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| Comparison of the chemical compounds in the coffee bean samples of different processing steps of the Arabica coffee wet processing experiments. The selected compounds were present at either lower concentrations in the green coffee beans (GB) than in the corresponding soaking beans (SB) (A) or higher concentrations in the GB than in the corresponding SB (B). The selected bean samples represent the end of the fermentations (FB; ), before and after soaking (•), and their corresponding GB (⊗) across the different processing variants. The freshly demucilaged beans and the GB produced in the control processes (C, black) are also included. Only the chemical compounds with consistent trends are shown.

| Comparison of the chemical compounds in the coffee bean samples of different processing steps of the Arabica coffee wet processing experiments. The selected compounds were present at either lower concentrations in the green coffee beans (GB) than in the corresponding soaking beans (SB) (A) or higher concentrations in the GB than in the corresponding SB (B). The selected bean samples represent the end of the fermentations (FB; ), before and after soaking (•), and their corresponding GB (⊗) across the different processing variants. The freshly demucilaged beans and the GB produced in the control processes (C, black) are also included. Only the chemical compounds with consistent trends are shown.

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Post-harvest wet coffee processing is a commonly applied method to transform coffee cherries into green coffee beans through depulping or demucilaging, fermentation, washing, soaking, drying, and dehulling. Multiple processing parameters can be modified and thus influence the coffee quality (green coffee beans and cup quality). The present study ai...

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... temporal metabolomic profiles of the fermenting beans from the DM and DP processes were similar. The compounds targeted could be divided into four groups, based on the temporal change of their profiles, namely (i) an off-phase evolution (in the case of sucrose versus the monosaccharides glucose and fructose), (ii) a rising trend, (iii) a decreasing trend, and (iv) a relatively stable concentration along the fermentations (Figure 7 and Supplementary Figure S6A). Concerning the first group, the glucose concentrations in the fermenting beans always evolved in the same phase as those of fructose, but off-phase with those of sucrose. ...
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... the washing step, the concentrations of certain compounds decreased in the coffee beans (Figure 7 and Supplementary Figures S6B,C). For example, the concentrations of glucose, fructose, mannitol, and lactic acid decreased, especially in the DP processes. ...
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... PCA based on a correlation matrix included the metabolomic data of the FB and SB from the DM and DP processes (Supplementary Figure S7A). Two PCs were obtained, explaining 41% of the total variance. ...
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... to the start of drying, most metabolites tended to degrade during drying, with several exceptions (Figure 7 and Supplementary Figure S8). The corresponding GB contained lower concentrations of glycerol, fumaric acid, lactic acid, succinic acid, trigonelline, alanine, and tryptophan (Figure 7A), as well as higher concentrations of compounds such as isocitric acid, 4,5-diCQA, aspartic acid, GABA, glutamic acid, proline, and serine (p < 0.05) (Figure 7B). ...
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... to the start of drying, most metabolites tended to degrade during drying, with several exceptions (Figure 7 and Supplementary Figure S8). The corresponding GB contained lower concentrations of glycerol, fumaric acid, lactic acid, succinic acid, trigonelline, alanine, and tryptophan (Figure 7A), as well as higher concentrations of compounds such as isocitric acid, 4,5-diCQA, aspartic acid, GABA, glutamic acid, proline, and serine (p < 0.05) (Figure 7B). In the control processes, the concentrations of glucose, fructose, succinic acid, mannitol, lactic acid, and alanine did not show significant differences before and after the drying step. ...
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... to the start of drying, most metabolites tended to degrade during drying, with several exceptions (Figure 7 and Supplementary Figure S8). The corresponding GB contained lower concentrations of glycerol, fumaric acid, lactic acid, succinic acid, trigonelline, alanine, and tryptophan (Figure 7A), as well as higher concentrations of compounds such as isocitric acid, 4,5-diCQA, aspartic acid, GABA, glutamic acid, proline, and serine (p < 0.05) (Figure 7B). In the control processes, the concentrations of glucose, fructose, succinic acid, mannitol, lactic acid, and alanine did not show significant differences before and after the drying step. ...
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... GB produced from the control processes contained higher concentrations of glucose, fructose, citric acid, malic acid, asparagine, and aspartic acid than all the other GB processed from the DM and DP processes (Figure 7). In contrast, the concentrations of mannitol, succinic acid, lactic acid, alanine, tyrosine, proline, glutamic acid, and glutamine were higher in the DM and DP beans than in the control GB, whereas beans from the DP1 process had the highest concentrations of mannitol and lactic acid. ...
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... PCA based on a correlation matrix of the same dataset resulted in two PCs, explaining 42% of the total variance (Supplementary Figure S7B). PC1 was characterized by positive loadings of mannitol, lactic acid, quinic acid, glutamic acid, isoleucine, and proline, and negative loadings of galactose, myo-inositol, serine, aspartic acid, and asparagine. ...
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... to the PCA analysis, two PCs covered 48% of the data variability (Supplementary Figure S7C). Smoothness (TX) was more associated with the positive values of PC1, whereas bitter and roasty (FL) notes were more associated with the negative values of PC1. ...

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... Post-harvesting is an important phase for obtaining specialty coffees. Various processing methods induce diverse metabolic reactions in coffee beans, which can affect the chemical composition and cupping quality of the final product (de Melo Pereira et al., 2019;Zhang, De Bruyn, Pothakos, Contreras, & Rizzello, 2019). Coffee fermentation involves the metabolic process in mucilage, which contains high concentrations of polysaccharides, simple carbohydrates, organic acids like citric acid, oxalic acid, lactic acid malic acid, free amino acids and phenolic compounds that can be utilized by bacteria and yeasts in successive fermentation (Silva et al., 2017;Waters, Arendt, & Moroni, 2017). ...
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... The diversity of microorganisms plays an important part in the endogenous metabolism of coffee beans, especially at the fermentation stage [60]. At this step, microorganisms are very prevalent, highly variable and difficult to predict [60,61]. ...
... The diversity of microorganisms plays an important part in the endogenous metabolism of coffee beans, especially at the fermentation stage [60]. At this step, microorganisms are very prevalent, highly variable and difficult to predict [60,61]. While other authors have discussed the microbial diversity associated to other components of the coffee plant, such as the rhizosphere, the episphere and endosphere [62][63][64][65][66][67][68], we have focused our review on the postharvest microbiota which, as described above, has been shown to be highly relevant to coffee quality and mycotoxin production. ...
... Up until the present, ten works have been published using next generation sequencing approaches to evaluate the impact of post-harvesting methods on coffee bean microbial community profiles (Table 2). These studies were all conducted with arabica coffee, yet they were dispersed across 3 continents including three studies in Ecuador [69][70][71], one in Brazil [72], one in Honduras [73], one in Mexico [74], one in Colombia [75], two in Australia [76,77] and one in China [60]. Of the 10, only two studies depended on shotgun metagenomic sequencing and for the targeted amplicon studies authors chose different variable regions of the 16S rRNA gene, and either ITS or 18S to probe fungi. ...
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