Microbial ecology and starter culture technology in coffee processing

Effects of Coffea canephora genotypes on the microbial community of soil and fruit

In recent years, the role of microbial communities in agricultural systems has received increasing attention, particularly concerning their impact on plant health and productivity. However, the influence of host plant genetic factors on the microbial composition of coffee plants remains largely unexplored. This study provides the first comprehensive investigation into how genotype affects the microbial communities present in the rhizosphere and fruits of Coffea canephora. Conducted on a commercial coffee farm in Brazil, we analyzed six genotypes of C. canephora var. Conilon. Soil and fruit samples were collected from which microbial DNA was extracted and sequenced, targeting the V3-V4 region of the 16 S rDNA and the ITS1 region for fungi. A total of 12,239,769 reads were generated from the 16 S rDNA and ITS1 regions. The PCoA revealed distinct patterns of beta diversity, with genotype 153 exhibiting significant isolation in soil bacterial communities. The dominant bacterial orders included Rhizobiales and Rhodobacterales, while the fungal community comprised diverse taxa from Saccharomycetales and Hypocreales. LEfSe analysis identified key metagenomic biomarkers, highlighting genotype Baiano 4 for its richness in fruit-associated taxa, whereas genotype 153 exhibited lower diversity in both soil and fruit samples. This work enhances our understanding of the microbiomes associated with different coffee genotypes, providing evidence of how host genetic variation influences microbial community composition. Our findings indicate that specific microbial taxa are enriched in the fruits and soil of various genotypes. Future research should focus on identifying these microorganisms and elucidating their specific functions within the rhizosphere and coffee fruits.

Coffee substitutes: A review of the technology, characteristics, application, and future perspective

Despite being one of the most frequently consumed beverages worldwide, there are concerns that excessive consumption of coffee can have adverse effects, especially concerning the addictive and stimulating effects of the alkaloid caffeine, which contributes to coffee's popularity. It is known to increase the risk of hypertension and heart rate among predisposed individuals, adversely affecting the nervous system. Even though they differ in nature from those found in coffee, coffee substitutes can be considered economically and health-wise as a favorable alternative to natural coffee brews. This review summarizes the state-of-the-art varieties of plants used as coffee substitutes and discusses their production technology, chemical composition, nutritional properties, health benefits, economic challenges, and rationale for choosing the plant as a substitute for coffee. Various instant products and coffee substitute blends are also available on the market especially based on different kinds of plants and herbs like ginger, rye, date pits, quinoa, lupine, chicory, barley, rye, oak, and so on. These coffee substitutes have several advantages especially having no caffeine and containing different beneficial phytochemicals, although the results of the difference between the levels of harmful compounds in coffee and coffee substitutes were contradictory. Therefore, it is no wonder that the development of coffee substitutes, which are beverages that are able to mimic the taste and aroma of coffee, is on the rise at present.

Genetic diversity of the fungal community that contributes to the sensory quality of coffee beverage after carbonic maceration and fermentation

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.

Developing defined starter culture for reproducible profile of flavour compound in Chinese xiaoqu baijiu fermentation

Defined starter cultures, containing selected microbes could reduce the complexity of natural starter, are beneficial for controllable food fermentations. However, there are challenges in identifying key microbiota and constructing synthetic microbiota for traditional food fermentations. Here, we aimed to develop a defined starter culture for reproducible profile of flavour compounds, using Chinese Xiaoqu Baijiu fermentation as a case. We classified all microbes into 4 modules using weighted correlation network analysis. Module 3 presented significant correlations with flavour compounds (P < 0.05) and the highest gene abundance related with flavour compound production. 13 dominant species in module 3 were selected for mixed culture fermentation, and each species was individually deleted to analyse the effect on flavour compound production. Ten species, presenting significant effects (P < 0.05) on flavour compound production, were selected for developing the starter culture, including Rhizopus oryzae, Rhizopus microsporus, Saccharomyces cerevisiae, Pichia kudriavzevii, Wickerhamomyces anomalus, Lactobacillus acetotolerans, Levilactobacillus brevis, Weissella paramesenteroides, Pediococcus acidilactici, and Leuconostoc pseudomesenteroides. After optimising the structure of the starter culture, the profile similarity of flavour compounds produced by the starter culture reached 81.88% with that by the natural starter. This work indicated feasibility of reproducible profile of flavour compounds with defined starter culture for food fermentations.

