The Role of Microbes in Coffee Fermentation and Their Impact on Coffee Quality

An interesting open source article on the basics of microbes and yeast in coffee fermentation.

I came across this good basic article on the role of microbes in coffee fermentationFermentation in coffee processing traditionally referred to the stage in wet-processing of the coffee. We now understand that fermentation happens more broadly in nearly all processes, including honey... ...more. I was interested in the fact they single out a particular strain, Rhizopus oligosporus, used in soy tempeh fermentation, as one with possible positive quality impacts on coffee.

One thing the article doesn’t address is the perception of flavor results from yeast-innoculated coffee by the professionals who make market decisions and the public who consumes the coffee. As people seek novel coffee experiences, it’s possible they can adapt to a wider range of flavors not traditionally thought of as “good” by experienced coffee tasters. In fact, it’s quite likely that a public who knows they are buying a “special process” coffee might actually require exotic flavors lest they feel ripped off!

At the same time I have noted a new generation of coffee tasters entering the field who don’t really have the background experience of comparing novel flavors to the orthodoxy of “good coffee”, ie, clean wet-processed, well processed lots from classic cultivars grown at high altitude. That baseline for quality has been toseed out the window in some areas of the coffee world, IMO. What replaces it is a search for more extreme flavors, bonafide taste experiences that pretty much anyone can “get”.

I am not sure where this puts us, but I don’t think it’s a good place necessarily. In any case this article predates our current situation in 2025, using established norms of what is considered “good tasting coffee” it seems to me. -Thompson

I am going to paste the short article here but some of the formatting doesn’t work, in particular the tables. So its best to view the PDF, linked here!

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The Role of Microbes in Coffee Fermentation and Their Impact on Coffee Quality

Mesfin Haile and Won Hee Kang, DepartmentA Department is the term used in some Latin American countries for a State or County. For example, Huila Department is the state in the South of Colombia. ...more of Horticulture and Bio-system Engineering, Kangwon National University, Chuncheon 24341, Republic of Korea Correspondence should be addressed to Won Hee Kang; [email protected] Received 16 November 2018; Revised 3 January 2019; Accepted 1 February 2019; Published 7 March 2019

Abstract: The Role of Microbes in Coffee Fermentation and Their Impact on Coffee Quality

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 processingThe removal of the cherry and parchment from the coffee seed.: Coffee is either wet-processed (also called washed or wet-milled) or dry-processed (also called wild, natural or natural... ...more methods used to obtain green coffeeGreen coffee refers to the processed seed of the coffee tree fruit. Coffee is a flowering shrub that produces fruit. The seeds of the fruit are processed, roasted,... ...more 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 mucilageMucilage indicates the fruity layer of the coffee cherry, between the outer skin and the parchment layer that surrounds the seed. It readily clings to the inner parchment... ...more by producing different enzymes (pectinase), acidsMany acids contribute to coffee flavor: acetic, malic, citric, quinic, tartaric, phosphoric, etc.: Many acids contribute to coffee flavor; malic, citric, quinic, tartaric, phosphoric, etc. See Acidity or... ...more, 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. Currently, green coffee beans obtained from farms that use any of the above processing methods are fermentedAs a defect flavor, a fruit quality in a coffee that is excessively ripe, toward rotten. Fermented flavor can be the result of poor wet-processing, over-ripe cherry, or... ...more with selected microorganisms to improve the flavour and aromaAroma refers to sensations perceived by the olfactory bulb and conveyed to the brain; whether through the nose or "retro-nasally": The aromatics of a coffee greatly influence its... ...more of the coffee. This is the result of a new insight into the development of unique flavoured coffee and into engaging with the coffee market to better benefit. This review gives a comprehensive overview of the fermentation process, micro- organisms and starter cultures, and fermentation’s impact on coffee quality. Future prospects are also discussed through the incorporation of recent research.

