The effects of yeasts involved in the fermentation of Coffea arabica in East Africa on growth and ochratoxin A (OTA) production by Aspergillus ochraceus

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.

Identification of antagonistic yeasts as potential biocontrol agents: Diverse criteria and strategies

Plant pathogenic and food spoilage microorganisms cause serious losses in crop production and severe damage during food manufacturing, transportation and storage. Synthetic antimicrobial agents are commonly used to control their propagation and harmful activities. However, the recent trend is shifting from chemicals towards safer and more eco-friendly alternatives. The use of antagonistic microorganisms as biological antimicrobial agents is becoming popular throughout the world to replace chemical agents. High numbers of microorganisms have turned out to exert adverse/inhibitory effects on other microorganisms including pathogens and spoiling strains. However, most of them are only active under laboratory conditions and their activity is sensitive to environmental changes. Only a small number of them can be used to manufacture biological protective products on an industrial scale. Therefore, there is a great need to identify additional antagonists. Yeasts have come to the forefront of attention because antimicrobial antagonism is fairly widespread among them. In the recent years, numerous excellent review articles covered various aspects of the phenomenon of antimicrobial antagonism of yeasts. However, none of them dealt with how antagonistic yeasts can be sought and identified, despite the high number and diverse efficiency of screening and identification procedures. As researchers working in different laboratories use different criteria and different experimental set-ups, a yeast strain found antagonistic in one laboratory may prove to be non-antagonistic in another laboratory. This review aims to provide a comprehensive and partially critical overview of the wide diversity of identification criteria and procedures to help researchers choose appropriate screening and identification strategies.

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.

Microbial Diversity Using a Metataxonomic Approach, Associated with Coffee Fermentation Processes in the Department of Quindío, Colombia

Coffee fermentation is a complex process, mainly involving bacteria and yeasts, whose interaction influences beverage quality. The way this process is conducted affects the interactions between these microorganisms. To identify microbial diversity in fermenting coffee, samples were collected from 20 farms in the Department of Quindío, Colombia. Metataxonomic analyses using high-throughput sequencing and volatile organic compound identification in green coffee beans were performed with HS-SPME and GC-MS. Potential relationships between some families and genera with different fermentation types and coffee quality were evaluated. In our results, samples presented with high richness and diversity were greater for bacteria than for yeast/fungi. The Enterobacteriaceae family dominated at the beginning of fermentation, while Leuconostoc, Lactobacillus, Gluconobacter, and Acetobacter genera dominated at the end, a finding related to pH reduction and final coffee quality. Overall, 167 fungal families were identified, but Saccharomyceaceae dominated from the beginning. Alcohols and esters were the main chemical classes identified in green coffee bean samples from these fermentations. These results will facilitate the identification process conditions that influence the presence and abundance of microorganisms related to quality as well as contributing to the design of strategies to conduct fermentations to improve the final quality of coffee.

Perfume Guns: Potential of Yeast Volatile Organic Compounds in the Biological Control of Mycotoxin-Producing Fungi

Pathogenic fungi in the genera Alternaria, Aspergillus, Botrytis, Fusarium, Geotrichum, Gloeosporium, Monilinia, Mucor, Penicillium, and Rhizopus are the most common cause of pre- and postharvest diseases of fruit, vegetable, root and grain commodities. Some species are also able to produce mycotoxins, secondary metabolites having toxic effects on human and non-human animals upon ingestion of contaminated food and feed. Synthetic fungicides still represent the most common tool to control these pathogens. However, long-term application of fungicides has led to unacceptable pollution and may favour the selection of fungicide-resistant mutants. Microbial biocontrol agents may reduce the incidence of toxigenic fungi through a wide array of mechanisms, including competition for the ecological niche, antibiosis, mycoparasitism, and the induction of resistance in the host plant tissues. In recent years, the emission of volatile organic compounds (VOCs) has been proposed as a key mechanism of biocontrol. Their bioactivity and the absence of residues make the use of microbial VOCs a sustainable and effective alternative to synthetic fungicides in the management of postharvest pathogens, particularly in airtight environments. In this review, we will focus on the possibility of applying yeast VOCs in the biocontrol of mycotoxigenic fungi affecting stored food and feed.