The Relationship between Microbial Communities in Coffee Fermentation and Aroma with Metabolite Attributes of Finished Products

Coffee is a critical agricultural commodity and is used to produce premium beverages enjoyed by people worldwide. The microbiome of coffee beans has proven to be an essential tool that improves the flavor profile of coffee by creating aromatic flavor compounds through natural fermentation. This study investigated the natural microbial consortium during the wet process fermentation of coffee onsite in Thailand in order to identify the correlation between microbial diversity and biochemical characteristics including flavor, aroma, and metabolic attributes. Our study found 64 genera of bacteria and 59 genera of yeast/fungi present during the fermentation process. Group of microbes, mainly yeast and lactic acid bacteria, that predominated in the process were significantly correlated with preferable flavor and aroma compounds, including linalyl formate, linalool, cis-isoeugenol, trans-geraniol, and (-)-isopulegol. Some of the detected metabolites were found to be active compounds which could play a role in health.

Fermentation of coffee fruit with sequential inoculation of Lactiplantibacillus plantarum and Saccharomyces cerevisiae: effect on sensory attributes and chemical composition of the beans

This study has innovative aspects related to the use of sequential inoculation technique in the coffee bean fermentation process: the inoculation of Lactiplantibacillus plantarum followed by Saccharomyces cerevisiae, in the fermentation of coffee fruit for the production of specialty natural coffees. The objective was to evaluate the effect of this technique and of the total fermentation time on the sensory attributes of the coffee beverage and on the organic acid profile, bioactive compounds, and fatty acid profile of the beans. The fermentation of coffee fruit with sequential inoculation resulted in greater acidity of the beverage and contributed to increases of up to 2 points in coffee fermented. The total fermentation time was directly related to the organic acid content, and the longer the total fermentation time was, the greater the organic acid content. The fatty acid content and bioactive compound content showed little variation among treatments.

Soybean fermentation: Microbial ecology and starter culture technology

Fermented soybean products, including Soya sauce, Tempeh, Miso, and Natto have been consumed for decades, mainly in Asian countries. Beans are processed using either solid-state fermentation, submerged fermentation, or a sequential of both methods. Traditional ways are still used to conduct the fermentation processes, which, depending on the fermented products, might take a few days or even years to complete. Diverse microorganisms were detected during fermentation in various processes with Bacillus species or filamentous fungi being the two main dominant functional groups. Microbial activities were essential to increase the bean's digestibility, nutritional value, and sensory quality, as well as lower its antinutritive factors. The scientific understanding of fermentation microbial communities, their enzymes, and their metabolic activities, however, still requires further development. The use of a starter culture is crucial, to control the fermentation process and ensure product consistency. A broad understanding of the spontaneous fermentation ecology, biochemistry, and the current starter culture technology is essential to facilitate further improvement and meet the needs of the current extending and sustainable economy. This review covers what is currently known about these aspects and reveals the limited available information, along with the possible directions for future starter culture design in soybean fermentation.

Identification of antioxidant and flavour marker compounds in Kalosi-Enrekang Arabica brewed coffee processed using different postharvest treatment methods

This research aims to predict the presence of marker compounds that differentiate tubruk brew from coffee beans with different postharvest processing. This research also aims to predict compounds correlating with antioxidant activity and sensory flavour attributes. This research used Kalosi-Enrekang Arabica coffee beans, which were processed with three different postharvest processing (honey, full-washed and natural), roasted at medium level, and brewed using the tubruk method. Each brew was analyzed for chemical profiles using LC-MS and GC-MS, antioxidant analysis using the DPPH IC50 and FRAP methods, and sensory analysis for flavour using the QDA and SCAA methods for cupping scores. OPLS-DA analysis revealed the presence of marker compounds from each brew, and the dried fruit flavour attribute was to be an inter-process marker. After that, OPLS analysis showed marker compounds that correlate to antioxidant activity and flavour attributes. Rhaponticin is thought to be one of the marker compounds in natural coffee brews and is one of the compounds that correlates to the antioxidant activity of the DPPH method (IC50); prunin is thought to be one of the marker compounds for full-washed coffee brews and is one of the compounds that correlates to the activity antioxidants of FRAP method. Triacetin, which is thought to be a marker compound in natural brewed coffee, correlates with fruity flavour. 3-acetylpyridine, as a marker in honey-brewed coffee, correlates with nutty flavour. Even though there are differences in dominant flavours, the cupping score shows the brew is categorized as a specialty. This research shows that different post-harvest processing processes influence the compound profile, antioxidant activity and flavour attributes of Tubruk brewed coffee.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13197-024-05948-8.

