Universidade de São Paulo - Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Brazil.
Food Research Center, Universidade de São Paulo - Faculdade de Ciências Farmacêuticas, Brazil.
Food Res Int. 2020 May;131:109034. doi: 10.1016/j.foodres.2020.109034. Epub 2020 Jan 27.
Cocoa fermentation is a spontaneous process shaped by a variable microbial ecosystem which is assembled due to cross-feeding relationship among yeasts and bacteria, resulting in a synchronized microbial succession started by yeasts, followed by lactic acid bacteria (LAB) and finalized by acetic acid bacteria (AAB). Several studies have indicated the effect of microbial interactions in food ecosystems highlighting the importance of quorum sensing (QS) in bacterial adaptation in harsh environments modulating several phenotypes such as biofilm formation, tolerance to acid stress, bacteriocin production, competence, morphological modifications, motility, among others. However, antagonic interactions also occur, and can be marked by Quorum Quenching (QQ) activity, negatively impacting QS regulated phenotypes. Our current knowledge regarding microbial cocoa composition and functioning is based on culture-based analysis and culture-independent PCR-based methods. Therefore, we set out to investigate the application of metagenomics analysis on a classical spontaneous cocoa fermentation in order to describe: (I) the microbial taxonomic composition; (II) the functional potential of the cocoa microbiome; (III) the microbiome putative QS potential; and (IV) the microbiome QQ potential. Both aims III and IV are related to the expression of effectors that may confer advantageous traits along fermentation which can explain their dominance in specific time zones during the entire process. We have observed a bacterial succession shaped by yeasts and filamentous fungi and then Enterobacteriaceales, LAB and AAB, as well as a diverse genetic metabolic potential related to proteins and carbohydrates metabolism associated to the yeast Saccharomyces cerevisiae and members of the Enterobacteriaceales order and LAB and AAB groups. In addition, in silico evidences of interspecific QS arsenal were found in members of the genera Enterobacter, Lactobacillus, Bacillus and Pantoea, while inferences of intraspecific QS potential were found in the members of the genera Bacillus, Enterobacter, Komagataeibacter, Lactobacillus and Pantoea. In addition, a QQ potential was detected in Lactobacillus and in AAB members. These findings indicate that QS and QQ may modulate bacterial dominance in different time points during fermentation, along with cross-feeding, being responsible for their maintenance in a large time range.
可可发酵是一个自发的过程，由一个可变的微生物生态系统塑造，这个生态系统是由于酵母和细菌之间的交叉喂养关系而组装在一起的，导致一个由酵母开始的同步微生物演替，随后是乳酸菌（LAB），最后是醋酸菌（AAB）。几项研究表明，微生物相互作用在食品生态系统中的影响突出了群体感应（QS）在细菌适应恶劣环境中的重要性，调节了生物膜形成、耐酸应激、细菌素产生、感受态、形态修饰、运动等多种表型。然而，拮抗相互作用也会发生，并可能由群体感应淬灭（QQ）活性标记，对 QS 调节的表型产生负面影响。我们目前对微生物可可组成和功能的了解是基于基于培养的分析和基于培养的 PCR 方法。因此，我们着手研究宏基因组分析在经典自然可可发酵中的应用，以描述：（I）微生物分类组成；（II）可可微生物组的功能潜力；（III）微生物组潜在的 QS 潜力；和（IV）微生物组的 QQ 潜力。目标 III 和 IV 都与效应子的表达有关，这些效应子可能在发酵过程中赋予有利的特性，从而解释它们在整个过程中特定时间点的优势。我们观察到一个由酵母和丝状真菌然后肠杆菌科、LAB 和 AAB 塑造的细菌演替，以及与酵母酿酒酵母和肠杆菌科、LAB 和 AAB 组的成员相关的蛋白质和碳水化合物代谢的多样化遗传代谢潜力。此外，在属 Enterobacter、Lactobacillus、Bacillus 和 Pantoea 的成员中发现了种间 QS 武器库的计算机证据，而在属 Bacillus、Enterobacter、Komagataeibacter、Lactobacillus 和 Pantoea 的成员中发现了种内 QS 潜力的推断。此外，在 LAB 和 AAB 成员中检测到了 QQ 潜力。这些发现表明，QS 和 QQ 可能在发酵过程中的不同时间点调节细菌的优势，同时还与交叉喂养一起，使它们在很长一段时间内得以维持。