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1. Introduction

Coffee is one of the most widely used nonalcoholic drinks, and its consumption is spreading globally. It is the second most important commodity exchanged in world markets, next to crude oil. BrazilBrazil is a coffee giant . As Frank Sinatra sang, "they grow an awful lot of coffee in Brazil".: Brazil is a coffee giant . As Frank Sinatra... ...more is the leading producer and exporter of CoffeaThe botanical genus colloquially referred to as the “coffea genus,” which is comprised of over 120 individual species. These are generally opposite-leaved, evergreen shrubs or small understory trees... ...more arabicaArabica refers to Coffea Arabica, the taxonomic species name of the genus responsible for around 75% of the worlds commercial coffee crop.: Arabica refers to Coffea Arabica, the... ...more [1], followed by IndonesiaUSDA is (obviously) the United States Department of Agriculture. USDA also had coffee plant breeding programs in the past and one variety they distributed to Indonesia and was... ...more, EthiopiaEthiopia, formerly known as Abyssinia, or a coffee cultivar: Ethiopia, or more specifically the Empire under Haile Selassie,  was known as Abyssinia. The name is Latin, derived from... ...more, the Philippines, MexicoMexican coffee originates from South-central to Southern regions of the country. For that reason, coffees from Coatepec and Veracruz are much different from Oaxacan Plumas, which are in... ...more, Vietnam, and 40 other countries. People drink coffee to relax and enjoy its diverse flavours and aromas. It has physiological and psychological effects be- yond its nutritional benefits. In recent years, an appreciation for quality coffee has lent importance to specialty coffees, which have unique aromas and remarkable flavours. These characteristics are linked to the areas where the coffees are grown and their cultivated genotypes [2]. Some researchers report significant differences among beverages from coffee that is processed using different methods [3, 4]. It is cur- rently believed that different processing methods induce different metabolic reactions in coffee fruits, which can affect the chemical compositions of the coffee beans and thereby their cuppingCupping is a method of tasting coffee by steeping grounds in separate cups for discrete amounts of ground coffee, to reveal good flavors and defects to their fullest.... ...more quality [5, 6].

Fermentation is a metabolic process that uses sugar, either in the absence (anaerobic) or presence (aerobic) of oxygen. Coffee fermentation is critical for removing mucilage from parchmentGreen coffee still in its outer shell, before dry-milling, is called Parchment coffee (pergamino). In the wet process, coffee is peeled, fermented, washed and then ready for drying... ...more coffee. Coffee mucilage con- tains polysaccharides (pectin), celluloseCellulose is the principle fiber of the cell wall of coffee. It is partially ordered (crystalline) and partially disordered (amorphous). The amorphous regions are highly accessible and react... ...more, and starch. The mucilage can prolong the time needed to dry the coffee beans and, in some cases, also lead to mould development, which reduces the final quality of the coffee. The fer- mentation process is facilitated by enzymes that naturally occur in the coffee fruit and microflora acquired from the environment.

Microorganisms (yeast, bacteria, and fungi) play a major role in degrading mucilage by producing various enzymes, alcohols, and acids during the fermentation pro- cess. There are several commercially available enzymes for coffee fermentation. The earliest was marketed under the trade name Benefax. Later brands have included Pectozyme, Cofepec, and Ultrazym, which are mixtures of pectinase, hemicellulose, and cellulose [7]. Current research indicates that coffee fermentation is becoming more popular for producing specialty coffeeSpecialty coffee was a term devised to mean higher levels of green coffee quality than average "industrial coffee" or "commercial coffee". At this point, the term is of... ...more. Vaast et al. [8] have reported that various physiological changes occur in grains during fer- mentation, such as decreases in water content and simple sugars and the development of aroma and flavour pre- cursors. 0erefore, the purpose of this review is to briefly explain the need for coffee fermentation and its impact on major coffee quality attributes, in company with recent research outcomes. 0is review will provide a clear un- derstanding of the role of microorganisms in coffee fer- mentation and can direct future research into commercializing potential starter cultures.

