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The growth of filamentous fungi during the spontaneous cocoa bean fermentation leads to inferior cocoa bean quality and poses a health risk for consumers due to the potential accumulation of mycotoxins. We recently developed anti-fungal cultures with the capacity to inhibit the growth of mycotoxigenic filamentous fungi on cocoa beans. However, it is not clear how these anti-fungal cultures affect the fermentation process and cocoa bean quality. The comparison of inoculated and spontaneous fermentation processes revealed that the co-cultures only marginally affected the fermentation process and cocoa bean quality.
Yet, how specific microbial communities and the changing chemical compositions of the beans determine the flavor of a cup of coffee remains underappreciated. Through a multiphasic approach, the establishment of the microbial communities, as well as their prevalence during wet processing of Coffea arabica , was followed at an experimental farm in Ecuador.
Also, the metabolites produced by the microorganisms and those of the coffee bean metabolism were monitored to determine their influence on the green coffee bean metabolite profile over time. The results indicated that lactic acid bacteria were prevalent well before the onset of fermentation and that the fermentation duration entailed shifts in their communities. The fermentation duration also affected the compositions of the beans, so that longer-fermented coffee had more notes that are preferred by consumers.
As a consequence, researchers and coffee growers should be aware that the flavor of a cup of coffee is determined before as well as during on-farm processing and that under the right conditions, longer fermentation times can be favorable, although the opposite is often believed.
The coffee postharvest processing is one of the key phases that convert the freshly harvested cherries into green coffee beans before roasting and brewing. Among multiple existing processing methods, the wet processing has been usually applied for Arabica coffee and produces decent quality of both green coffee beans and the cup of coffee.
In the present case study, wet processing was followed by a multiphasic approach through both microbiological and metabolomic analyses. The impacts of each processing step, especially the fermentation duration, were studied in detail.
Distinct changes in microbial ecosystems, processing waters, coffee beans, and sensory quality of the brews were found. Thus, through fine-tuning of the parameters in each step, the microbial diversity and endogenous bean metabolism can be altered during coffee postharvest processing and hence provide potential to improve coffee quality.
A cup of coffee is the endpoint of a complex chain of events. This chain includes postharvest processing, roasting, and brewing. Postharvest processing consists of several steps performed on-farm after the coffee cherries have been harvested, and it yields the green coffee beans that can be roasted 1 , 2. During this processing, an interplay between microbial activities and endogenous bean metabolism takes place, which results in a specific flavor precursor profile of the green coffee beans 2 , 3 Coffee cherries can be processed in different ways 1.
Wet processing is usually implemented for Coffea arabica cherries to produce high-grade Arabica coffee. During wet processing, the harvested coffee cherries are depulped, spontaneously fermented underwater, soaked, and dried 4 , 5. The fermentation step aims to remove the mucilage that is firmly attached to the beans. This fermentation is performed by microorganisms that originate from the cherry surfaces, plantation environment, or processing equipment. As processing progresses, microbial communities grow due to variable selective pressures from intrinsic e.
How these factors shape these communities remains to be elucidated. Due to this uncertainty, researchers have already tried to standardize the fermentation process by adding selected microbial strains to the fermentation mass, without managing specific operational practices 9 , — Since metabolites of microbial origin such as organic acids can be present on the green coffee beans, the mechanisms shaping the coffee ecosystem need to be better understood 3.
As coffee beans are still metabolically active during postharvest processing, they respond to various abiotic stresses, such as those caused by depulping at the start of the processing, anoxic and acidic conditions during underwater fermentation, and drought stress upon drying 12 , These stress-related metabolic responses will also change the metabolite composition of the green coffee beans.
However, the evolution of such compounds along the entire postharvest processing chain has not been studied extensively. During roasting, the chemical profiles of the green coffee beans, which are determined not only by cultivar and geography but also by postharvest processing as described above, transform into the characteristic coffee flavor 17 , — Ultimately, gauging the effect of postharvest processing on the coffee cup quality requires sensory analysis by a trained panel.
However, reports on the relationship between the sensory data and the fermentation process postharvest effect are scarce 7 , Given this complex and interlinked postharvest processing of coffee, an integrated systematic study of the relationship between the coffee processing microbiota, endogenous bean metabolism, operational practices, and cup quality was necessary.
