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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.
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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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Context 1
... 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. ...
Context 6
... 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. ...
Context 7
... 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. ...
Context 8
... 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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... Through various investigations that have explored fermentation behaviors in coffee, it is known that the temperature evolves depending on several factors, such as the initial quality of the coffee, the temperature of the environment and the amount of coffee, among other factors [34][35][36][37]. In controlled processes, agitation is necessary to achieve temperature homogenization in the coffee mass, which is a challenge considering the changing physical properties of coffee beans suspended in the hydrolyzed mucilage [19]. ...
Temperature control is the starting point for the development of controlled fermentation and improving coffee quality. The characteristics of coffee varieties can influence fermentation behavior. To evaluate the effect of the coffee variety on the behavior of controlled fermentation and on coffee quality, a completely randomized design was used with three varieties (Castillo, Cenicafé1 and Tabi) and two control temperatures (15 and 30 °C). Spontaneous fermentation was the control for each controlled process. The fermentation time, pH, glucose and lactic acid contents, as well as, the count of mesophiles, yeasts, lactic acid bacteria (LAB) and acetic acid bacteria (AAB), were assessed. The sensory quality of the coffee was classified as very good and excellent based on the variety, with averages above 82 Specialty Coffee Association (SCA) points. The highest values were for the Cenicafé1 variety. Fermentation behaviors were similar among varieties but not based on the given condition. Compared with spontaneous fermentation, the treatment at 15 °C prolonged the degradation of mucilage in more than 24 h; additionally, there were differences in the final pH values, less than 3.5 and close to 4.0, respectively. Quality was not significantly different between the controlled fermentation and the spontaneous fermentation (Wilcoxon test p > 0.05) or between fermentation temperatures (Kruskal–Wallis test p > 0.05).
... The composition of the microbial community in each fermentation process varies depending on the geographical location, processing method, coffee variety and state of maturity of the coffee fruits at the time of harvest. Factors such as soil, water, tools, insects and human manipulation also influence the types of microorganisms that are abundant during fermentation [9,17,[19][20][21]. These factors also influence the fermentation stage because changes within the same process, such as the consumption of some nutrients and changes in pH and temperature, modify the structures of the microbial population [22]. ...
... The physicochemical analysis of the mucilage showed that for the three coffee varieties, the pH decreased while the production of organic acids increased with increasing fermentation time. The increase in organic acids was associated with the metabolism of the different microorganisms present during fermentation, and it has been recognized that the presence of these acids can impact the final quality of coffee [9,10]. The concentration and type of organic acid are related to the sensory perception of beverages, such as aroma [46]. ...
... Additionally, mixed-acid bacteria, represented by the Enterobacteriaceae family, were found in the fermentation process; in total, eight genera and seven species were found, and these taxa were also reported in Brazil, Australia, Ecuador and China [9,13,16]. ...
The microbial composition and physical-chemical characteristics were studied during the coffee fermentation of three Coffea arabica L. varieties, Var. Tabi, Var. Castillo General® and Var. Colombia. Mucilage and washed coffee seeds samples were collected at different stages of fermentation. Mucilage microbiology characterization and metataxonomic analysis were performed using 16S rDNA sequencing to determine bacterial diversity and ITS sequencing for fungal diversity. Additionally, the microorganisms were isolated into pure cultures. The molecular diversity analyses showed similarities in microorganisms present during the fermentation of Var. Castillo General and Var. Colombia, which are genetically closely related; mixed-acid bacteria (Enterobacteriaceae, Tatumella sp.) and lactic acid bacteria (Leuconostoc sp., Weissella sp. and Lactobacillaceae) were common and predominant, while in Var. Tabi, acetic acid bacteria (Gluconobacter sp. and Acetobacter sp.) and Leuconostoc sp. were predominant. At the end of the fermentation period, the fungi Saccharomycodaceae, Pichia and Wickerhamomyces were found in Var. Castillo General and Var. Colombia, while in Var. Tabi, Saccharomycodaceae, Pichia and Candida were recorded. Sensory analyses of the coffee beverages were carried out (SCA methodology) for all samples. Var. Tabi had the highest SCA score, between 82.7 and 83.2, while for Var. Colombia, the score ranged between 82.1 and 82.5. These three coffee varieties showed potential for the production of specialty coffees influenced by spontaneous fermentation processes that depend on microbial consortia rather than a single microorganism.