2. Coffee Fermentation Process

Fermentation is a chemical processA decaffeination method where beans are soaked in hot water, which is then treated with a chemical that bonds to caffeine (either methylene chloride or ethyl acetate).: A... ...more in which complexThe co-presence of many aroma and flavor attributes, with multiple layers. A general impression of a coffee, similar to judgments such as "balanced" or "structured" ...more molecules are broken down into simpler molecules, pro- ducing liquid products and gasses (volatile compounds). Coffee fruits are processed by one of three methods im- mediately after harvesting to allow spontaneous or in- digenous fermentation to occur. 0e three different coffee processing methods are referred to as dry, wet, and semidry. Depending on the processing type, the length of time needed for fermentation varies. 0e main purpose of the fermen- tation process in all methods is to remove the mucilage layer, which is rich in polysaccharides (pectin), and to decrease the water content of the coffee beans. However, if carefully managed, fermentation also has a positive impact on the coffee’s quality attributes.

Wet processing is largely used for Arabica coffee. Im- mediately after harvesting, the ripe coffee fruits go through a flotation process to clean debris and remove floatersFloaters are defective coffee cherries or depulped seeds that float to the surface of a water bath.: During the wet-process method, coffee cherry or the de-pulped (without skin)... ...more (low- densityThe density of a coffee bean is often taken as a sign of quality, as a more dense bean will roast more with a better dynamic. The density... ...more fruits). 0e coffee fruit is then pulped, put through a 24- to 48-hour underwater tank fermentation process, and dried until the moisture content reaches 10%–12% [9, 10]. In dry processing, the coffee fruits are cleaned and floaters are separated immediately after harvesting, and the entire coffee fruits are dried in the sun on platforms and/or on the floor without prior removal of the pulp [11]. Semidry processing is a combination of both methods, in which the coffee fruits are depulped but the fermentation process occurs directly under the sun on a platform [12].

2.1. Composition of Mucilage. Coffee mucilage is a viscous liquid residue produced in the coffee industry that is dis- posed of without treatment directly into watercourses, causing serious contamination problems. 0e physical and chemical properties of coffee mucilage vary according to species and varietyA botanical variety is a rank in the taxonomic hierarchy below the rank of species and subspecies and above the rank of form (form / variety / subspecies... ...more. Studies have shown that the mucilage/ water ratio increases as altitude increases [13]. Mucilage is composed of water (84.2%), protein (8.9%), reducing sugar (4.1%), pectates (0.91%), and ash (0.7%) [14]. Knowing these compositions is essential for the understanding of coffee fermentation. 0e chemical composition and composition of mucilage before and after fermentation are described in Tables 1 and 2, respectively.

3. Microbial Enzymes and Starter Cultures for Coffee Fermentation

3.1. Enzymes Produced during Coffee Fermentation. Previous reports have identified over 50 yeasts and bacterial species that are present during coffee fermentation [15, 16]. Silva et al. [17] mention that the microorganisms in coffee fermentation contribute to the production of ethanol and lactic, butyric, acetic, and other higher carboxylic acids during the fermentation of pectinaceous sugars. Coughlan and Mayer [18] report that a variety of extracellular en- zymes are generated by cellulolytic Bacillus species, which potentially contribute to the breakdown of cellulose and pectin substances that exist in the skin, pulp, and mucilage of coffee cherries [11].

The ethree most important enzymes produced by mi- croorganisms for degrading pectin substances during coffee fermentation are pectin lyase, polygalacturonase, and pectin methyl esterase. Pectin lyase catalyses pectin degradation by trans-elimination, releasing unsaturated galacturonic acids [19]. Polygalacturonase is the main enzyme involved in coffee fermentation. It catalyses the hydrolysis of α-1,4 glycosidic bonds into pectic acid (polygalacturonic acid) [20]. Pectin methyl esterase is responsible for the de- esterification of the methoxyl group of the pectin, form- ing pectic acid and methanol [21].

3.2. Starter Cultures for Coffee Fermentation. A starter culture is a microbiological culture that accelerates the fermentation process. In the food fermentation industry, starter cultures are widely known for use in cheese, yogurt, beer, and wine [22, 23]. 0e use of starter culture in a controlled coffee fermentation may ensure the best quality of coffee and increase the economic benefits for the growers [24]. As Corsetti et al. [25] have mentioned, the microor- ganisms selected for starter cultures are expected to have certain characteristics, such as being nonpathogenic, non- toxigenic, and adaptable to the raw materials and process. 0ey should also produce sensory quality, prolong shelf life, reduce the processing time, and repress the development of food-related pathogenic microorganisms. Only limited studies have been reported on the use of a starter culture for coffee fermentation. 0e first study, by Agate and Bhat [26], effectively introduced a coffee fermentation starter culture. 0is study demonstrated that the addition of a mixture of three Saccharomyces species (viz., S. marxianus, S. bayanus, and S. cerevisiae var. ellipsoideus) facilitated the fermenta- tion process by quickening the degradation of the mucilage layer.

