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Bacterial (A) and fungal (B) amplicon sequencing variants (ASVs) detected during fermentation of depulped (DP) and demucilaged (DM) beans of the Arabica coffee wet processing experiments. To simplify visualization, individual ASVs were grouped by genus and represented in a dedicated panel. The different colors denote the different fermentation variants (blue for the DP trials and orange for the DM trials).

Bacterial (A) and fungal (B) amplicon sequencing variants (ASVs) detected during fermentation of depulped (DP) and demucilaged (DM) beans of the Arabica coffee wet processing experiments. To simplify visualization, individual ASVs were grouped by genus and represented in a dedicated panel. The different colors denote the different fermentation variants (blue for the DP trials and orange for the DM trials).

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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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... The abundance of aldehydes decreased during fermentation, drying, and roasting, which indicates that processing influenced the volatile profile. In addition, using different metabolic pathways, the starter cultures contributed to the biotransformation of these compounds present in green coffee, which consequently enabled the production of distinct volatile compounds during roasting [30,44,45]. The most abundant compound at the end of fermentation was benzeneacetaldehyde, which gave the coffee a green, honeylike aroma. ...
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One strategy for adding unique characteristics and flavors to improve coffee quality is the selection of starter microorganisms. Here, we aimed to evaluate the effect of Saccharomyces cerevisiae LNFCA11 and Kluyveromyces lactis B10 as starter cultures on the quality of four different wet-fermented coffee varieties. Microbiological, molecular, and chemical analyses were carried out to identify yeast, bacteria, volatile compounds, carbohydrates and bioactive compounds in coffee. Sensory analysis was performed by Q-graders certified in coffee. Starter yeasts affected bioactive and volatile compounds as well as sensory descriptors in the coffee varieties. S. cerevisiae CA11 allowed a higher content of trigonelline and chlorogenic acid in MGS Paraíso 2 (P2) and Catuai Amarelo IAC62 (CA62) varieties. K. lactis B10 fermentation resulted in higher chlorogenic acid only on the P2 cultivar and MGS Catucaí Pioneira (CP). In addition, 5-methyl-2-furfuryl alcohol and n-hexadecanoic acid were produced exclusively by yeast fermentation compared to spontaneous fermentation. The coffee cultivars P2 presented more complex sensory descriptors and the attributes of aroma, acidity, and balance when fermented with S. cerevisiae CA11. Sensory descriptors such as lemongrass, citrus, and lemon with honey were related to K. lactis B10. Starter cultures allowed the coffees to be classified as specialty coffees. The fermentation showed that the choice of starter yeast depends on the desired sensory descriptors in the final product.
... Very recently, not only accumulation of the stress marker GABA was confirmed for coffee beans submitted to postharvest treatment, but also that of the imino acid proline, another typical stress metabolite (Zhang, De Bruyn, Pothakos, Torres et al., 2019;Zhang, De Bruyn, Pothakos, Contreras et al., 2019). ...
... Yeast included Pichia, Candida, Arxula, and Saccharomycopsis. In addition, Cladosporium, Furthermore, the microbial community is a dynamic change process during primary processing [37]. For example, Acetobacteraceae (Acetobacter, Gluconobacter, and Kozakia), Enterobacteria, L. pseudomesenteroides, P. kluyveri, Hanseniaspora uvarum, and C. quercitrusa had high counts during the pooling, de-pulping, and fermentation in wet processing in China. ...
... In addition, Pseudomonas fluorescens, P. fulva, Gluconobacter frateurii, G. oxydans, G. cerinus, Kluyvera intermedia, and K. cryocrescens were also present [45]. In addition, Zhang et al. [37] found that lactic acid bacteria and aerobic microorganisms were the most prevalent microbial groups, while yeasts and enterobacteria were less common. Even filamentous fungi were not found. ...