Exploring the microbiome of coffee plants: Implications for coffee quality and production

Coffee stands as one of the world's most popular beverages, and its quality undergoes the influence of numerous pre- and post-harvest procedures. These encompass genetic variety, cultivation environment, management practices, harvesting methods, and post-harvest processing. Notably, microbial communities active during fermentation hold substantial sway over the ultimate quality and sensory characteristics of the final product. The interaction between plants and microorganisms assumes critical significance, with specific microbes assuming pivotal roles in coffee plant growth, fruit development, and, subsequently, the fruit's quality. Microbial activities can synthesize or degrade compounds that influence the sensory profile of the beverage. However, studies on the metabolic products generated by various coffee-related microorganisms and their chemical functionality, especially in building sensory profiles, remain scarce. The primary aim of this study was to conduct a literature review, based on a narrative methodology, on the current understanding of the plant-microorganism interaction in coffee production. Additionally, it aimed to explore the impacts of microorganisms on plant growth, fruit production, and the fermentation processes, directly influencing the ultimate quality of the coffee beverage. Articles were sourced from ScienceDirect, Scopus, Web of Science, and Google Scholar using specific search terms such as "coffee microorganisms", "microorganisms-coffee interactions", "coffee fermentation", "coffee quality", and 'coffee post-harvest processing". The articles used were published in English between 2000 and 2023. Selection criteria involved thoroughly examining articles to ensure their inclusion was based on results about the contribution of microorganisms to both the production and quality of the coffee beverage. The exploration of microorganisms associated with the coffee plant and its fruit presents opportunities for bioprospecting, potentially leading to targeted fermentations via starter cultures, consequently generating new profiles. This study synthesizes existing data on the current understanding of the coffee-associated microbiome, its functionalities within ecosystems, the metabolic products generated by microorganisms, and their impacts on fermentation processes and grain and beverage quality. It highlights the importance of plant-microorganism interactions in the coffee production chain.

Yeasts are essential for mucilage degradation of coffee beans during wet fermentation

During wet fermentation, mucilage layers in coffee cherries must be removed completely. To explain mucilage degradation, several controversial hypotheses have been proposed. The aim of this work was to improve our understanding of the kinetics of mucilage breakdown. Pulped coffee beans were wet fermented with seven different treatments for 36 h. Endogenous bacteria and yeasts are selectively suppressed, and pectinases or lactic acid are added. They also involve maintaining the beans at pH 7 throughout fermentation and using spontaneous fermentation without additives as a control. During spontaneous fermentation, yeast and lactic acid bacteria were detected and significantly increased to 5.5 log colony-forming units (CFU)/mL and 5.2 log CFU/mL, respectively. In the first 12 h of fermentation, there was a significant degree of endogenous pectinolytic activity, which resulted in partly destroyed beans in the absence of microorganisms. By adding pectinase and lactic acid to the fermentation mass, the breakdown process was accelerated in less than 8 h. When yeast was present throughout the fermentation, complete degradation was achieved. Bacteria played no critical role in the degradation. Klebsiella pneumoniae and Erwinia soli were found in a lower population and showed weaker pectinolytic activities compared to Hanseniaspora uvarum and Pichia kudriavzevii. During wet fermentation, mucilage degradation appears to be mediated by endogenous enzymes at the early stage, whereas microbial contributions, mainly yeasts, occur subsequently. H. uvarum and P. kudriavzevii may be promising candidates to be tested in future studies as coffee starter cultures to better control the mucilage degradation process.

Isolation of Yeast and LAB from Dry Coffee Pulp and Monitoring of Organic Acids in Inoculated Green Beans

Yeast and lactic acid bacteria (LAB) are known to play an important role in the fermentation process of coffee post-harvest. This study aimed to isolate and screen yeast and LAB to be applied in lab-scale refermentation of commercial green coffee beans and coffee pulp with the aim of modifying the composition of organic acids (OAs) in coffee beans. Yeast and LAB strains were isolated from green coffee beans and dry coffee pulp and identified, and their effect on OA concentration in the coffee beans was quantified. In addition, the effects of different fermentation conditions (additional carbon source, different inoculum dose, and different types of coffee pulp) were evaluated based on OA quantification. Nine yeast isolates of Rhodotorula mucilaginosa and Wickerhamomyces anomalus were identified, and 11 LAB isolates of the species Enterococcus mundtii were identified. Of the 7 OAs quantified, quinic acid was the most abundant. The inoculation of isolated yeasts and LAB led to higher concentrations of OAs, showing the potential to realize modification of the OA composition of green coffee beans by re-fermentation with coffee-originated isolates.

Coffee fermentation process: A review

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.

Effects of Different Probiotics on the Volatile Components of Fermented Coffee Were Analyzed Based on Headspace-Gas Chromatography-Ion Mobility Spectrometry

Headspace-gas chromatography-ion mobility spectrometry (HS-GC-IMS) was used to study the effects of four kinds of probiotics on the volatile components of fermented coffee. The fingerprints showed that 51 compounds were confirmed and quantified, including 13 esters, 11 aldehydes, 9 alcohols, 6 ketones, 3 furans, 5 terpenes (hydrocarbons), 2 organic acids, 1 pyrazine, and 1 sulfur-containing compound. After fermenting, the aroma of the green beans increases while that of the roasted beans decreases. After roasting, the total amount of aroma components in coffee beans increased by 4.48-5.49 times. The aroma differences between fermented and untreated roasted beans were more significant than those between fermented and untreated green beans. HS-GC-IMS can distinguish the difference in coffee aroma, and each probiotic has a unique influence on the coffee aroma. Using probiotics to ferment coffee can significantly improve the aroma of coffee and provide certain application prospects for improving the quality of commercial coffee beans.