A study was also conducted on the microbial and physicochemical characteristics of coffee fermentation by inoculating pectinolytic microbes isolated from sponta- neous fermentation (viz., Lactobacillus brevis L166, Erwinia herbicola C26, B. subtilis C12, and Kluyveromyces fragilis K211) [27]. However, the authors reported that the in- oculation of the pectinolytic microbes did not speed up the degradation of the polysaccharide compounds or modify the organolepticOrganoleptic refers to any sensory properties of, in this case, the coffee beverage. It involves flavor, color, odor and mouthfeel. Organoleptic testing involves inspection through visual examination, smelling... ...more characteristics of the beverage. 0ey suggested that it would be better to use lactic acid bacteria instead in order to remain as close as possible to natural fermentation.

Recently, coffee fermentation using aromatic yeasts to develop flavour has been studied during dry [28], semidry [28], and wet [29] processing. A large microbial diversity is usually observed in coffee fermentation; however, most of these indigenous microorganisms presumably do not have important characteristics for improving the final coffee product, and a few species were chosen based on their final impacts on the coffee’s flavour and aroma. 0e microbial ecology of the indigenous yeasts from which starter cultures were selected is reported in Tables 3 and 4.

4. Coffee Fermentation’s Impacts on Flavour and Aroma

4.1. 0e Positive Impact of Fermentation on Coffee Flavour and Aroma. Around the globe, coffee is popular as a non- alcoholic drink because of its pleasant aroma and refreshing flavours. Joe ̈t et al. [31] report that coffee beans themselves contain all the precursors required to provide the standard coffee flavour and aroma during roasting. However, the fermentation process can increase the diversity of coffee aroma and flavour compounds. As mentioned by Tressi [32] and Farah et al. [33], more than 700 volatile and nonvolatile compounds that contribute to coffee flavour have been identified. 0e coffee’s species, variety, geographic originIn coffee talk, it refers to a coffee-producing region or country; such as, "I was just at origin." Of course "Origin" for most product we use is not... ...more, and level of roasting determine the constitution and quantity of the flavour resulting from these compounds [34]. A supporting report indicates that factors during the preharvest and postharvest processes also critically affect the coffee aroma [35].

During coffee fermentation, microorganisms produce diverse metabolites. Microbial activity and the extent of fermentation determine the concentrations of free sugars (e.g., glucose and fructose) and free amino acids that con- tinue to surround the bean and subsequently contribute to the production of MaillardAn important reaction in coffee roasting that results in the browning of the green coffee seed.: The Maillard reaction is a chemical reaction between an amino acid and... ...more compounds and volatiles during the roasting process [36]. Pederson and Breed [37] sum- marized early studies on the implication that fermentation improves coffee quality. Wet-processed coffee has superior aroma qualities to dry-processed coffee because of the ar- omatic compounds produced during the removal of the mucilage layer in wet processing [38]. 0e selection of ap- propriate microorganisms that have a positive impact on coffee flavour and aroma during fermentation is critical, and the fermentation process should be controlled to achieve this positive impact.

4.2. 0e Negative Impact of Fermentation on Coffee Flavour and Aroma. 0e major challenge in coffee fermentation, according to several studies, is the difficulty of controlling the process. Overfermentation is one of several dilemmas described by coffee farmers and scientists [39–41]. 0e fermentation process must be well controlled to ensure the development of beneficial microorganisms that produce a high-quality beverage with a good aroma. When fermen- tation fails, it results in the development of spoilage mi- croorganisms that adversely affect the coffee’s aroma and flavour. Coffee beans resulting from such fermentations are often referred to as “stinkers” [42, 43]. Underfermented coffee beans contain residual mucilage and sugar that prevent drying and create a conducive environment for the development of spoilage bacteria and fungi. Overfermen- tation encourages the production of undesirable chemical compounds, notably propionic and butyric acids, which confer off-flavours, such as an onion taste [44–47]. Lopez et al. [41] report that these acids should not be present in a concentration greater than 1mg·mL−1. Species of the Ba- cillus genus, especially B. megaterium, may be responsible for the propionic acid found in coffees processed via dry or natural processing [11].