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Based on coffee’s unique and fascinating flavor, coffee has become the most popular nonalcoholic drink in the world and is a significant agricultural economic crop in tropical- and subtropical-planted coffee countries and regions. It is also beneficial for human health because of its rich active compounds, such as caffeine, chlorogenic acids, trigonelline, tryptophan alkaloids, diterpenes, melanoidins, etc. These compounds often relate to the prevention of cardiovascular disease, Alzheimer’s disease, and antibacterial, anti-diabetic, neuroprotection, and anti-cancer activities. The formation of coffee’s flavor results from various influence factors, including genetics, shade, elevation, post-harvest processing, fermentation, roasted methods, etc. The first stage of coffee production is obtaining green coffee beans through the primary process. Fermentation is critical in the primary process of coffee, which is often related to yeasts, bacteria, and filamentous fungi. Therefore, microorganisms play a key role in coffee fermentation and coffee flavor. To provide an understanding of the role of microorganisms in coffee fermentation, the coffee fermentation overview and microbial characteristics in different coffee primary processing methods and different coffee fermentation regions were reviewed in this paper. Brazil and China are the main study countries in coffee fermentation, which contribute a large number of technologies and methods to improve coffee flavor by fermentation. Different primary processing methods (wet, dry, or semi-dry processing) and coffee producer countries had obvious microbial community characteristics. Moreover, the application of yeast and bacteria for improving coffee flavor by microbial fermentation was also introduced.
... Wet processing generally increases coffee quality because of the better preservation of the intrinsic flavor and aroma of the coffee bean (de Oliveira Junqueira et al., 2019;Hamdouche et al., 2016;Lee et al., 2015). Wet postharvest processing includes a complex chain of steps, such as depulping, spontaneous fermentation, soaking, and drying, as performed on farms (Duong et al., 2020;Zhang et al., 2019a). During this process, the fermentation step is aimed at removing the mucilage (which is primarily composed of simple sugars and pectin substances) attached to the beans by the action of microorganisms from the cherry surfaces, the plantation environment, or processing equipment (Carvalho et al., 2018;Zhang et al., 2019b). ...
... This approach provides access to and information on the functional gene composition of microbial communities and consequently provides a much broader description than phylogenetic surveys do (Gilbert et al., 2011). Nevertheless, this great potential of metagenomics has not been exploited in coffee fermentation except in Zhang et al. (2019a) in China and Pothakos et al. (2020) in Ecuador. ...
... Numerous analyses, including microbiological (culturedependent and amplicon sequencing; Fernandez-Güimac et al., 2023) and metabolomic analyses, have been conducted on the coffee fermentation process in northern Peru. However, the diversity and functional role of the bacterial microbiota in the coffee fermentation process remain to be fully revealed, despite some studies highlighting its noteworthiness when using shotgun metagenomics in Ecuador (Pothakos et al., 2020) and China (Zhang et al., 2019a). Accordingly, this study provides insights into the bacterial diversity and functional composition during the SFP and LFP in northern Peru. ...
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Peru is the ninth‐largest coffee producer and the largest organic coffee exporter worldwide. Specific modifications in the microbial consortia during fermentation control the flavor of coffee. It is still unclear how fermentation duration affects microbial communities. This study aimed to provide insights into the diversity and functional behavior of the bacterial microbiome during coffee fermentation in northern Peru using shotgun metagenomics. Accordingly, metagenomic DNA was extracted and sequenced from samples of the liquid fraction during the short fermentation process (SFP) in Amazonas (6 and 12 h) and long fermentation process (LFP) in Cajamarca (6, 12, 18, 24, and 36 h). Our findings indicate that common (e.g., Acetobacter, Lactobacillus, Leuconostoc, and Weissella) and unique (e.g., Acidiphilium and Methylobacterium) acid‐tolerant bacteria from the SFP and LFP play crucial roles and have a positive impact on the sensory qualities of coffee. Specifically, the LFP from San Ignacio might be associated with the high sensory quality of coffee based on the release of catalytic, hydrolase, oxidoreductase, transferase, and transporter enzymes in the InterPro and KEGG profiles. Additionally, these bacterial microorganisms metabolize several compounds (e.g., isoleucine, betaine, galactose, tryptophan, arginine, and cobalamin) into volatile compounds, mainly in the LFP, enhancing the flavor and aroma of coffees. This characteristic suggests that the LFP has a stronger effect on coffee quality than does the SFP on the basis of bacterial diversity and functional prediction. These findings provide new perspectives on the potential biotechnological uses of autochthonous microorganisms to produce superior‐quality coffee beans from northern Peru.