Control of toxigenic Aspergillus spp. in dried figs by volatile organic compounds (VOCs) from antagonistic yeasts

Aspergillus flavus and Aspergillus niger are fungi which can contaminate dried figs before and after harvest and consequently produce aflatoxins (AFs) and ochratoxin A (OTA). Many approaches have been applied to minimise the growth of these filamentous fungi, mainly involving the use of synthetic fungicides which are limited due to their negative impact on human health and the environment. In this context, biocontrol is a recent approach that needs to be explored. This study evaluated the potential of three volatile organic compounds (VOCs), octanoic acid (OA), 2-phenylethyl acetate (2PEA) and furfuryl acetate (FA), produced by Hanseniaspora uvarum and Hanseniaspora opuntiae yeasts on the growth, germination, gene expression and production of AFs and OTA by A. flavus M144 and A. niger M185 on dried fig-based agar and the incidence rates in dried figs. Two of the three VOCs evaluated (2PEA and FA) effectively controlled A. flavus M144 and A. niger M185 by using at least amounts of 50 μL (715 μL/L in the headspace) for FA and 100 μL (1430 μL/L in the headspace) for 2PEA in dried figs. One of the mode of actions of both compounds consists in early repressing the expression of genes involved in the biosynthesis of AFs (aflR) and OTA (pks) of A. flavus and A. niger, respectively. The results of this study support the application of 2PEA and FA at the early post-harvest stages of dried figs to control mycotoxin accumulation.

Fungal diversity and mycotoxins detected in maize stored in silo-bags: a review

Silo-bags are hermetic storage systems that inhibit fungal growth because of their atmosphere with low humidity, as well as low pH and O₂ concentrations, and a high CO₂ concentration. If a silo-bag with stored maize loses its hermetic nature, it favors the development of fungi and the production of mycotoxins. To the best of our knowledge, this is the first review on the diversity of fungal species and mycotoxins that were reported in maize stored under the environmental conditions provided by silo-bags. The genera Penicillium, Aspergillus and Fusarium were found more frequently, whereas Acremonium spp., Alternaria sp., Candida sp., Cladosporium sp., Debaryomyces spp., Epiconum sp., Eupenicillium spp., Eurotium sp., Eurotium amstelodami, Hyphopichia spp., Hyphopichia burtonii, Moniliella sp., Wallemia sp. and genera within the orden Mucorales were reported less recurrently. Despite finding a great fungal diversity, all of the studies focused their investigations on a small group of toxins: fumonisins (FBs), aflatoxins (AFs), deoxynivalenol (DON), zearalenone (ZEA), patulin (PAT), toxin T2 (T2) and ochratoxin (OT). Of the FBs, fumonisin B₁ and fumonisin B₂ presented higher incidence percentages, followed by fumonisin B₃ . Of the AFs, the only one reported was aflatoxin B_1. The mycotoxins DON, ZEA and OT were found with lower incidences, whereas PAT and T2 were not detected. Good management practices of the silo-bags are necessary to achieve a hermetically sealed environment, without exchange of gases and water with the external environment during the storage period. © 2022 Society of Chemical Industry.

An entropy driven catalytic reaction powered DNA motor for simultaneous detection of ochratoxin A and chloramphenicol in food

An entropy driven catalytic reaction powered DNA motor was proposed for simultaneous detection of ochratoxin A (OTA) and chloramphenicol (CAP) in food. The dumbbell hairpin structure was formed by the two aptamers of OTA and CAP. The dumbbell hairpin can be opened by the interaction of OTA and CAP with their aptamers. The tails of the end of dumbbell hairpin sequence can induce the entropy driven catalytic reactions on the AuNPs, causing the sustained releasing of the fluorophore labeled DNA sequences. The recovery of fluorescent intensities can be used for quantitative detection of OTA and CAP. The limit of detection reached 2 pM for OTA and 6 pM for CAP respectively, which was great improved by entropy driven amplification of the self-powdered DNA motor. This strategy is simple and sensitive and only needs one-step operation. It exhibits promising potentiality in food quality control and food security supervision.

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.

