This work aimed at studying the unconfirmed hypothesis predicting the existence of a connection between coffee farm microbiome and the resulting spontaneous fermentation process. Using Illumina-based amplicon sequencing, 360 prokaryotes and 397 eukaryotes were identified from coffee fruits and leaves, over-ripe fruits, water used for coffee de-pulping, depulped coffee beans, soil, and temporal fermentation samples at an experimental farm in Honduras. Coffee fruits and leaves were mainly associated with high incidence of Enterobacteriaceae, Pseudomonas, Colletotrichum, and Cladosporium. The proportion of Enterobacteriaceae was increased when leaves and fruits were collected on the ground compared to those from the coffee tree. Coffee farm soil showed the richest microbial diversity with marked presence of Bacillus. Following the fermentation process, microorganisms present in depulped coffee beans (Leuconostoc, Gluconobater, Pichia, Hanseniaspora, and Candida) represented more than 90% of the total microbial community, which produced lactic acid, ethanol, and several volatile compounds. The community ecology connections described in this study showed that coffee fruit provides beneficial microorganisms for the fermentation process. Enterobacteria, Colletotrichum, and other microbial groups present in leaves, fruit surface, over-ripe fruits, and soil may transfer unwanted aromas to coffee beans, so they should be avoided from having access to the fermentation tank.

中文翻译：

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设施特定的“房屋”微生物组确保将功能性微生物群落维持在咖啡豆发酵中：对源跟踪的影响

这项工作旨在研究未经证实的假设，该假设预测咖啡农场微生物组与由此产生的自发发酵过程之间存在联系。在洪都拉斯的一个实验农场，使用基于 Illumina 的扩增子测序，从咖啡果实和叶子、过熟的果实、用于咖啡脱浆的水、脱浆的咖啡豆、土壤和临时发酵样品中鉴定出 360 种原核生物和 397 种真核生物。咖啡果实和叶子主要与肠杆菌科、假单胞菌属、炭疽菌属和枝孢菌属的高发病率有关. 与咖啡树相比，在地上采集叶子和果实时，肠杆菌科细菌的比例增加。咖啡农场土壤显示出最丰富的微生物多样性，其中显着存在芽孢杆菌。在发酵过程之后，脱浆咖啡豆中存在的微生物（明串珠菌属、葡糖菌属、毕赤酵母属、汉森氏菌属和念珠菌属）占整个微生物群落的 90% 以上，这些微生物群落会产生乳酸、乙醇和几种挥发性化合物。本研究中描述的群落生态联系表明，咖啡果实为发酵过程提供了有益的微生物。肠杆菌，炭疽菌和其他存在于叶子、果实表面、过熟果实和土壤中的微生物群可能会将不需要的香气转移到咖啡豆中，因此应避免它们进入发酵罐。