... Consumers are very interested in the special coffee flavor. However, a cup of a high-quality coffee beverage is comprehensively affected by many factors, such as genetic attributes, growing conditions, harvesting, post-harvest coffee processing, storage, roasting, and the brewing steps of coffee beverages [1][2][3][4]. Coffee beans are surrounded by skin, pulp, mucilage, parchment, and silver skin. Therefore, post-harvesting primary processing (wet, dry, or semi-dry processing) is the first step of coffee processing used to obtain green coffee beans [5] which can significantly influence coffee's flavor [6,7]. ...
... Dry processing is often used for C. robusta, while wet processing is often used for C. arabica [5]. Washed or wet processing, a traditional post-harvest coffee processing technique, includes de-pulping, fermentation, washing, drying, and other main operations [2]. Fermentation is a critical operation, as it can remove the pulp and mucilage by enzymes from the coffee fruit and microflora from the environment, and since mucilage is composed of protein, this reduces sugar, pectates, and ash [14,15]. ...
... However, traditional coffee fermentation is carried out in a developed environment; microbial communities often are influenced by environmental factors, such as the coffee region, temperature, altitude, pH, and so on. Therefore, the control of fermentation conditions is a prerequisite for improving coffee quality, such as suitable fermentation duration, processing type, application of soaking, etc. [2,16]. For example, a long fermentation duration would produce positive fruity and acid notes along with negative cereal and floral notes in the coffee flavor [2]. ...
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The washed process is one of the traditional post-harvest processes of coffee beans, which include selective harvesting, flotation, pulping, submerged fermentation underwater, washing, and drying operations. During the washed processing, fermentation underwater can remove coffee mucilage and change metabolites by microorganisms. Therefore, coffee fermentation is a key factor influencing coffee’s flavor. To compare the influence of fermentation duration in an open environment of Coffea arabica in 48 h during the washed processing on the coffee’s flavor, the sensory characteristics of the coffee at different fermentation durations were evaluated using the Specialty Coffee Association of America (SCAA) cupping protocol. Moreover, ultra performance liquid chromatography–triple quadrupole mass spectrometry (UHPLC–MS/MS) and gas chromatography–mass spectrometry (GC–MS) were combined to analyze and compare the chemical compounds of coffee samples from fermentation durations of 24 h (W24) and 36 h (W36) during the washed processing method. The results showed that W36 had the highest total cupping score with 77.25 in all different fermentation duration coffee samples, and 2567 non-volatile compounds (nVCs) and 176 volatile compounds (VCs) were detected in W36 and W24 during the washed processing method. Furthermore, 43 differentially changed non-volatile compounds (DCnVCs) and 22 differentially changed volatile compounds (DCVCs) were detected in W36 vs. W24. Therefore, suitable fermentation duration in an open environment is beneficial to coffee flavor, judging by chemical compound changes. For the washed primary processing of C. arabica from Yunnan, China, 36 h fermentation was the suitable fermentation duration in an open environment, which presented potential value as the reference for washed coffee processing in the food industry.
... The potential of metabolomics as a robust, efficient, and sensitive analytical tool in food science has been widely recognized for its application to studies on food processing and transformation (Utpott et al., 2022). Zhang et al. (2019) used a metabolomic approach to study the effect of the coffee fermentation process on the quality of the final product, confirming that a longer fermentation time leads to a more fruity and acidic product. Chen et al. (2020) investigated the effect of the drying process on the nonvolatile compounds of white tea through metabolomics and proteomics approaches, and their study showed that the drying process slightly contributes to the formation of the flavor of white tea but contributes more to the formation of white tea aroma than to the formation of white tea flavor. ...
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Panax notoginseng (Burk.) F. H. Chen (PN), commonly known as PN, is a nutritious natural food with a long history of consumption and has traditionally been used for dietary purposes in the form of dried processed products. Currently, developed a dry processing at short time and room temperature (DRST), which is characterized by high efficiency and low cost. However, there are few studies on the impact of DSRT. In this study, the effects of conventional hot air drying (DHA) and the innovative drying technology DSRT on the key components of PN were evaluated for the first time. The results showed that DRST could obtain processed PN products with smaller particle sizes and that DRST‐treated PN could increase the content of five saponins by 1.38% for Ginsenoside Rg1, 0.1% for Ginsenoside Re, 0.83% for Ginsenoside Rb1, 0.16% for Ginsenoside Rd, and 0.36% for PN saponin R1, relative to the content of five saponins that could be increased by conventional DHA. The metabolome results yielded a total of 1401 metabolites identified and analyzed, and 201 metabolites showed significant differences between the two techniques, which were expressed as amino acids, flavonoids, and other nutrient‐active components. The results of this study indicate that the PN products produced by DRST technology have higher nutritional quality compared to traditional processing. This study provides support in the processing of PN and the development of PN products.