Effect of green and roasted coffee storage conditions on selected characteristic quality parameters

The paper attempts to determine the best storage conditions for green and roasted coffee beans. Coffee beans were processed in various ways-some of them were washed or left in their natural state after harvesting, then they were stored in two types of packaging with different permeability, i.e. jute bag and GrainPro polymer bag, ensuring stable conditions in three temperature chambers, i.e. - 10, 10 and 20 °C. The grains treated in this way were evaluated after 3, 6, 9, and 12 months. The selection of the analyzed parameters (in roasted coffee-cupping and 3 selected volatile organic compounds; in green coffee-average water activity, content of volatile fatty acids, 6 selected volatile organic compounds) was to monitor the ongoing processes, and thus the qualitative changes taking place in grains. The research shows that grain stored at 20 °C ages the fastest. Grains stored in - 10 °C and 10 °C chambers perform similarly well. The evaluation of the parameters shows that among the grains stored in these two chambers, the method of grain processing (Natural/Washed) had a greater impact on the results, while the type of packaging did not differentiate the grains to such a significant extent.

Unlocking the Aromatic Potential of Native Coffee Yeasts: From Isolation to a Biovolatile Platform

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.

Study on coffee quality improvement by self-induced anaerobic fermentation: Microbial diversity and enzymatic activity

The postharvest fermentation process of coffee has rapidly advanced in the last few years due to the search for quality and diversity of sensorial profiles. A new type of fermentation, named self-induced-anaerobic fermentation (SIAF), is a promising process that has been increasingly used. This study aims to evaluate the sensorial improvement of coffee beverages during SIAF and the influence of microorganism's community and enzymatic activity. The SIAF process was conducted in Brazilian farms for up to 8 days. The sensorial quality of coffee was evaluated by Q-graders; the microbial community was identified by the high-throughput sequencing of 16S rRNA and ITS regions; and the enzymatic activity (invertase, polygalacturonase, and endo-β-mannanase) was also investigated. SIAF increased up to 3.8 points in the total score of sensorial evaluation (compared to the non-fermented sample), in addition to presenting more flavor diversity (especially within the fruity and sweetness descriptors). The high-throughput sequencing identified 655 bacterial and 296 fungal species during the three processes. The bacteria Enterobacter sp., Lactobacillus sp., Pantoea sp., and the fungi Cladosporium sp. and Candida sp. were the predominant genera. Fungi that are potential producers of mycotoxin were identified throughout the process, which indicates a risk of contamination since some of them are not degraded in the roasting process. Thirty-one species of microorganisms were described for the first time in coffee fermentation. The microbial community was influenced by the place where the process was carried out, mainly in relation to the diversity of fungi. Washing the coffee fruits before fermenting led to a fast reduction of pH; a fast development of Lactobacillus sp. and a fast dominance of Candida sp.; a reduction of the fermentation time necessary to achieve the best sensorial score; an increase in the invertase activity in the seed; a more expressive invertase activity in the husk; and a decreasing trend in polygalacturonase activity in the coffee husk. The increase in endo-β-mannanase activity suggests that coffee starts germinating during the process. SIAF has a huge potential to increase the quality and add value to coffee, but further studies must be conducted to access its safety. The study allowed a better knowledge of the spontaneous microbial community and the enzymes that were present in the fermentation process.

Detection of Markers in Green Beans and Roasted Beans of Kalosi-Enrekang Arabica Coffee with Different Postharvest Processing Using LC-MS/MS

Our study is aimed at evaluating the effect of postharvest processing (natural, honey, and fully washed) on the compounds profile in green beans and roasted beans of Kalosi-Enrekang Arabica coffee and determining the marker compounds for each process. These beans were extracted using boiling water, and the extract was analyzed using LC-MS/MS. The results of this work confirmed the significant impact of postharvest processing on compounds in the coffee beans, and each process has a marker compound. Green beans by natural processing have 3 marker compounds, honey processing has 6 marker compounds, and fully washed processing has 2 marker compounds. Meanwhile, roasted beans by natural processing have 4 marker compounds, honey processing has 5 marker compounds, and fully washed processing has 7 marker compounds. In addition, our research identified caffeoyl tyrosine in green beans from natural and honey processing, which was previously only identified in Robusta coffee. These marker compounds can differentiate postharvest processing (natural, honey, and fully washed). These results can also help understand the effect of postharvest processing on the chemical composition of green and roasted beans.

