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. Currently, green coffee beans obtained from farms that use any of the above processing methods are fermented with selected microorganisms to improve the flavour and aroma 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, microorganisms and starter cultures, and fermentation’s impact on coffee quality. Future prospects are also discussed through the incorporation of recent research.

We examined the antioxidant activity, total polyphenol content (TPC), total flavonoid content (TFC), total tannin content (TTC) and physical characteristics of green coffee beans fermented with selected yeasts. There was no significant (p > 0.05) interaction effect between yeast-fermented coffee extracts and duration of fermentation on antioxidant activity (oxygen radical absorbance capacity [ORAC] and superoxide dismutase-like [SOD-like] activity). However, the mean of the antioxidant activity (ORAC and SOD-like activity) significantly (p < 0.05) increased in the fermented coffee extracts compared to unfermented coffee. There were significant (p < 0.05) interaction effects between yeast-fermented coffee extracts and duration of fermentation (24 h and 48 h) on the TPC, TFC, TTC and pH of the fermented solution and on the colors of the ground-roasted coffee. The TPC showed a pattern of increase in samples Ferm-1 and Ferm-3 as fermentation time increased from 24 h to 48 h. However, a decreasing TPC trend was observed in Ferm-2 as the number of fermentation hours increased from 24 to 48. The fermented coffee beans had a significantly higher flavonoid content than the unfermented coffee beans, while fermentation significantly decreased the tannin content compared to that in unfermented coffee.

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.

Coffee is one of the most important agricultural commodities in the world. The coffee quality is associated with pre-harvest and post-harvest management activities. Each step starting from selecting the best coffee variety for plantation until the final coffee drink preparation determines the cupping quality. The overall coffee quality influenced by the factors which involve in changes the physicochemical properties and sensorial attributes, including the post-harvest operations. The postharvest processing activities contribute about 60% of the quality of green coffee beans. The post-harvest operations include pulping, processing, drying, hulling, cleaning, sorting, grading, storage, roasting, grinding, and cupping. This chapter comprises the harvest and post-harvest operations of coffee and their impacts on coffee quality.

There are different types of coffee processing methods. The wet (WP) and dry processing (DP) methods are widely practiced in different parts of coffee-growing countries. There is also a digestive bioprocessing method in which the most expensive coffee is produced. The elephant dung coffee is produced using the digestive bioprocessing method. In the present experiment, the antioxidant activity and volatile compounds of coffee that have been processed using different methods were compared. The antioxidant activity, total phenolic content (TPC), total flavonoid content (TFC), and total tannin content (TTC) of green coffee beans from all treatments were higher as compared to roasted coffee beans. Regarding the green coffee beans, the 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging activity of elephant dung coffee beans was higher as compared to that of the DP and WP coffee beans. The green coffee beans had higher DPPH activity and ferric reducing antioxidant power (FRAP) value compared to the roasted coffee beans. The green beans of elephant dung coffee had a high TPC than the beans obtained by WP and DP methods. TFC in elephant dung coffee in both green and roasted condition was improved in contrast to the beans processed using dry and wet methods. The elephant dung coffee had an increased TTC in comparison to the DP and WP coffee (green beans). About 37 volatile compounds of acids, alcohols, aldehydes, amide, esters, ethers, furans, furanones, ketones, phenols, pyrazines, pyridines, Heterocyclic N, and pyrroles functional classes have been found. Some of the most abundant volatile compounds detected in all treatments of coffee were 2-furanmethanol, acetic acid, 2-methylpyrazine, 2,6-dimethylpyrazine, pyridine, and 5-methylfurfural. Few volatile compounds have been detected only in elephant dung coffee. The principal component analysis (PCAs) was performed using the percentage of relative peak areas of the volatile compound classes and individual volatile compounds. This study will provide a better understanding of the impacts of processing methods on the antioxidants and volatile compounds of coffee.

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A few yeast species have been tested frequently to improve the tastes, flavors, and other important quality parameters of coffee. However, continuing evaluations of different yeast species for fermenting green coffee beans will have a significant positive contribution to the coffee industry. This experiment was conducted to evaluate the antioxidant properties, total phenol content (TPC), total flavonoid content (TFC), total tannin content (TTC), and the consumer acceptability of fermented green coffee beans with Wickerhamomyces anomalu. The coffee beans were roasted at different roasting conditions (light, medium, and dark). There was no significant (p > 0.05) difference between the yeast-fermented and non-fermented coffee with regard to the oxygen radical absorbance capacity (ORAC) values in medium and dark roasted coffee. Similarly, the superoxide dismutase-like (SOD)-like activity did not significantly differ in all roasting conditions. However, the SOD-like activity was significantly different (p < 0.05), particularly within light roasted and medium roasted, and between light roasted and dark roasted in both the control and fermented coffee extracts. The 2, 2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging assay and ferric reducing antioxidant power (FRAP) were improved in fermented coffee beans. There was a significant (p ≤ 0.05) difference between the yeast-fermented and non-fermented coffee with respect to the TPC and TFC in all roasting types and the TTC in the light and dark roasting conditions. The fermentation of green coffee beans with W. anomalus increased the TPC and TFC. However, the TTC was lower in the fermented coffee beans compared to the non-fermented coffee beans in medium and dark roasted coffee. In general, fermentation of green coffee beans with W. anomalus has the potential to improve the functionality of coffee beans.

One of the most serious pepper diseases is Phytophthora blight, which is caused by Phytophthora capsici. It is crucial to assess the resistance of pepper genetic resources to Phytophthora blight, understand the genetic resistances, and develop markers for selecting resistant pepper materials in breeding programs. In this study, the resistance of 342 pepper accessions to P. capsici was evaluated. The disease severity score method was used to evaluate the phenotypic responses of pepper accessions inoculated with the KCP7 isolate. A genome-wide association study (GWAS) was performed to identify single nucleotide polymorphisms (SNPs) linked to P. capsici (isolate KCP7) resistance. The pepper population was genotyped using the genotype-by-sequencing (GBS) method, and 45,481 SNPs were obtained. A GWAS analysis was performed using resistance evaluation data and SNP markers. Significantly associated SNPs for P. capsici resistance at 4 weeks after inoculation of the GWAS pepper population were selected. These SNPs for Phytophthora blight resistance were found on all chromosomes except Chr.05, Chr.09, and Chr.11. One of the SNPs found on Chr.02 was converted into a high-resolution melting (HRM) marker, and another marker (QTL5-1) from the previous study was applied to pepper accessions and breeding lines for validation and comparison. This SNP marker was selected because the resistance phenotype and the HRM marker genotype matched well. The selected SNP was named Chr02-1126 and was located at 112 Mb on Chr.02. The Chr02-1126 marker predicted P. capsici resistance with 78.5% accuracy, while the QTL5-1 marker predicted resistance with 80.2% accuracy. Along with the marker for major quantitative traits loci (QTLs) on Chr.05, this Chr02-1126 marker could be used to accurately predict Phytophthora blight resistance in pepper genetic resources. Therefore, this study will assist in the selection of resistant pepper plants in order to breed new phytophthora blight-resistant varieties.