... Coffees from different environments have diverse and specific microbial communities (Martinez et al. 2017;Veloso et al. 2020). Post-harvest processing techniques, such as different types and fermentation times, can also affect the diversity of microorganisms (Martinez et al. 2017;Zhang et al. 2019). Harvest and post-harvest processes are essential for the specialty of coffee. ...
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Understanding the effects of microorganisms on coffee fermentation is crucial to ensure sensory quality and food security. The analysis of the dynamics of the microbial community during fermentation can contribute to a better understanding of the beneficial and harmful effects of microorganisms and help select starter cultures to improve coffee quality. Furthermore, the anaerobic environment produced by carbonic maceration of the coffee fruits inhibits aerobic respiratory processes and stimulates fermentative metabolism, modulating the microbial community during coffee fermentation. This study evaluated the effects of carbonic maceration in the fungal community dynamics during the fermentation of Coffea arabica fruits at 18, 28, and 38 °C for 24, 48, 72, 96, and 120 h. Fungal diversity was accompanied by high-throughput sequencing (NGS) of the Internal Transcribed Spacer (ITS) region. During the coffee fermentation, the fungal community changed over time, with the most significant changes occurring at 18 and 28 °C after 72 h. However, at 38 °C, there were greater variations in fungal composition and fungal diversity was highest after 120 h. The yeast Pichia cephalocereana was predominant in the fermentations. These results indicated that temperature and fermentation conditions influence the fungal community during coffee fermentation. Lower temperatures might favor a more stable microbial environment, while higher temperatures lead to more intense changes. Thus, our data from NGS can help in the identification, isolation, and metabolic characterization of fungi for the fermentation of coffee fruits.
... Coffee processing methods can produce various avors and aromas, ranging from the earthy and bitter notes often associated with Robusta coffee to the fruity and acidic pro les of the preferred Arabica [19]. For example, fermentation and washing of the coffee have been reported to contribute to the fruity avor of Arabica coffee [18,20]. Therefore, the use of a sensory descriptive method is a key tool to better understand and differentiate between coffee samples [21,22] but is best used in conjunction with the standard coffee cupping method [23]. ...
... To enhance the sensory quality and marketability of Robusta coffee, the Washed processing method could improve the sensory pro le perception towards coffee consumers. Additionally, it has been shown that in Arabica, longer fermentation times result in a fruitier and more acidic cup [20]. Furthermore, as stated earlier, the germination of fermenting coffee beans has previously been associated with fruity avors in Arabica [50]. ...
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Coffee processing involves various steps, from harvest to the storage of dried green coffee beans, each of which can significantly affect the beans' chemical composition and sensory qualities. Yet, a comprehensive evaluation that includes the coffee's genetic background and chemical, sensory, and biological aspects is still uncommon for Robusta coffee. Four Robusta ( C. canephora ) genotypes from the Democratic Republic of the Congo were subjected to five different coffee processing methods: Strip-picked, unsorted, sundried cherries; Overripe, sorted, sundried cherries; ripe, sorted, sundried (Natural) cherries; ripe, sorted, Pulped, sundried parchment; and ripe, sorted, wet fermented (Washed), sundried parchment were processed separately. The resulting green beans underwent sensory descriptive cupping, seed germination tests, and metabolite profiling using LC-HRMS. The Pulped and Washed methods produced coffees with higher sensory attributes scores, while the Overripe method was associated with the sensory ‘potato taste’ defect. Washed coffee was characterized by smooth, fruity, cocoa notes, and was negatively correlated with rough mouthfeel, tobacco, and leather flavors. The Pulped and Washed method had significantly higher germination success after four months of storage. The processing method influenced caffeine concentration in green beans, depending on the genotype, while trigonelline levels varied significantly between genotypes but not between processing methods. The grouping of the metabolite profiles of roasted coffee and green beans was consistent with their genetic background rather than the processing method. Overall, we demonstrate that genotype plays a significant role in mediating the outcomes of different processing methods.