Sensory Analysis of Full Immersion Coffee: Cold Brew Is More Floral, and Less Bitter, Sour, and Rubbery Than Hot Brew

Cold brew coffee is often described as sweeter or less acidic than hot brew coffee. Such comparisons, however, are potentially confounded by two key effects: different brew temperatures necessarily change the extraction dynamics and potentially alter the resulting brew strength, and different consumption temperatures are well known to affect perceived flavor and taste. Here, we performed a systematic study of how extraction temperature affects the sensory qualities of full immersion coffee. The investigation used a 3 × 3 × 3 factorial design, with coffee from three different origins representing different post-harvest methods (washed, honey-processed, and wet-hulled), each roasted to three different levels (light, medium, and dark), and each brewed at three different temperatures (4 °C, 22 °C, and 92 °C). All coffees were brewed to equilibrium, then diluted to precisely 2% total dissolved solids (TDS) and served at the same cold temperature (4 °C). We find that four attributes exhibited statistically significant variations with brew temperature for all origins and roast levels tested, with bitter taste, sour taste, and rubber flavor all higher in hot brewed coffees, and floral flavor higher in cold brewed coffee. However, there were strong interactions with origin and roast, with several additional attributes significantly impacted by temperature for specific origins and roast levels. These results provide insight on how brew temperature can be used to modulate the flavor profile of full immersion coffee.

A Systematic Mapping Study of Coffee Quality throughout the Production-to-Consumer Chain

Coffee is one of the most consumed beverages in the world and is crucial in the economy of many developing countries. The search to improve coffee quality comes from many fronts, as do the many ways to measure quality and the factors that affect it. Several techniques are used to measure the different metrics to assess coffee quality, across different types of coffee samples and species, and throughout the entire process from farm to cup. In this work, we conducted a systematic mapping study of 1,470 articles to identify the aspects of quality that are the most important in the scientific literature to evaluate coffee throughout the processing chain. The study revealed that cup quality and biochemical composition are the most researched quality attributes. The main objective of the reviewed studies is the correlation between different quality measurements. The most used techniques are the analytical chemistry methods. The most studied species is Coffea arabica. The most used sample presentation is green coffee. The postharvest stage is the most researched, in which quality control receives more attention. In the preharvest stage, management practices stand out. Finally, the most used type of research was the evaluation research.

The periodic table of fermented foods: limitations and opportunities

Fermentation is one of the oldest methods of food processing and accounts for a substantial proportion of human foods, including not only staple foods such as bread, cereal porridges or fermented legumes but also fermented vegetables, meats, fish and dairy, alcoholic beverages as well as coffee, cocoa and condiments such as vinegar, soy sauce and fish sauces. Adding the regional varieties to these diverse product categories makes for an almost immeasurable diversity of fermented foods. The periodic table of fermented foods aims to map this diversity on the 118 entries of the periodic table of chemical elements. While the table fails to represent the diversity of fermented foods, it represents major fermentation substrates, product categories, fermentation processes and fermentation organisms. This communication not only addresses limitations of the graphical display on a "periodic table of fermented foods", but also identifies opportunities that relate to questions that are facilitated by this graphical presentation: on the origin and purpose of food fermentation, which fermented foods represent "indigenous" foods, differences and similarities in the assembly of microbial communities in different fermentations, differences in the global preferences for food fermentation, the link between microbial diversity, fermentation time and product properties, and opportunities of using traditional food fermentations as template for development of new products. KEY POINTS: • Fermented foods are produced in an almost immeasurable diversity. • Fermented foods were mapped on a periodic table of fermented foods. • This table facilitates identification of communalities and differences of products.

Influence of Environmental Microbiota on the Activity and Metabolism of Starter Cultures Used in Coffee Beans Fermentation

Microbial activity is an integral part of agricultural ecosystems and can influence the quality of food commodities. During on-farm processing, coffee growers use a traditional method of fermentation to remove the cherry pulp surrounding the beans. Here, we investigated the influence of the coffee farm microbiome and the resulting fermentation process conducted with selected starter cultures (Pichia fermentans YC5.2 and Pediococcus acidilactici LPBC161). The microbiota of the coffee farm (coffee fruits and leaves, over-ripe fruits, cherries before de-pulping, depulped beans, and water used for de-pulping beans) was dominated by Enterobacteriaceae and Saccharomycetales, as determined by llumina-based amplicon sequencing. In addition, 299 prokaryotes and 189 eukaryotes were identified. Following the fermentation process, Pichia and the family Lactobacillaceae (which includes P. acidilactici) represented more than 70% of the total microbial community. The positive interaction between the starters resulted in the formation of primary metabolites (such as ethanol and lactic acid) and important aroma-impacting compounds (ethyl acetate, isoamyl acetate, and ethyl isobutyrate). The success competitiveness of the starters towards the wild microbiota indicated that coffee farm microbiota has little influence on starter culture-added coffee fermentation. However, hygiene requirements in the fermentation process should be indicated to prevent the high microbial loads present in coffee farm soil, leaves, fruits collected on the ground, and over-ripe fruits from having access to the fermentation tank and transferring undesirable aromas to coffee beans.