... Various microbes, including LAB, acetic acid bacteria, enterobacteria, and yeasts, are normally found in green beans as part of the normal flora, and their interactions during fermentation need to be controlled (Zhang et al., 2019). Previous studies have attempted to develop flavors and metabolites through the fermentation process of green beans, with a primary focus on using single-species starters and Arabica coffee (Lee et al., 2016a(Lee et al., , 2016b2017a, 2017b. ...
... Yunnan province is the primary coffee plantation province in China, accounting for more than 95% of China's coffee plantation area, making coffee one of the most important economic sources in the province. Zhang et al. studied the influence of processing conditions on coffee quality and metabolomic profiles in traditional wet-processing methods and reported that Leuconostoc and Lactococcus were active in C. arabica fermentation in China [13]. This study analyzed the microbiota and metabolites of coffee beans during washed processing to further study coffee quality and the functions of microbiota. ...
... In India, Saccharomyces, Shizosaccharomyces, Bacillus, Lactobacillus, Leuconostoc, Pseudomonas, and Flavobacterium are dominant genera during initial fermentation stages [18]. In China, Enterobacter, Bacillus, Pseudomonas, Gluconobacter, Kluyvera, and Candida are dominant in the wet processing of C. arabica [13]. Based on the results of this study, Achromobacter, Tatumella, Weissella, Streptococcus, and Trichocoleus were found to be predominant in the bacterial community, while Cystofilobasidu, Hanseniaspora, Lachancea, Wickerhamomyces, and Aspergillus were predominant in the fungal community during complete washed processing. ...
Coffee fermentation is crucial for flavor and aroma, as microorganisms degrade mucilage and produce metabolites. This study aimed to provide a basis for understanding the impact of microorganisms on Coffea arabica from Yunnan, China, during washed processing. The microbial community structure and differentially changed metabolites (DCMs) of C. arabica beans during washed processing were analyzed. The results indicated that the top five predominant microorganisms at the genera level were Achromobacter, Tatumella, Weissella, Streptococcus, and Trichocoleus for bacteria and Cystofilobasidium, Hanseniaspora, Lachancea, Wickerhamomyces, and Aspergillus for fungi. Meanwhile, the relative content of 115 DCMs in 36 h samples decreased significantly, compared to non-fermentation coffee samples (VIP > 1, p < 0.05, FC < 0.65), and the relative content of 28 DCMs increased significantly (VIP > 1, p < 0.05, FC > 1.5). Furthermore, 17 DCMs showed a strong positive correlation with microorganisms, and 5 DCMs had a strong negative correlation (p < 0.05, |r| > 0.6). Therefore, the interaction and metabolic function of microbiota play a key role in the formation of coffee flavor, and these results help in clarifying the fermentation mechanisms of C. arabica and in controlling and improving the quality of coffee flavor.
... In this sense, concentration changes may be related to the presence of oxygen, enzymes, microorganisms and sunlight during the drying of coffee beans. Therefore, these processes and environmental conditions determine the rate at which chemical, metabolic and microbiological reactions occur in coffee beans (Kwon et al., 2015;Zhang, De Bruyn, Pothakos, Contreras, et al., 2019;Zhang, De Bruyn, Pothakos, Torres, et al., 2019). ...
Solar drying and forced convection of hot air (mechanical drying) are traditionally used for the drying process of coffee beans. This work describes the changes of the concentration of sucrose and 11 fatty acids contained in Castillo® variety coffee beans during the drying process using HPLC and CG MS. A single‐factor experimental design with three blocks was carried out like this: three solar and three mechanical drying. A phenomenological mathematical model was developed allowing to know the evolution of chemical compounds concentration over time by using a parameter called characteristic time, which can be experimentally measured. For the 18‐h mechanical drying, sucrose concentration increased by 14.55 ± 0.20 mg/g db, while palmitic and linoleic fatty acids decreased by 0.372 ± 0.013 mg/g dry basis (db). For solar drying of 94, 120, and 218 h the initial sucrose concentration was reduced by 24.81 ± 0.23, 29.28 ± 0.27, and 47.10 ± 0.21 mg/g db, likewise palmitic and linoleic fatty acids were reduced by 0.442 ± 0.010, 0.680 ± 0.012, and 1.088 ± 0.014 mg/g db. These results suggest that a short drying time leads to a higher concentration of the analyzed chemical compounds in the coffee beans.