... The presence of this compound in high concentration suggests that the wine-based green beans have a distinct fermented flavor. The length of fermentation also influences the activity of microorganisms like acetic acid bacteria and Enterobacteriaceae; the longer the fermentation period, the greater the likelihood of acetic acid formation [22][23][24]. Isoamyl alcohol is the dominant volatile compound in Arabica coffee green beans and the fermentation process increases its concentration [25,26]. Phenylethyl alcohol compound is associated with a sweet aroma and floral, honey-like flavor [21,27]. ...
Article
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Whether the post-harvest process will greatly influence volatile or non-volatile coffee chemical compounds. Four post-harvest coffee processing techniques, namely natural, honey, fullwash, and wine, were evaluated in this study. This research aims to authenticate the volatile and non-volatile compounds of Robusta Jawa Bogor green bean as a differentiator in natural, fullwash, honey, and wine processing. Using HS-SPME-GC-MS and LC-MS, we identified a total of 128 volatile compounds (113 in natural, 111 in honey, 100 in fullwash, and 126 in wine), as well as 105 non-volatile compounds (77 in natural, 73 in honey, 66 in fullwash, and 93 in wine). The study found volatile compounds like ethyl cinnamate potential marker for honey processing. A potential marker for natural and wine processing is 1- isopropyl-3 methylbenzene. Some potential markers for wine processing are (E)-4-hexen-1-ol, 5-methyl-2-hexanol, diethyl succinate, ketoisophorone, and 4-ethyl-2-methoxyphenol. Non-volatile compounds like 1-naphthoic, [4]-gingerol, and theophylline are non-volatile markers for natural processing. Succinic acid is a non-volatile marker for natural and wine processing. While maleic acid and adenosine are markers for honey processing, adenine is a marker for wine processing. In contrast, fullwash does not have any volatile and non-volatile marker. Due to post-harvest-process variations, the obtained results assist in authenticating the chemical compounds of Robusta Java Bogor green beans.
... This practice continues to present day and applies to instant coffee. Later, the solutions that involved adding other aromas, such as vanilla, nut, chocolate, rum, cherry, and several others were developed [27]. However, coffee connoisseurs look for natural and more healthy solutions than flavoring by adding artificial substances. ...
Article
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Over the years, many methods of refining green beans have been developed, including maceration aimed at enriching the coffee aroma and improving the overall quality. This study aimed to evaluate the influence of different methods of maceration (fruit and wine) and the addition of food flavors to coffee beans on antioxidant activity, caffeine, phenolic and organic acid content, as well as health-promoting properties. This research showed that the use of the maceration in melon and apple fruit pulp (100 g of fruit pulp per 100 g of green coffee, incubated for 24 h, coffee roasting at 230 °C, control trial roasted coffee) ensured the highest polyphenol (hydroxycinnamic acids and their esters—chlorogenic acids) content (in melon pulp—13.56 g/100 g d.b. (dry bean); in apple pulp—13.22 g/100 g d.b., p < 0.05 (one-way ANOVA)) and antioxidant activity. Melon (92.11%, IC50 = 3.80 mg/mL extract) and apple (84.55%, IC50 = 4.14 mg/mL) showed the highest α-amylase (enzyme concentration 10 μmol/mL) inhibition activity (0.5 mg/mL for both fruits). The addition of food flavors reduced the total content of chlorogenic acids to the range of 4.64 to 6.48 g/100 g d.b. and increased the content of acrylamide and 5-HMF, which positively correlated with a low antioxidant potential compared to the macerated samples and the control. Studies have shown that coffee macerated in the pulp of melon and apple fruit, due to its great potential to inhibit α-amylase in vivo, may have a preventive effect on type II diabetes. This study complements the current knowledge on the potential health-promoting properties of coffee flavored using different methods; further research should include more advanced models for testing these health-promoting properties. Statistical analysis was based on the determination of the average values of six measurements and their standard deviation, as well as on the one-way ANOVA (analysis of variation) and the Pearson correlation coefficient, using Statistic 10.0 software. The significance was defined at p ≤ 0.05.