Prevalence of toxigenic fungi and mycotoxins in Arabic coffee (Coffea arabica): Protective role of traditional coffee roasting, brewing and bacterial volatiles

Fungal infection and synthesis of mycotoxins in coffee leads to significant economic losses. This study aimed to investigate the prevalence of toxigenic fungi, their metabolites, and the effect of traditional roasting and brewing on ochratoxin A (OTA) and aflatoxins (AFs) contents of naturally contaminated coffee samples. In addition, in vivo biocontrol assays were performed to explore the antagonistic activities of Bacillus simplex 350–3 (BS350-3) on the growth and mycotoxins synthesis of Aspergillus ochraceus and A. flavus. The relative density of A. niger, A. flavus, Penicillium verrucosum and A. carbonarius on green coffee bean was 60.82%, 7.21%, 3.09% and 1.03%, respectively. OTA contents were lowest in green coffee beans (2.15 μg/kg), followed by roasted (2.76 μg/kg) and soluble coffee (8.95 μg/kg). Likewise, AFs levels were highest in soluble coffee (90.58 μg/kg) followed by roasted (33.61 μg/kg) and green coffee (9.07 μg/kg). Roasting naturally contaminated coffee beans at three traditional methods; low, medium and high, followed by brewing resulted in reduction of 58.74% (3.50 μg/kg), 60.88% (3.72 μg/kg) and 64.70% (4.11 μg/kg) in OTA and 40.18% (34.65 μg/kg), 47.86% (41.17 μg/kg) and 62.38% (53.73 μg/kg) AFs contents, respectively. Significant inhibitions of AFs and OTA synthesis by A. flavus and A. carbonarius, respectively, on infected coffee beans were observed in presence of Bacillus simplex BS350-3 volatiles. Gas chromatography mass spectrochemistry (GC-MS/MS) analysis of head-space BS350-3 volatiles showed quinoline, benzenemethanamine and 1-Octadecene as bioactive antifungal molecules. These findings suggest that marketed coffee samples are generally contaminated with OTA and AFs, with a significant level of roasted and soluble coffee contaminated above EU permissible limits for OTA. Further, along with coffee roasting and brewing; microbial volatiles can be optimized to minimize the dietary exposure to mycotoxins.

Microbial diversity associated with spontaneous coffee bean fermentation process and specialty coffee production in northern Colombia

Coffee fermentation involves the action of microorganisms, whose metabolism has a significant influence on the composition of the beans and, consequently, on the beverage's sensory characteristics. In this study, the microbial diversity during the wet fermentation of Coffea arabica L. in the Sierra Nevada of Santa Marta (SNSM) in Colombia was explored by high-throughput sequencing and the resulting cup quality through the standards of the Specialty Coffee Association. The taxonomic assignment of sequence reads showed a high microbial diversity comprised of 695 bacterial and 156 fungal genera. The microbial community was dominated by the Lactic Acid Bacteria (LAB) Leuconostoc, the yeast Kazachstania, and the Acetic Acid Bacteria (AAB) Acetobacter. Co-occurrence relationships suggested synergistic patterns between populations of LAB-AAB, yeasts-AAB, Leuconostoc-Prevotella, LAB-ABB-Selenomonas, and yeasts-fungi-nonLAB-nonAAB, which may result in the production of metabolites that positively impact the sensory attributes of coffee. The beverages produced were classified as specialty coffees, and their score was positively influenced by the fungal richness and the abundance of unclassified Lactobacillales, Pichia, and Pseudomonas. The findings show the richness and microbial diversity of the SNSM and serve as input for future research such as the analysis of microbial-derived metabolites and the establishment of starter cultures in coffee processing that guarantee the generation of high-quality beverages, the standardization of processes, the reduction of economic losses, and the production of value-added products that allow taking advantage of specialty coffee market.

