to the majority of researchers, systematic studies of fermentative cultures are becoming more frequent (Pswarayi and Ganzle, 2019;Weckx et al, 2019;Arikan et al, 2020;Comasio et al, 2020;Fernandez-Nino et al, 2021).…”