Practical Applications
The coffee drying process impacts the concentration of chemical compounds that are of great interest in forming coffee aroma and flavor in the roasting process. This study highlights the impact of drying time on the concentration of sucrose and fatty acids in coffee beans. The main application of this research shows how in solar and mechanical drying variations organic compounds occur. The presence of these organic compounds in coffee beans is of great interest for the later coffee roasting process. The proposed phenomenological mathematical model allows a physical understanding in the effect of drying time on the concentration of sucrose and 11 fatty acids.
... Previous research has identified a relationship between elevation and the chemical and microbiological compositions of coffee [3,4,[6][7][8][9][10][11][12]. On the other hand, the processing method used has an important role in determining quality [5,7,[13][14][15], especially with the use of the wet process, which is capable of generating a coffee beverage with balanced attributes and better acidity levels [6,16,17]. In the wet process, the elimination of mesocarp or mucilage through fermentation has great potential to positively impact the quality of coffee due to the formation of compounds that enhance the aroma and flavor of the drink; these compounds are formed from the biochemical transformations of mucilage substrates produced by the microorganisms present [6,18]. ...
... These compounds are the precursors of the compounds that are formed in the roast and are finally perceived in the drink [20]. However, modifications of the matrix of compounds of green coffee beans lead to the production of alcohols, esters, and ketones, among others, during fermentation [13,14,21]. Gas chromatography coupled with mass spectrometry (GC-MS) is the most commonly used technique for the analysis of volatile organic compounds in green, roasted, and beverage coffee. ...
... Gas chromatography coupled with mass spectrometry (GC-MS) is the most commonly used technique for the analysis of volatile organic compounds in green, roasted, and beverage coffee. Headspace solid-phase microextraction (HS-SPME) in conjunction with GC-MS has identified changes in the chemical composition of green coffee due to the modification of fermentation parameters, time, and type of process [13,22,23], or due to the identification of defects [24]. The compounds identified by these and other techniques such as Near-infrared spectroscopy (NIR-HSI) or Fourier-transform infrared spectroscopy (FITR) [25,26] have been related to beverage attributes such as aroma and flavor. ...
Controlled fermentation processes have high potential for improving coffee quality. The effect of fermentation temperature on beverage quality was investigated with coffee cultivated at elevations between 1166 and 1928 m. A completely randomized design was carried out at five elevation ranges at 200 m intervals in five farms per elevation range, and two temperatures (15 °C and 30 °C), which were maintained in a temperature-controlled bioreactor. Each temperature-controlled fermentation batch had a spontaneous fermentation batch (control treatment). Microbial identification of LAB and yeast was performed using a Biolog™ MicroStation™ ID System, and cup quality tests were performed following the SCA protocol. Tests conducted at 15 °C showed higher microbial community activity on the substrates used, indicating greater transformation potential than those conducted at 30 °C or those of spontaneous fermentation. According to Wilcoxon and Kruskal–Wallis tests, temperature-controlled fermentation resulted in high-quality coffee for all elevation ranges, with coffee from higher elevations and processed at controlled temperatures of 15 °C receiving the highest cup scores compared to coffee that was subjected to 30 °C. These results suggest that controlled temperature can be used to design standardized fermentation processes in order to enhance coffee quality through differentiated sensory profiles.
... It is known that the coffee processing method influences the endogenous metabolic factors in coffee fruit and exogenous factors such as microbial ecology and fermentation conditions and consequently causes changes in the biochemical composition of coffee (Lee et al., 2015;Pereira et al., 2021). Therefore, the type of process has a strong influence on coffee quality, from changes in coffee flavors and aromas to the dominance rate of these attributes in the final beverage (Hameed et al., 2018;Pereira et al., 2022;Zhang et al., 2019). ...