Coffee Microbiota and Its Potential Use in Sustainable Crop Management. A Review

Intensive coffee production is accompanied by several environmental issues, including soil degradation, biodiversity loss, and pollution due to the wide use of agrochemical inputs and wastes generated by processing. In addition, climate change is expected to decrease the suitability of cultivated areas while potentially increasing the distribution and impact of pests and diseases. In this context, the coffee microbiota has been increasingly studied over the past decades in order to improve the sustainability of the coffee production. Therefore, coffee associated microorganisms have been isolated and characterized in order to highlight their useful characteristics and study their potential use as sustainable alternatives to agrochemical inputs. Indeed, several microorganisms (including bacteria and fungi) are able to display plant growth-promoting capacities and/or biocontrol abilities toward coffee pests and diseases. Despite that numerous studies emphasized the potential of coffee-associated microorganisms under controlled environments, the present review highlights the lack of confirmation of such beneficial effects under field conditions. Nowadays, next-generation sequencing technologies allow to study coffee associated microorganisms with a metabarcoding/metagenomic approach. This strategy, which does not require cultivating microorganisms, now provides a deeper insight in the coffee-associated microbial communities and their implication not only in the coffee plant fitness but also in the quality of the final product. The present review aims at (i) providing an extensive description of coffee microbiota diversity both at the farming and processing levels, (ii) identifying the “coffee core microbiota,” (iii) making an overview of microbiota ability to promote coffee plant growth and to control its pests and diseases, and (iv) highlighting the microbiota potential to improve coffee quality and waste management sustainability.

Biocontrol potential of native yeast strains against Aspergillus flavus and aflatoxin production in pistachio

ASPERGILLUS FLAVUS

is the main aflatoxin producer in food and feed and has wide ecological niches. Contamination of food products such as pistachio nuts and aflatoxin secretion directly affects food safety and international food product trades. Abilities of 13 yeast strains isolated from 200 soil and pistachio nut samples collected in Iranian orchards to reduce the growth of A. flavus as well as aflatoxin production were assessed in dual culture, volatile and non-volatile compounds tests. The growth of A. flavus was reduced by 32-60%, 13-31% and 40-61% in dual culture, volatile and non-volatile compounds, respectively, while aflatoxin B1 production was diminished by 90.6-98.3%. Based on these assays, five yeast strains were selected for co-inoculation experiments using soil, pistachio hulls and leaf. A significant reduction in colony-forming units (CFU) ranging from 23% to 110% (p < .05) was observed. Molecular, physiological and morphological identification revealed these were strains of Pichia kudriavzevii and Lachansea thermotolerans. Aflatoxin biocontrol with yeast strains possesses many advantages including the ease of commercial production and organic application which is an environmental approach. More investigation is required to understand the efficiency of selective strains to inhibit A. flavus and aflatoxin production as well as withstand predominant abiotic stress in pistachio orchards and mass production in field application.

Biocontrol ability and volatile organic compounds production as a putative mode of action of yeast strains isolated from organic grapes and rye grains

The inhibiting activity of three yeast strains belonging to Pichia kudriavzevii, Pichia occidentalis, and Meyerozyma quilliermondii/Meyerozyma caribbica genera against common plant pathogens representing Mucor spp., Penicillium chrysogenum, Penicillium expansum, Aspergillus flavus, Fusarium cereals, Fusarium poae, as well as Botrytis cinerea genera was investigated. The yeast strains tested had a positive impact on growth inhibition of all target plant pathogens. The degree of inhibition was more than 50% and varied depending on both the yeast antagonist and the mold. Ethyl esters of medium-chain fatty acids, phenylethyl alcohol, and its acetate ester prevailed among the analyzed volatile organic compounds (VOCs) emitted by yeasts in the presence of the target plant pathogens. Due to the method used, assuming no contact between the antagonist and the pathogen, the antagonistic activity of the yeast strains studied resulted mainly from the production of biologically active VOCs. Moreover, the antagonistic activity was not only restricted to a single plant pathogen but effective towards molds of different genera, making the yeast strains studied very useful for potential application in biological control.

The Aspergilli and Their Mycotoxins: Metabolic Interactions With Plants and the Soil Biota