As described by Silva et al. [11], propionic acid is detected in high concentrations only when the fermen- tation process proceeds for longer than its optimum du- ration. Enterobacteriaceae and acetic acidAcetic acid can lead to vinegar-like flavors in over-mature coffees, or bitterness in high quantities. But in moderate amounts it adds a positive winey note to the cup.... ...more bacteria lead to the production of excessive acetic acid during prolonged fermentation in dry processing [11]. Bade-Wegner et al. [47] state that overfermentation may also produce short- chain fatty acids and their estersAn ester is an often fragrant organic or partially organic compound formed by the reaction between an acid (including amino acids) and an alcohol. They play a smaller... ...more, such as 2-methyl butanoic acid ethyl ester, 3-methyl butanoic acid ethyl ester, and cyclohexanoic acid ethyl ester. 0ese can be detrimental to coffee quality if they are present at concentrations higher than 1.8, 13.9, and 14 mg·kg−1, respectively. Furthermore, the growth of filamentous fungi and mycotoxins, which can generate off-flavours, should be controlled by the management of the fermentation and drying processes [48–52].

Species identified

Lactobacillus plantarum, L. brevis, Lactococcus lactis, Leuconostoc mesenteroides, Pichia anomala, P. caribbica, Rhodotorula mucilaginosa, Saccharomyces sp., S. bayanus, S. cerevisiae, Candida ernobii,
C. fukuyamaensis, C. membranifaciens, C. carpophila, Hanseniaspora uvarum, Torulaspora delbrueckii, Arxula sp., Kloeckera sp., and Kluyveromyces sp.

Debaryomyces hansenii, D. polymorphus, D. polymorphus, Pichia guilliermondii, P. guilliermondii, P. burtonii, P. anomala, P. burtonii, P. sydowiorum,
P. subpelliculosa, Candida saitoana, C. fermentati,
C. membranifaciens, Stephanoascus smithiae, Saccharomyces cerevisiae, Arxula adeninivorans, and A. adeninivorans

Pichia fermentans, P. guilliermondii, P. caribbica, Hanseniaspora opuntiae, Candida glabrata, C. quercitrusa, and Saccharomyces sp.

Selected species

Saccharomyces cerevisiae

Pichia guilliermondii Pichia fermentans

and Saccharomyces sp.

Reference

Vilela et al. [12]; Silva et al. [15]

Silva et al. [11]; Silva et al. [15]

Pereira et al. [29]; Pereira et al. [16]

5. Green Coffee Bean Fermentation with Selected Microorganisms and Its Future Prospects

A study was conducted by Kwak et al. [53] on the effect of the yeast fermentationYeast fermentation involves adding different types of external yeasts to the fermentation stage of wet processing in order to help control the outcome, and ultimately, how the coffee... ...more of green coffee beans on their antioxidant activity and consumer acceptability. 0ey reported that 24 h yeast fermentation induced a notable increase in antioxidant activity and total polyphenol and flavonoid contents. 0e consumer acceptance of the fermented coffee beans was slightly lower than that of the controls (nonfermented), with the exception of one fermented coffee beans (fermented with Saccharomyces species), which gained approximately 39.4% of consumers’ preference over the controls [53].