Evolution of Food Fermentation Processes and the Use of Multi-Omics in Deciphering the Roles of the Microbiota

Food fermentation has been practised since ancient times to improve sensory properties and food preservation. This review discusses the process of fermentation, which has undergone remarkable improvement over the years, from relying on natural microbes and spontaneous fermentation to back-slopping and the use of starter cultures. Modern biotechnological approaches, including genome editing using CRISPR/Cas9, have been investigated and hold promise for improving the fermentation process. The invention of next-generation sequencing techniques and the rise of meta-omics tools have advanced our knowledge on the characterisation of microbiomes involved in food fermentation and their functional roles. The contribution and potential advantages of meta-omics technologies in understanding the process of fermentation and examples of recent studies utilising multi-omics approaches for studying food-fermentation microbiomes are reviewed. Recent technological advances in studying food fermentation have provided insights into the ancient wisdom in the practice of food fermentation, such as the choice of substrates and fermentation conditions leading to desirable properties. This review aims to stimulate research on the process of fermentation and the associated microbiomes to produce fermented food efficiently and sustainably. Prospects and the usefulness of recent advances in molecular tools and integrated multi-omics approaches are highlighted.

From Plantation to Cup: Changes in Bioactive Compounds during Coffee Processing

Coffee is consumed not just for its flavor, but also for its health advantages. The quality of coffee beverages is affected by a number of elements and a series of processes, including: the environment, cultivation, post-harvest, fermentation, storage, roasting, and brewing to produce a cup of coffee. The chemical components of coffee beans alter throughout this procedure. The purpose of this article is to present information about changes in chemical components and bioactive compounds in coffee during preharvest and postharvest. The selection of the appropriate cherry maturity level is the first step in the coffee manufacturing process. The coffee cherry has specific flavor-precursor components and other chemical components that become raw materials in the fermentation process. During the fermentation process, there are not many changes in the phenolic or other bioactive components of coffee. Metabolites fermented by microbes diffuse into the seeds, which improves their quality. A germination process occurs during wet processing, which increases the quantity of amino acids, while the dry process induces an increase in non-protein amino acid γ-aminobutyric acid (GABA). In the roasting process, there is a change in the aroma precursors from the phenolic compounds, especially chlorogenic acid, amino acids, and sugars found in coffee beans, to produce a distinctive coffee taste.

Preparation of Activated Carbons from Spent Coffee Grounds and Coffee Parchment and Assessment of Their Adsorbent Efficiency

The valorization of coffee wastes through modification to activated carbon has been considered as a low-cost adsorbent with prospective to compete with commercial carbons. So far, very few studies have referred to the valorization of coffee parchment into activated carbon. Moreover, low-cost and efficient activation methods need to be more investigated. The aim of this work was to prepare activated carbon from spent coffee grounds and parchment, and to assess their adsorption performance. The co-calcination processing with calcium carbonate was used to prepare the activated carbons, and their adsorption capacity for organic acids, phenolic compounds and proteins was evaluated. Both spent coffee grounds and parchment showed yields after the calcination and washing treatments of around 9.0%. The adsorption of lactic acid was found to be optimal at pH 2. The maximum adsorption capacity of lactic acid with standard commercial granular activated carbon was 73.78 mg/g, while the values of 32.33 and 14.73 mg/g were registered for the parchment and spent coffee grounds activated carbons, respectively. The Langmuir isotherm showed that lactic acid was adsorbed as a monolayer and distributed homogeneously on the surface. Around 50% of total phenols and protein content from coffee wastewater were adsorbed after treatment with the prepared activated carbons, while 44, 43, and up to 84% of hydrophobic compounds were removed using parchment, spent coffee grounds and commercial activated carbon, respectively; the adsorption efficiencies of hydrophilic compounds ranged between 13 and 48%. Finally, these results illustrate the potential valorization of coffee by-products parchment and spent coffee grounds into activated carbon and their use as low-cost adsorbent for the removal of organic compounds from aqueous solutions.

Coffee and Yeasts: From Flavor to Biotechnology

Coffee is one of the most consumed beverages in the world, and its popularity has prompted the necessity to constantly increase the variety and improve the characteristics of coffee as a general commodity. The popularity of coffee as a staple drink has also brought undesired side effects, since coffee production, processing and consumption are all accompanied by impressive quantities of coffee-related wastes which can be a threat to the environment. In this review, we integrated the main studies on fermentative yeasts used in coffee-related industries with emphasis on two different directions: (1) the role of yeast strains in the postharvest processing of coffee, the possibilities to use them as starting cultures for controlled fermentation and their impact on the sensorial quality of processed coffee, and (2) the potential to use yeasts to capitalize on coffee wastes—especially spent coffee grounds—in the form of eco-friendly biomass, biofuel or fine chemical production.