Species of the highly diverse fungal genus Aspergillus are well-known agricultural pests, and, most importantly, producers of various mycotoxins threatening food safety worldwide. Mycotoxins are studied predominantly from the perspectives of human and livestock health. Meanwhile, their roles are far less known in nature. However, to understand the factors behind mycotoxin production, the roles of the toxins of Aspergilli must be understood from a complex ecological perspective, taking mold-plant, mold-microbe, and mold-animal interactions into account. The Aspergilli may switch between saprophytic and pathogenic lifestyles, and the production of secondary metabolites, such as mycotoxins, may vary according to these fungal ways of life. Recent studies highlighted the complex ecological network of soil microbiotas determining the niches that Aspergilli can fill in. Interactions with the soil microbiota and soil macro-organisms determine the role of secondary metabolite production to a great extent. While, upon infection of plants, metabolic communication including fungal secondary metabolites like aflatoxins, gliotoxin, patulin, cyclopiazonic acid, and ochratoxin, influences the fate of both the invader and the host. In this review, the role of mycotoxin producing Aspergillus species and their interactions in the ecosystem are discussed. We intend to highlight the complexity of the roles of the main toxic secondary metabolites as well as their fate in natural environments and agriculture, a field that still has important knowledge gaps.

Scent of a Killer: Microbial Volatilome and Its Role in the Biological Control of Plant Pathogens

The use of synthetic fungicides represents the most common strategy to control plant pathogens. Excessive and/or long-term distribution of chemicals is responsible for increased levels of environmental pollution, as well as adverse health consequence to humans and animals. These issues are deeply influencing public perception, as reflected by the increasing demand for safer and eco-friendly agricultural commodities and their by-products. A steadily increasing number of research efforts is now devoted to explore the use of safer and innovative approaches to control plant pathogens. The use of microorganisms as biological control agents (BCAs) represents one of the most durable and promising strategies. Among the panoply of microbial mechanisms exerted by BCAs, the production of volatile organic compounds (VOCs) represents an intriguing issue, mostly exploitable in circumstances where a direct contact between the pathogen and its antagonist is not practicable. VOCs are potentially produced by all living microorganisms, and may be active in the biocontrol of phytopathogenic oomycetes, fungi, and bacteria by means of antimicrobial activity and/or other cross-talk interactions. Their biological effects, the reduced residuals in the environment and on agricultural commodities, and the ease of application in different agricultural systems make the use of VOCs a promising and sustainable approach to replace synthetic fungicides in the control of plant pathogens. In this review, we focus on VOCs produced by bacteria and fungi and on their role in the cross-talk existing between the plant pathogens and their host. Biologic systemic effect of the microbial volatile blends on both pathogen and host plant cells is also briefly reviewed.

Inhibition of growth and ochratoxin A production in Aspergillus species by fungi isolated from coffee beans

Ochratoxin A (OTA) is a mycotoxin found in several agricultural commodities. Produced by Aspergillus spp., it is nephrotoxic and hepatotoxic and can be carcinogenic. Preventive measures are preventing fungal growth and OTA production. In this study, fungal strains (Rhizopus oryzae, Lichtheimia ramosa, Aspergillus westerdijkiae, Aspergillus niger, Aspergillus tamarii, Aspergillus sp., and Aspergillus fumigatus) isolated from coffee beans were identified for their abilities to inhibit the growth of Aspergillus ochraceus, Aspergillus westerdijkiae, Aspergillus carbonarius, and Aspergillus niger, and OTA production. All fungi strains tested were able to inhibit growth of the four Aspergillus species and OTA production, where A. niger showed the best results in both tests. L. ramosa showed the lowest growth-reducing potential, while the other fungal strains had a growth-reducing potential higher than 70% against all Aspergillus species tested. Regarding OTA production, L. ramosa and Aspergillus sp. completely inhibited the mycotoxin production by A. ochraceus and non-toxigenic strain A. niger completely inhibited OTA production by A. niger. Our findings indicate that the strains tested can be used as an alternative means to control growth of OTA-producing fungi and production of the mycotoxin in coffee beans.

Microbial Ecology of Fermented Vegetables and Non-Alcoholic Drinks and Current Knowledge on Their Impact on Human Health