Rhizopus oligosporus is a common fungal species widely used as a starter culture in fermented foods, such as soy tempeh (a traditional fermented soybean product). During fermentation by R. oligosporus, extracellular enzymes, such as proteases [54], and polysaccharide-degrading enzymes, such as xylanase, polygalacturonase, cellulase, arabinase, b-D- glucosidase, and a-D galactosidase [55], are secreted. A study was conducted on the effect of the solid-state fermen- tation of green coffee beans by R. oligosporus on their volatile and nonvolatile profile. As reported by Lee et al. [56], during fermentation, some volatiles were broken down, while the production of others could be correlated with the metabolism of aroma precursors by R. oligosporus. Fermentation with R. oligosporus significantly improved the compositions of the aroma precursors in green coffee beans, and these compounds

are responsible for the production of potent classes of odorants (pyrazines, thiols, furanones, and guaiacols) that give rise to the characteristic coffee aroma during roasting [56].

Coffee enjoys wide global acceptance, and small im- provements in coffee quality can make a significant differ- ence and expand market opportunity. Because green coffee beans are used for fermentation instead of parchment coffee (with mucilage), this can be done by coffee-processing companies. However, the isolation and identification of microorganisms that significantly impact coffee sensory quality should be further investigated for the development of a starter culture. Future research may also investigate the commercialization of the aroma and flavour modulation of green coffee beans via fermentation.

6. Conclusion

Fermentation is crucial in coffee processing, not only to remove mucilage, but also, if well controlled, to create es- sential sensory quality characteristics. However, it has a disadvantage that if fermentation proceeds beyond the recommended time, microorganisms can also reduce the quality by creating off-flavours and undesirable character- istics. Of the diverse microflora found in natural coffee fermentation, a few may be selected for use as a starter culture. However, the potential use of starter cultures for coffee fermentation is not yet well studied. Most microor- ganisms isolated from spontaneous coffee fermentation lack attributes for improving coffee’s sensory quality selection of food-grade microorganisms and their use in fermenting green coffee beans require further research. 0is review provides precise information about the role of mi- croorganisms in coffee fermentation and their impact on coffee flavour and aroma. Other molecular sciences can contribute to an understanding of the chemical compounds produced during fermentation and their impact on coffee quality, leading to the availability of more credible and advanced information. Integrating multidisciplinary re- search will be helpful in more detailed studies.

Acknowledgments

0is study was supported by 2018 research grant from the Kangwon National University (no. 520180086).

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Table 3: 0e list of developed culture and their characteristics and effect on coffee fermentation.

Starter culture Saccharomyces cerevisiae,

Candida parapsilosis, and Pichia guilliermondii

Pichia fermentans and Saccharomyces sp.

Pichia fermentans

ScreeningRunning coffee through a screen with holes of a fixed size to sort beans for size.: Running coffee through a screen with holes of a fixed size to... ...more criteria

Pectinolytic activity and production of organicGrown without the use of artificial fertilizers, herbicides, etc.: Organic coffee has been grown according to organic farming techniques, typically without the use of artificial fertilizers. Some farms... ...more acids and volatile aroma compounds

Pectinolytic activity, growth capacity under stress conditions, and production of volatile aroma compounds

Pectinolytic activity, growth capacity under stress conditions, and production of volatile aroma compounds

Effect on coffee quality

Production of high-quality coffee beverages with special aroma of caramelCaramel is a desirable form of sweetness found in the flavor and aroma of coffee, and is an extension of roast taste. Extremely light or dark coffees will... ...more, herbs, and fruits

Production of coffee beverages with high sensory scores for fruityIn some coffee taster’s lexicon, “fruity” means the coffee is tainted with fruit, and “fruited” means a coffee is graced by positive fruit notes. We don't exactly see... ...more, butteryA mouthfeel description indicating thickness and creaminess, and can also be a flavor description.: Buttery is primarily a mouthfeel description indicating thickness and creaminess. It indicates a high... ...more, and fermented aroma

Production of high-quality coffee beverages with intense perception of “vanillaVanilla notes in coffee are often related to caramelization notes, as butter and vanilla can be found in flavors and aromatics of roast reactions from reducing of sugars. ...more” tests and “floralFloral notes in coffee exemplify the connection between taste and smell. Describing the taste of a specific flower is near impossible...we always default to “it tastes like it... ...more” aroma

References

Silva et al. [15]; Evangelista et al. [30]; Evangelista et al. [28]

Pereira et al. [29] Pereira et al. [16]

Table 4: Microbial ecology of yeasts and bacteria of coffee fermentation from which starter culture selected.