Isolation of microorganisms from the feces of ring-tailed coati related to the production of "misha coffee" in the central forest of Peru and evaluation of some features of technological importance

A diversity of yeasts and lactic bacteria were isolated from the feces of ring-tailed coaties bred in captivity and related to the production of "misha coffee". Isolation of yeasts was carried out using oxytetracycline-glucose-yeast extract agar containing 100 mg/L oxytetracycline and, lactic bacteria using de Man-Rogosa and Sharpe agar containing 20 mg/L of vancomicin. Then, isolates were biochemically analysed using API strips (ID 32C for yeasts and 50CHL for lactic bacteria) followed by 16S and 26S rRNA gene sequencing. Among the yeasts, Debaryomyces hansenii, Pichia kluyveri, Pichia kudriavzevii, and Candida sorboxilosa were the most frequent, whereas Weissella cibaria, Weissella paramesenteroides, Enterococcus thailandicus and Enterococcus faecalis were the most important lactic bacteria. Cultivation of the isolated yeasts under agitated conditions, showed that Pichia kluyveri LBFT.Lev3 (0.15 ± 0.01 h^-1) and Pichia kudriavzevii LBTF.Lev7 (0.14 ± 0.01 h^-1) had higher specific growth rates than Debaryomyces hansenii LBFT.Lev9 (0.09 ± 0.01 h^-1), whereas cultivation of lactic bacteria under static fashion showed that Weisella paramesenteroides LBTF.Bal2 (0.16 ± 0.01 h^-1) and Weisella cibaria LBTF.Bal3 (0.18 ± 0.01 h^-1) had better growth than Enterococcus thailandicus LBTF.Bal1 (0.1 ± 0.015 h^-1) and Enterococcus faecalis LBTF.Bal7 (0.14 ± 0.01 h^-1). Additionally, evaluation of pectinolytic activity revealed that Pichia kudriavzevii LBTF.Lev7 and Debaryomyces hansenii LBFT.Lev9 were able to use pectin as carbon source for their growth. On the other hand, W. cibaria LBTF.Bal3, E. thailandicus LBTF.Bal1 and W. paramesenteroides LBTF.Bal2 showed inhibitory activity against S. mutans ATCC 35668, B. subtilis subsp. spizizenii ATCC 6633 and Staph. epidermidis ATCC 14990. Results of this study are useful for the search of potential application of the isolated yeasts and lactic bacteria in coffee and other food fermentations.

Transfer kinetics of labeled aroma compounds from liquid media into coffee beans during simulated wet processing conditions

The transfer kinetics of three labelled compounds (butanal, 2-phenyethanol, isoamyl acetate) was studied from a liquid medium into the coffee beans during simulated wet processing using four media (M) (M1: contained dehulled beans, M2: contained demucilaginated beans, M3: contained depulped beans, M4: contained depulped beans with yeast). Trials were carried out at 25 °C, under agitation and for five time periods (0, 6, 12, 24 and 48 h), and then the labelled volatiles were analyzed by SPME-GC-MS. The three labelled molecules were transferred into the coffee beans with different mass transfer rates; reaching at 12hrs in the M4, 0.2 ± 0.03, 11.2 ± 0.66 and 1.3 ± 0.04 µg/g of coffee respectively for butanal, 2-phenyethanol and isoamyl acetate. The parchment resistance significantly affected the mass transfer of the 2-phenylethanol. Butanal and isoamyl acetate underwent metabolic reactions, which decreased their amount in the coffee beans. Furthermore, an interaction between molecules and the yeast was observed and decreased significantly the butanal's transfer.

Comparison of Batch and Continuous Wet-Processing of Coffee: Changes in the Main Compounds in Beans, By-Products and Wastewater

Many technical challenges still need to be overcome to improve the quality of the green coffee beans. In this work, the wet Arabica coffee processing in batch and continuous modus were investigated. Coffee beans samples as well as by-products and wastewaters collected at different production steps were analyzed in terms of their content in total phenols, antioxidant capacity, caffeine content, organic acids, reducing sugars, free amino group and protein content. The results showed that 40% of caffeine was removed with pulp. Green coffee beans showed highest concentration of organic acids and sucrose (4.96 ± 0.25 and 5.07 ± 0.39 g/100 g DW for the batch and continuous processing). Batch green coffee beans contained higher amount of phenols. 5-caffeoylquinic Acid (5-CQA) was the main constituent (67.1 and 66.0% for the batch and continuous processing, respectively). Protein content was 15 and 13% in the green coffee bean in batch and continuous processing, respectively. A decrease of 50 to 64% for free amino groups during processing was observed resulting in final amounts of 0.8 to 1.4% in the processed beans. Finally, the batch processing still revealed by-products and wastewater with high nutrient content encouraging a better concept for valorization.