Fermented foods are currently experiencing a re-discovery, largely driven by numerous health benefits claims. While fermented dairy, beer, and wine (and other alcoholic fermented beverages) have been the subject of intensive research, other plant-based fermented foods that are in some case widely consumed (kimchi/sauerkraut, pickles, kombucha) have received less scientific attention. In this chapter, the current knowledge on the microbiology and potential health benefits of such plant-based fermented foods are presented. Kimchi is the most studied, characterized by primarily acidic fermentation by lactic acid bacteria. Anti-obesity and anti-hypertension properties have been reported for kimchi and other pickled vegetables. Kombucha is the most popular non-alcoholic fermented drink. Kombucha's microbiology is remarkable as it involves all fermenters described in known fermented foods: lactic acid bacteria, acetic acid bacteria, fungi, and yeasts. While kombucha is often hyped as a "super-food," only antioxidant and antimicrobial properties toward foodborne pathogens are well established; and it is unknown if these properties incur beneficial impact, even in vitro or in animal models. The mode of action that has been studied and demonstrated the most is the probiotic one. However, it can be expected that fermentation metabolites may be prebiotic, or influence host health directly. To conclude, plant-based fermented foods and drinks are usually safe products; few negative reports can be found, but more research, especially human dietary intervention studies, are warranted to substantiate any health claim.

Farm to Consumer: Factors Affecting the Organoleptic Characteristics of Coffee. II: Postharvest Processing Factors

The production and consumption of coffee are increasing despite the roadblocks to its agriculture and global trade. The unique, refreshing, and stimulating final cupping quality of coffee is the only reason for this rising production and consumption. Coffee quality is a multifaceted trait and is inevitably influenced by the way it is successively processed after harvesting. Reportedly, 60% of the quality attributes of coffee are governed by postharvest processing. The current review elaborates and establishes for the first time the relationship between different methods of postharvest processing of coffee and its varying organoleptic and sensory quality attributes. In view of the proven significance of each processing step, this review has been subdivided into three sections, secondary processing, primary processing, and postprocessing variables. Secondary processing addresses the immediate processing steps on the farm after harvest and storage before roasting. The primary processing section adheres specifically to roasting, grinding and brewing/extraction, topics which have been technically addressed more than any others in the literature and by industry. The postprocessing attribute section deals generally with interaction of the consumer with products of different visual appearance. Finally, there are still some bottlenecks which need to be addressed, not only to completely understand the relationship of varying postharvest processing methods with varying in-cup quality attributes, but also to devise the next generation of coffee processing technologies.

Relationship between drought and preharvest aflatoxin contamination in groundnut (Arachis hypogaea L.)

Groundnut is a commercial oilseed crop that is prone to infection by Aspergillus flavus or Aspergillus parasiticus. Drought impairs the defence mechanism of the plant and favours the production of aflatoxin by the fungus. Aflatoxin is a carcinogen and its presence in food and feed causes significant economic loss. The answer to the question, ‘how drought tolerance and aflatoxin resistance are related?’ is not clear. In this review paper, the relationship of drought and preharvest aflatoxin contamination (AC), the relationship of drought tolerance traits and AC, and the approaches to enhance resistance to AC are discussed using up-to-date literature. Factors leading to AC are drought, high geocarposphere temperature, kernel/pod damage, and reduced phytoalexin synthesis by the plant. If the fungus colonises a kernel with reduced water activity, the plant cannot synthesise phytoalexin and then, the fungus synthesises aflatoxin. Breeding for resistance to AC is complicated because aflatoxin concentration is costly to measure, highly variable, and influenced by the environment. Since drought tolerant cultivars have resistance to AC, traits of drought tolerance have been used as indirect selection tools for reduced AC. The genetics of aflatoxin resistance mechanisms have not been made clear as the environment influences the host-pathogen relationship. Host-pathogen interactions under the influence of environment should be studied at molecular level to identify plant resistant factors using the tools of genomics, proteomics, and metabolomics in order to develop cultivars with durable resistance. Many candidate genes involved in host-pathogen interactions have been identified due to improvements in fungal expressed sequence tags, microarrays, and genome sequencing techniques. Moreover, research projects are underway on identifying genes coding for antifungal compounds, resistance associated proteins and quantitative trait loci associated with aflatoxin resistance. This review is expected to help those who wish to work on reducing AC in groundnuts.

Integration of transcriptome and proteome data reveals ochratoxin A biosynthesis regulated by pH in Penicillium citrinum

Proteomics and transcriptomics of P. citrinum under pH 5 (highest OTA-production) and pH 3 (not produce OTA) were analyzed to reveal the possible mechanism of OTA biosynthesis in P. citrinum.

