This review provides an overview of the application of next-generation sequencing (NGS) technologies for microbiome analysis of cocoa beans fermentation. The cocoa-producing regions where NGS has been applied include Brazil, Ghana, Ivory Coast, Cameroon, Nicaragua, and Colombia. The data collected were processed by principal component analysis (PCA) and Venn diagrams to perform a multivariate association between microbial diversity and cocoa-producing regions. NGS studies have confirmed the dominance of three major microbial groups revealed by culture-dependent approaches, i.e., lactic acid bacteria, acetic acid bacteria, and yeasts. However, a more complex microbial diversity has been revealed, comprising sub-dominant populations, late-growing species, and uncultivable microorganisms. A total of 99 microbial genera and species were for the first time reported in cocoa beans fermentation, such as Brevibacillus sp., Halomonas meridiana, Methylobacterium sp., Novosphingobium sp., and Paenibacillus pabuli. PCA and Venn diagrams showed that species composition is rarely fixed and often experiences fluctuations of varying degrees and at varying frequencies between different cocoa-producing regions. Understanding these differences will provide further directions for exploring the functional and metabolic activity of rare and abundant taxa, as well as their use as starter cultures to obtain high-quality cocoa beans.

Graphic abstract

中文翻译：

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全球可可发酵微生物组：通过下一代测序技术揭示新的分类群和微生物功能

本综述概述了新一代测序 (NGS) 技术在可可豆发酵微生物组分析中的应用。已应用 NGS 的可可产区包括巴西、加纳、科特迪瓦、喀麦隆、尼加拉瓜和哥伦比亚。收集的数据通过主成分分析 (PCA) 和维恩图进行处理，以在微生物多样性与可可产区之间进行多变量关联。NGS 研究证实了依赖培养的方法所揭示的三个主要微生物群的优势，即乳酸菌、醋酸菌和酵母菌。然而，已经揭示了更复杂的微生物多样性，包括次优势种群、晚生物种和不可培养的微生物。Brevibacillus sp.、Halomonas meridiana、Methylobacterium sp.、Novosphingobium sp. 和Paenibacillus pabuli。PCA 和维恩图表明，物种组成很少是固定的，并且在不同的可可产区之间经常经历不同程度和不同频率的波动。了解这些差异将为探索稀有和丰富类群的功能和代谢活动以及将它们用作获得优质可可豆的起始培养物提供进一步的方向。

图形摘要