Occurrence of ochratoxin A and its stereoisomeric degradation product in various types of coffee available in the Czech market

Ochratoxin A (OTA) belongs among the most frequently occurring mycotoxins in coffee. In order to investigate its contamination levels in products currently available in the market, a broad set of coffee samples (103 in total) collected between 2016 and 2018 in the Czech Republic was investigated. Aqueous-methanolic extracts purified by using immunoaffinity columns were analysed by ultra-performance liquid chromatography coupled with tandem mass spectrometry (U-HPLC-MS/MS). The undertaken study revealed a relatively low OTA contamination of roasted coffee (in the range 0.2-2.5 μg/kg with the mean concentration of 0.6 μg/kg, and 71% of positive samples). The roasted coffee samples did not exceed the maximum limit of 5 μg/kg set by 1881/2006/EC. With regard to instant coffee samples, OTA concentrations were considerably higher. All the samples were positive, with a mean concentration of 2.9 μg/kg (ranging from 0.6 to 12.8 μg/kg, with 100% of positive samples). One of the analysed samples of instant coffee even exceeded the maximum limit of 10 μg/kg (1881/2006/EC). The study further revealed a relatively high incidence of 14-(R)-OTA, stereoisomer of OTA (14-(S)-OTA), originating as its main degradation product. Its identity was confirmed by high resolution mass spectrometry (HRMS/MS). Most of the samples positive for OTA were also positive for this diastereoisomer, with signal intensities of approx. one-third to one half of the signal of 14-(S)-OTA.

Influence of Various Processing Parameters on the Microbial Community Dynamics, Metabolomic Profiles, and Cup Quality During Wet Coffee Processing

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 aimed to explore the impacts of these parameters, including processing type (depulping or demucilaging), fermentation duration, and application of soaking, on the microbial community dynamics, metabolite compositions of processing waters (fermentation and soaking) and coffee beans, and resulting cup quality through a multiphasic approach. A large-scale wet coffee processing experiment was conducted with Coffea arabica var. Catimor in Yunnan (China) in duplicate. The fermentation steps presented a dynamic interaction between constant nutrient release (mainly from the cherry mucilage) into the surrounding water and active microbial activities led by lactic acid bacteria, especially Leuconostoc and Lactococcus. The microbial communities were affected by both the processing type and fermentation duration. At the same time, the endogenous coffee bean metabolism remained active at different stages along the processing, as could be seen through changes in the concentrations of carbohydrates, organic acids, and free amino acids. Among all the processing variants tested, the fermentation duration had the greatest impact on the green coffee bean compositions and the cup quality. A long fermentation duration resulted in a fruitier and more acidic cup. As an ecological alternative for the depulped processing, the demucilaged processing produced a beverage quality comparable to the depulped one. The application of soaking, however, tempered the positive fermentation effects and standardized the green coffee bean quality, regardless of the preceding processing practices applied. Lastly, the impact strength of each processing parameter would also depend on the coffee variety used and the local geographical conditions. All these findings provide a considerable margin of opportunities for future coffee research.

Isolation, Identification, and Characterization of Pectinolytic Yeasts for Starter Culture in Coffee Fermentation

This experiment was carried out to identify and select pectinolytic yeasts that have potential use as a starter culture for coffee fermentation during wet processing. The coffee fruit was fermented for 48 h at 28 °C and a sample was taken from the fermented solution and spread onto yeast extract-peptone-dextrose agar (YPDA) media and incubated at 28 °C. A total of 28 yeasts were isolated, eight of which had the ability to produce pectinase enzymes. The species of those eight yeasts were molecularly identified and confirmed. These yeasts are Wickerhamomyces anomalus (strain KNU18Y3), Saccharomycopsis fibuligera (strain KNU18Y4), Papiliotrema flavescens (strain KNU18Y5 and KNU18Y6), Pichia kudriavzevii (strain KNU18Y7 and KNU18Y8), and Saccharomyces cerevisiae (strain KNU18Y12 and KNU18Y13). The pectin degradation index of S. fibuligera (strain KNU18Y4), W. anomalus (strain KNU18Y3), and P. flavescens (strain KNU18Y6) were higher compared to the others, at 178%, 160%, and 152%, respectively. The pectinase enzyme assays were made on two growth media: coffee pulp media (CPM) and synthetic pectin media (SPM). S. fibuligera (strain KNU18Y4) and W. anomalus (strain KNU18Y3) had great potential in producing polygalacturonase (PG) and pectin lyase (PL) compared to others in both media. However, S. cerevisiae strains (KNU18Y12 and KNU18Y13) produced higher pectin methylesterase (PME). Using MEGA 6 software, the phylogenetic trees were constructed to determine the evolutionary relationship of newly identified yeasts from our experiment and previously published yeast species. The sequences of the yeasts were deposited in the National Center for Biotechnology Information (NCBI) database.