Isolation, selection and evaluation of antagonistic yeasts and lactic acid bacteria against ochratoxigenic fungus Aspergillus westerdijkiae on coffee beans

In this study, yeasts and lactic acid bacteria (LAB) were isolated from coffee fruits and identified via biochemical and molecular approaches. The isolates represented the Pichia, Debaryomyces, Candida, Clavispora, Yarrowia, Sporobolomyces, Klyveromyces, Torulaspora and Lactobacillus genera. Four isolates, namely Pichia fermentans LPBYB13, Sporobolomyces roseus LPBY7E, Candida sp. LPBY11B and Lactobacillus brevis LPBB03, were found to have the greatest antagonist activity against an ochratoxigenic strain of Aspergillus westerdijkiae on agar tests and were selected for further characterization. Applications of P. fermentans LPBYB13 in coffee cherries artificially contaminated with A. westerdijkiae showed efficacy in reducing ochratoxin A (OTA) content up to 88%. These results highlight that P. fermentans LPBYB13 fulfils the principle requirements of an efficient biological control of aflatoxigenic fungi in coffee beans and may be seen as a reliable candidate for further validation in field conditions.

SIGNIFICANCE AND IMPACT OF THE STUDY

Studies based on microbial ecology and antagonistic interactions are important for the development of new strategies in controlling aflatoxin contamination of crops and are relevant to further biotechnological applications. This study shows that coffee fruit is a potential source for the isolation of microbial strains with antifungal ability. A new yeast strain, Pichia fermentans LPBYB13, showed efficacy in reducing growth and ochratoxin A production of Aspergillus westerdijkiae in coffee beans. Our results should encourage the use of this yeast strain on a large scale for biocontrol of aflatoxigenic fungi in coffee beans.

What's Inside That Seed We Brew? A New Approach To Mining the Coffee Microbiome

Coffee is a critically important agricultural commodity for many tropical states and is a beverage enjoyed by millions of people worldwide. Recent concerns over the sustainability of coffee production have prompted investigations of the coffee microbiome as a tool to improve crop health and bean quality. This review synthesizes literature informing our knowledge of the coffee microbiome, with an emphasis on applications of fruit- and seed-associated microbes in coffee production and processing. A comprehensive inventory of microbial species cited in association with coffee fruits and seeds is presented as reference tool for researchers investigating coffee-microbe associations. It concludes with a discussion of the approaches and techniques that provide a path forward to improve our understanding of the coffee microbiome and its utility, as a whole and as individual components, to help ensure the future sustainability of coffee production.

Biotechnological advances for combating Aspergillus flavus and aflatoxin contamination in crops

Aflatoxins are toxic, carcinogenic, mutagenic, teratogenic and immunosuppressive byproducts of Aspergillus spp. that contaminate a wide range of crops such as maize, peanut, and cotton. Aflatoxin not only affects crop production but renders the produce unfit for consumption and harmful to human and livestock health, with stringent threshold limits of acceptability. In many crops, breeding for resistance is not a reliable option because of the limited availability of genotypes with durable resistance to Aspergillus. Understanding the fungal/crop/environment interactions involved in aflatoxin contamination is therefore essential in designing measures for its prevention and control. For a sustainable solution to aflatoxin contamination, research must be focused on identifying and improving knowledge of host-plant resistance factors to aflatoxin accumulation. Current advances in genetic transformation, proteomics, RNAi technology, and marker-assisted selection offer great potential in minimizing pre-harvest aflatoxin contamination in cultivated crop species. Moreover, developing effective phenotyping strategies for transgenic as well as precision breeding of resistance genes into commercial varieties is critical. While appropriate storage practices can generally minimize post-harvest aflatoxin contamination in crops, the use of biotechnology to interrupt the probability of pre-harvest infection and contamination has the potential to provide sustainable solution.

Coffee fermentation and flavor--An intricate and delicate relationship

The relationship between coffee fermentation and coffee aroma is intricate and delicate at which the coffee aroma profile is easily impacted by the fermentation process during coffee processing. However, as the fermentation process in coffee processing is conducted mainly for mucilage removal, its impacts on coffee aroma profile are usually neglected. Therefore, this review serves to summarize the available literature on the impacts of fermentation in coffee processing on coffee aroma as well as other unconventional avenues where fermentation is employed for coffee aroma modulation. Studies have noted that proper control over the fermentation process imparts desirable attributes and prevents undesirable fermentation which generates off-flavors. Other unconventional avenues in which fermentation is employed for aroma modulation include digestive bioprocessing and the fermentation of coffee extracts and green coffee beans. The latter is an area that should be explored further with appropriate microorganisms given its potential for coffee aroma modulation.