In recent years, the importance of controlling coffee fermentation in the final quality of the beverage has been recognized. The literature review was conducted in the Science Direct and Springer databases, considering studies published in the last ten years, 74 references were selected. Several studies have been developed to evaluate and propose fermentation conditions that result in sensory improvements in coffee. So, this review aims to describe detailed the different protocols for conducting the coffee fermentation step and how they could influence the sensory quality of coffee based on the Specialty Coffee Association protocol. We propose a new way to identify coffee post-harvest processing not based on the already known wet, dry and semi-dry processing. The new identification is focused on considering fermentation as a step influenced by the coffee fruit treatment, availability of oxygen, water addition, and starter culture utilization. The findings of this survey showed that each type of coffee fermentation protocol can influence the microbiota development and consequently the coffee beverage. There is a migration from the use of processes in open environments to closed environments with controlled anaerobic conditions. However, it is not possible yet to define a single process capable of increasing coffee quality or developing a specific sensory pattern in any environmental condition. The use of starter cultures plays an important role in the sensory differentiation of coffee and can be influenced by the fermentation protocol applied. The application of fermentation protocols well defined is essential in order to have a good product also in terms of food safety. More research is needed to develop and implement environmental control conditions, such as temperature and aeration, to guarantee the reproducibility of the results.
... Due to their pectinolytic activity, they play an essential role in the degradation of fruit mucilage and the production of aroma precursors, such as reducing sugars, amino acids, and chlorogenic acids (de Carvalho Neto et al., 2017;Lee et al., 2015). The most-reported yeast genera in coffee fermentation are Pichia, Candida, Saccharomyces, and Hanseniaspora (de Oliveira Junqueira et al., 2019;Martins et al., 2020;Zhang et al., 2019) and have shown high potential as starter cultures (de Melo Pereira et al., 2014, 2015Elhalis et al., 2021;Silva et al., 2013). When inoculated during fermentation, these individual or mixed microbial cultures increase the control and efficiency of the process since they enable standardization of production and avoid possible effects on the final product, which ensures that high-quality coffee is obtained and the increased economic benefits for growers. ...
The post-harvest processing of coffee plays a crucial role in developing high-quality beverages with differential sensory attributes. The present study aims to determine the yeast diversity associated with spontaneous wet fermentation of Colombian coffee and to analyze the composition of green coffee and the sensory quality of the beverage. It was found that the yeast community is made up of 46 species, many of which are reported for the first time in coffee fermentation, as is the case of Kazachstania humilis, which leads the entire fermentation process. The contents of sugars and total soluble proteins in green coffee beans showed a dependence on fermentation time, where glucose and fructose decrease and sucrose and TSP increase. Amino acids generally did not show significant differences with respect to time; however, alanine was the most abundant, followed by glutamic acid and aspartic acid. Finally, the beverages obtained were classified as specialty coffees with distinctive fruity, floral, chocolatey, and sweet attributes, whose quality scores were positively correlated with gamma-aminobutyric acid, TSP, Picha mandshurica, and sucrose. These findings provide new insights into the microbial diversity in coffee fermentation, the content of sugars, proteins, and amino acids in green coffee, and their contribution to the generation of differential sensory profiles. The new yeasts reported in this study may be explored as starter cultures in further studies.
... The processed beans are subjected to solar or mechanical drying until reaching a humidity between 10% and 12% (dry parchment coffee) and then are subjected to the subsequent processes of threshing, roasting, grinding, and beverage preparation. To remove the mucilage, which is a gelatinous substance with a high water content that is rich in isms in fermentation [9,13,14,20]. The general conclusion of these studies is the need to expand the information on the diversity, richness, abundance, and dynamics of the microbiota involved in coffee fermentation, in different regions and production conditions or contrasting ones, and to perform wider taxonomic characterizations. ...