Therefore, this study aimed to decode the complete wet processing chain of Arabica coffee under different operational practices, starting from the harvesting of the coffee cherries through on-farm processing until coffee roasting and brewing Fig. This was tackled through a multiphasic approach, monitoring the coffee microbiota on-farm microbiological analysis and high-throughput sequencing , the coffee bean composition meta-metabolomics , and the final quality of the coffee brews sensory analysis.
The abbreviations of the different samples are indicated as well. The dark blue line represents the standard fermentation process S , and the light blue line represents the extended fermentation process E. Sample codes starting with F correspond to fermentation samples, followed by a number corresponding to the fermentation duration in hours.
Sample codes starting with SS denote soaking samples after standard fermentation and sample codes starting with SE denote soaking samples after extended fermentation, followed by a number corresponding to the soaking duration in hours. Sample codes starting with DS denote drying samples after standard fermentation and sample codes starting with DE denote drying samples after extended fermentation, followed by a number corresponding to the drying duration in hours. Samples SB and EB denote green coffee bean samples resulting from the standard fermentation process and the extended fermentation process, respectively.
The sampling points for each analysis type are colored based on their location in the processing chain. Gray sampling points denote samples that were not included for analysis.
The pooled cherries and depulped beans showed high counts of all microbial groups targeted, namely, lactic acid bacteria LAB , acetic acid bacteria AAB , enterobacteria, and yeasts Fig. Isolate identification and amplicon sequencing of targeted genes of the whole-community DNA affirmed the community members of these groups belong to the Acetobacteraceae encompassing Acetobacter, Gluconobacter , and Kozakia , enterobacteria, Leuconostoc pseudomesenteroides , Pichia kluyveri particularly found by amplicon sequencing , Hanseniaspora uvarum, and Candida quercitrusa Fig.
These high counts persisted once the depulped beans were submerged in the fermentation tank particularly LAB and enterobacteria. From here on, LAB asserted their quantitative prevalence over other microbial groups during the standard fermentation S. This prevalence was further developed during the extended fermentation E and was retained until the end of fermentation F. During this phase, a shift from L. Conversely, the counts of enterobacteria and AAB showed a continuous decrease during the standard and extended fermentations.
No major shifts occurred within the community compositions of these groups. The yeast counts and communities remained relatively stable during these phases, although Starmerella bacillaris particularly found through isolate identification became more pronounced as fermentation progressed and Saccharomycopsis crataegensis was encountered occasionally. Lactococcus lactis was prevalent transiently during the standard fermentation 12 to 24 h.
Other species were sporadically encountered, such as Leuconostoc fallax at 16 h and Pediococcus pentosaceus at 48 h. Hence, the initial occurrence of enterobacteria and to a lesser degree, AAB and the prevalence of Leuconostoc accompanied by the transient occurrence of Lactococcus characterized the standard fermentation. The continued but diminishing prevalence of Leuconostoc and the subsequent prevalence of Lactobacillus characterized the extended fermentation.
Microbial counts during coffee cherry pooling, depulping, fermentation, soaking, and drying. Counts of 2. Sample abbreviations are as in the legend for Fig. Isolate identification during coffee cherry pooling, depulping, fermentation, and soaking.
Isolates are grouped into major microbial categories acetic acid bacteria, lactic acid bacteria, and yeasts. Colors denote the different species identified, and the size of the dots is relative to the number of isolates picked up and identified. The number of isolates picked up and identified at each time point is represented inside each dot.
Distribution of amplicon sequence variants ASVs of the V4 region of the 16S rRNA gene bacteria and the internal transcribed spacer ITS1 region of the fungal ribosomal transcribed unit yeasts and molds during coffee cherry pooling, depulping, fermentation, soaking, on the processing apparatus, in the processing environment, and in the postfermentation waters.
The relative values of these counts were comparable to those found during fermentation. Leuconostoc pseudomesenteroides and P. Notably, a higher abundance of Lactobacillus was found by amplicon sequencing when performing soaking after the extended fermentation reflecting its higher prevalence at the end of the extended fermentation.
Minor variations were found for other communities, such as enterobacteria and Lactococcus. Within the yeast communities, P. This was in contrast with that at the end of soaking, i.
The loss of viability was faster and more pronounced after the extended fermentation than after the standard fermentation. The microbial contamination of the processing apparatus cherry storage bags, depulper exit shaft, empty fermentation tank, and empty soaking tank and environmental samples plantation soil, coffee tree flowers, coffee tree leaves, and fresh cherries from the coffee trees was generally soil or plant associated but was variable for the different pieces of apparatus analyzed Fig.