An overview on mycotoxin contamination of foods in Africa

Mycotoxins are fungal secondary metabolites that contaminate various feedstuffs and agricultural crops. The contamination of food by mycotoxins can occur before production, during storage, processing, transportation or marketing of the food products. High temperature, moisture content and water activity are among the predisposing factors that facilitate the production of mycotoxins in food. Aflatoxins, ochratoxins, fumonisins, deoxynivalenol and zearalenone are all considered the major mycotoxins produced in food and feedstuffs. In Africa, mycotoxin contamination is considered to be a major problem with implications that affect human and animal health and economy. Aflatoxin-related hepatic diseases are reported in many African countries. Ochratoxin and fumonisin toxicity in humans and animals is widespread in Africa. The available, updated information on the incidence of mycotoxin contamination, decontamination and its public health importance in Africa is lacking. The aim of this review is to highlight, update and discuss the available information on the incidence of mycotoxins in African countries. The public health implications and the recommended strategies for control of mycotoxins in food and agricultural crops are also discussed.

Effects of lactic acid bacteria and Saccharomyces cerevisiae on growth of Aspergillus westerdijkiae and ochratoxin A production and toxicity

The aim of this study was to examine three strains of the yeast Saccharomyces cerevisiae and three strains of lactic acid bacteria belonging to the genus Lactobacillus for their antifungal activity against the ochratoxin A producer Aspergillus westerdijkiae, as well as for their effect on OTA genotoxicity and cytotoxicity. When inoculated simultaneously, fungal growth was completely inhibited by S. cerevisiae. In the case of lactic acid bacteria, growth inhibition also occurred but to a less extent. A significant decrease in toxin production in co-culture with the yeast strains and LAB was observed. The supernatant of 24-h-old cultures of yeast strains in medium with OTA did not influence significantly the viability of porcine kidney epithelial LLC-PK1 cell line, whereas the supernatant from the LAB increased the viability compared to the control. Regarding genotoxicity, a decreased fragmentation of DNA was observed in the presence of the supernatant from wine and brewing yeasts, and Lactobacillus brevis strains. Based on the results obtained, it might be concluded that S. cerevisiae yeasts and lactic acid bacteria could be used to minimise the negative effect of OTA on humans and animals.

Development and validation of a method for detection and quantification of ochratoxin A in green coffee using liquid chromatography coupled to mass spectrometry

A method using Liquid Chromatography Tanden Mass Spectrometry (LC-MS/MS) with matrix-matched calibration curve was developed and validated for determining ochratoxin A (OTA) in green coffee. Linearity was found between 3.0 and 23.0 ng.g-1. Mean recoveries ranged between 90.45% and 108.81%; the relative standard deviation under repeatability and intermediate precision conditions ranged from 5.39% to 9.94% and from 2.20% to 14.34%, respectively. The limits of detection and quantification were 1.2 ng.g-1 and 3.0 ng.g-¹, respectively. The method developed was suitable and contributed to the field of mycotoxin analysis, and it will be used for future production of the Certified Reference Material (CRM) for OTA in coffee.

Seven naphtho-γ-pyrones from the marine-derived fungus Alternaria alternata: structure elucidation and biological properties

Eight bioactive pyrone derivatives were identified from the culture of Alternaria alternata strain D2006, isolated from the marine soft coral Denderonephthya hemprichi, which was selected as its profound antimicrobial activities. The compounds were assigned as pyrophen (1), rubrofusarin B (2), fonsecin (3), and fonsecin B (5) beside to the four dimeric naphtho-γ-pyrones; aurasperone A (6), aurasperone B (7), aurasperone C (8), and aurasperone F (9). Structures of the isolated compounds were identified on the basis of 1D and 2D NMR spectroscopy and mass (EI, ESI, HRESI) data, and by comparison with the literature. Configuration of the four dimeric naphtho-γ-pyrones 6-9 was analyzed by CD spectra, exhibiting an identical stereochemistry.