## 3 Results and Discussion
### Farm Microbiome
1 = Soil; 2 = Leaves collected from the ground; 3 = Fruits collected from the ground; 4 = Leaves collected from the coffee tree; 5 = Cherries collected from the coffee tree; 6 = Cherries before de-pulping; 7 = Over-ripe fruits; 8 = Depulped beans; 9 = Water used for de-pulping beans. Figure 2: Composition of bacteria (**A**) and fungi (**B**) from coffee farm samples. Only microorganisms with prevalence superior to 2% are showed. The complete list of minor microbial groups is reported in the Supporting Information (Table S1). High incidence of Enterobacteriaceaeaceae has already been reported in grape and coffee plantations [9; 10; 24]. In vineyards, this family is considered beneficial because they produce proteases, chitinases and glucanases, which make them excellent antagonistic microorganisms [25]. In addition, over 80% of the bacterial community of coffee fruits collected on the ground and over-ripe fruits was composed of Enterobacteriaceaeae and _Erwinia_, showing the ability of this group to secrete hydrolytic enzymes to support their growth on decaying organic matter [26]. However, these microorganisms are not undesirable in coffee fermentation, as a correlation analysis performed by [PERSON] et al. [9] showed that the main alcohols and esters produced from the course of the fermentation process were not associated with enterobacteria. In addition, Enterobacteriaceae are mainly associated formation of off-flavor metabolites, such as 3-isopropyl-2-methoxy-5-methylpyrazine, 2,3-butanediol and butyric acid [27]. _Leuconostoc_ was observed in the coffee cherries before de-pulping (53.48%), depulped beans (20.24%) and in the water used for de-pulping beans (25.60%) (Figure 2A). After harvesting, coffee fruits are usually placed in storage bags for a few hours until they are processed. During this period, micro-cracks can be generated in the fruit skin and several amino acids and phosphorylated carbohydrates present in the coffee pulp become accessible to the epiphyic microbiota of the cherries. The abundance of _Leuconostoc_ in these samples may be associated with its ability to produce a wide range of saccharolytic enzymes, as well as having an elaborate carbohydrate uptake system [7]. Shotgun metagenomic analysis of a coffee fermentation identified a gene that encodes hexose 6 phosphate: phosphate antiporter (_ulupT_). This transporter may favor _Leuconostoc_ proliferation since phosphorylated hexoses can be transported into bacterial cells without ATP consumption [7]. The coffee farm soil showed a rich and complex microbial diversity, with 214 bacterial groups (Table S1). The high diversity found in the soil was also observed in other coffee-producing regions, such as China, Ecuador, Mexico, Brazil, and Honduras [9; 10; 28; 29; 30]. However, most of the bacterial groups that have been identified in coffee farm soils (e.g., _Amycolatopsis_, _Bacillus_, _Bradyrhizobium_, _Pseudolabtrys_, _Rhodoplanes_, and _Splingomonas_) are not associated with the fermentation process, so it should be avoided from having access to the fermentation tank. Figure 3: Principal component analysis, based on Weighted UniFrac Distances, according to microbial diversity and abundance. (**A**) Bacterial analysis, (**B**) Fungal analysis. 1 = Soil; 2 = Leaves collected from the ground; 3 = Fruits collected from the ground; 4 = Leaves collected from the coffee tree; 5 = Cherries collected from the coffee tree; 6 = Cherries before de-pulping; 7 = Over-ripe fruits; 8 = Depulped beans; 9 = Water used for de-pulping beans; F0 = Fermentation (0 h). Interestingly, coffee leaves showed a relatively high population of _Lactococcus_ and _Lactobacillus_, which had not been reported so far. The ability of these strains to grow on leaves suggests that these microorganisms possess a metabolic versatility not yet explored, as LAB are auxotrophic for some amino acids and vitamins that are not bioavailable in coffee leaves [9; 10; 28; 29; 30; 31].