Notably, taxa that were found extensively during fermentation e. These taxa were sporadically encountered in relatively high relative abundances in the coffee phyllosphere e. Coffee cherries that were attached to the trees displayed microbial counts that spanned a wide range see Fig.
Differences in community compositions of the different samples were elucidated by principal-component analysis PCA see Fig. The fermentation and soaking water samples formed a cluster distinct from the environmental samples. This separation was substantiated by network analysis, through which these environmental samples were disjoined from all other types of samples and were connected with different microbial communities see Fig. The overall sequencing error rate of all amplicons was 0.
All of the microbial groups followed were able to grow on the appropriate agar media when plating samples from coffee cherries inside the sterile plastic bags used for an imitation of the harvesting-depulping interval of the coffee postharvest processing chain see Fig.
However, the most rapid and most substantial increase approximately 2. The LAB community profiles of the postfermentation water PFW; mixture of fermentation water and wash water samples were similar to those at the end of the standard fermentation Fig. S2 and S3. These profiles were characterized by a relatively high prevalence of Leuconostoc , Lactococcus , lactobacilli, enterobacteria, and Pichia. In contrast to the standard fermentation profile, taxa unique to the PFW were found, notably, Clostridium.
The nonamino acid compounds quantified in the fermentation water samples W were divided into three clusters according to hierarchical clustering analysis of the heatmap data A1 to A3 based on their profiles during fermentation Fig. Cluster A1 compounds, represented by sucrose, citric acid, malic acid, and acetaldehyde, reached high concentrations after 12 to 24 h of fermentation and were depleted toward the end F In comparison, cluster A3 compounds, represented by glucose and fructose, also reached the highest concentrations after 12 h of fermentation F Yet, these compounds remained at relatively high concentrations toward the end of the extended fermentation.
For example, glucose and fructose concentrations reached 3. In contrast, cluster A2 compounds lactic acid and mannitol were characterized by their continuous accumulation throughout fermentation. The accumulation of these compounds increased after 16 h of fermentation F16 , resulting in a 2- to 8-fold increase at the end of the extended fermentation F As a result, the most abundant compounds in F64W were lactic acid 8.
Compounds originating from the coffee plant, such as quinic acid, caffeine, trigonelline, and succinic acid, also displayed small increments in their concentrations. Chlorogenic acids CGAs were not found in the fermentation water samples.
Hierarchical clustering analysis and heatmap visualization of selected quantified chemical compound profiles column dendrogram in fermentation and soaking waters FW and SW a and coffee beans B b along the wet coffee processing chain.
Cocoa and coffee are two beverages derived from beans which are processed by fermentation, drying, roasting and grinding. This is in contrast to black tea which is derived from leaves which undergo withering, rolling, an enzymatic oxidative process, and drying. Fermentation of cocoa and coffee involves a number of groups of microorganisms including fungi, yeasts, acetic acid bacteria and lactic acid bacteria. In this chapter, an account of the process of coffee and cocoa fermentation will be given and the role played by the lactic acid bacteria will be described. Unable to display preview.
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Coffee is one of the most important and widely used commercial crops in the world. After ripe coffee cherries are harvested, coffee must pass through several steps to become green raw coffee beans. Commonly, there are three different processing methods used to obtain green coffee beans from coffee cherries, namely, the wet, dry, and semidry methods. Microorganisms yeasts and bacteria play a major role in coffee fermentation process by degrading mucilage by producing different enzymes pectinase , acids, and alcohols. Starter culture development is crucial and is done by selecting microorganisms that have certain characteristics, such as mucilage degradation ability, tolerance to stress during fermentation, the ability to suppress the growth of pathogenic fungi, and a positive impact on the sensory quality of the coffee.
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The first stage of chocolate production consists of a natural, seven-day microbial fermentation of the pectinaceous pulp surrounding beans of the tree Theobroma cacao. There is a microbial succession of a wide range of yeasts, lactic-acid, and acetic-acid bacteria during which high temperatures of up to 50 degrees C and microbial products, such as ethanol, lactic acid, and acetic acid, kill the beans and cause production of flavor precursors. Over-fermentation leads to a rise in bacilli and filamentous fungi that can cause off-flavors.
Джабба, - проворковала женщина в ответ. - Это Мидж. - Королева информации! - приветствовал ее толстяк. Он всегда питал слабость к Мидж Милкен. Умница, да к тому же единственная женщина, не упускавшая случая с ним пококетничать.
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