... In total, we studied 20 representative farms (sampling units) located in 12 municipalities of the Department of Quindío, in the central coffee zone of Colombia ( Figure 1). Fermentation 2023, 9, x FOR PEER REVIEW 3 of 20 Several studies have been carried out examining fermentation types, based on a single coffee variety, origin, or a specific farm, so the results are specific in that regard [21,22,[26][27][28][29]. Consequently, there are still discrepancies regarding the role of predominant microorganisms in fermentation [9,13,14,20]. The general conclusion of these studies is the need to expand the information on the diversity, richness, abundance, and dynamics of the microbiota involved in coffee fermentation, in different regions and production conditions or contrasting ones, and to perform wider taxonomic characterizations. ...
... For most types of fermentation samples, predominant genera were common, such as lactic acid bacteria (LAB), including Leuconostoc and Lactobacillus, acetic acid bacteria (AAB), such as Gluconobacter and Acetobacter, and OTUs from the family Enterobacteriaceae, in which Tatumella and Pantoea were also found. Other genera present at proportions less than 3% included Pseudomonas, Rosenbergiella, Frateuria, Lactococcus, Zymomonas, and Weisella, some of which have been reported as natural coffee microbiota or in fermentation processes of coffee and other products [9,13,14,22,27,53,54]. Similarly, predominant and common fungal genera between fermentations were represented by the Saccharomycedaceae family, specifically Pichia and Candida genera. ...
Coffee fermentation is a complex process, mainly involving bacteria and yeasts, whose interaction influences beverage quality. The way this process is conducted affects the interactions between these microorganisms. To identify microbial diversity in fermenting coffee, samples were collected from 20 farms in the Department of Quindío, Colombia. Metataxonomic analyses using high-throughput sequencing and volatile organic compound identification in green coffee beans were performed with HS-SPME and GC-MS. Potential relationships between some families and genera with different fermentation types and coffee quality were evaluated. In our results, samples presented with high richness and diversity were greater for bacteria than for yeast/fungi. The Enterobacteriaceae family dominated at the beginning of fermentation, while Leuconostoc, Lactobacillus, Gluconobacter, and Acetobacter genera dominated at the end, a finding related to pH reduction and final coffee quality. Overall, 167 fungal families were identified, but Saccharomyceaceae dominated from the beginning. Alcohols and esters were the main chemical classes identified in green coffee bean samples from these fermentations. These results will facilitate the identification process conditions that influence the presence and abundance of microorganisms related to quality as well as contributing to the design of strategies to conduct fermentations to improve the final quality of coffee.
... Yeast Isolate Recovery and Identification from Dry and Semidry Postharvest Processes. Subsequently to enumeration, 15 colonies of yeasts were isolated on YPD agar plate spots corresponding to high dilutions, 21 independently of their phenotype. ...
... The composition of CFSM was based on the metabolite analysis of fresh coffee fruit, mucilage, and fermentation water during coffee fermentations. 21,22 This medium aimed at providing a carbon and nitrogen source, organic acids, growth factors, and other coffeerelated compounds in order to mimic the coffee fermentation matrix. Growth factors, such as MnSO 4 , MgSO 4 , and soy peptone, were included to support strain growth as a substitute to unknown growth agents present in coffee fruits. ...
Postharvest processing of coffee has been shown to impact cup quality. Yeasts are known to modulate the sensory traits of the final cup of coffee after controlled fermentation at the farm. Here, we enumerated native coffee yeasts in a Nicaraguan farm during dry and semidry postharvest processing of Arabica and Robusta beans. Subsequently, 90 endogenous yeast strains were selected from the collected endogenous isolates, identified, and subjected to high-throughput fermentation and biovolatile generation in a model system mimicking postharvesting conditions. Untargeted volatile analysis by SPME-GC-MS enabled the identification of key aroma compounds generated by the yeast pool and demonstrated differences among strains. Several genera, including Pichia, Candida, and Hanseniaspora, showed both strain- and species-level variability in volatile generation and profiles. This fermentation platform and biovolatile database could represent a versatile opportunity to accelerate the development of yeast starter cultures for generating specific and desired sensory attributes in the final cup of coffee.
