Bioactive profile and microbiological safety of Coffea arabica and Coffea canephora beverages obtained by innovative cold extraction methods (cold brews)

Coffee cold brews have been gaining prominence and popularity among consumers worldwide. However, only a few studies have systematically analyzed their chemical composition or evaluated microbiological safety aspects. This study aimed to evaluate the survival of Bacillus cereus and Escherichia coli in cold brews prepared from roasted and ground Coffea arabica and C. canephora seeds using the following preparation methods: immersion without filter (INF), immersion in a cotton filter bag (ICF), vacuum (Vac.) and cold dripping (Drip.). Traditional hot dripping methods using filter paper (HDFP) and cotton filter (HDCF) were also tested for comparison. Water at 4 °C or 25 °C was intentionally contaminated (105 CFU/mL) with cells of Escherichia coli ATCC 25922 (EC) and Bacillus cereus F4433 (BC) before coffee extraction and refrigeration at 4 °C. Coffee concentrations of 5, 10, and 15% were tested. Analyses of pH, soluble solids, nine chlorogenic acids and two lactones (CGA), caffeine, trigonelline, and melanoidins were performed. Results were compared by ANOVA, followed by the Fisher's test, Pearson correlation, Variable Importance in Projection (VIP), and Cluster analyses, with a significance level of 5%. EC and BC were not detected (<10 CFU/mL and < 1 CFU/mL, respectively) after preparing C. arabica and C. canephora hot brews. In cold brews, the higher the extraction of soluble solids and bioactive compounds (with the highest occurring at 25 °C), the lower the counts of inoculated microorganisms during 24 h of storage. BC was not detected after 24 h of extraction and/or storage in the drinks obtained by ICF and Drip. at 5%, 10%, and 15% and INF and Vac. at 15%. EC was not detected in ICF and Drip. at 10 and 15%, and in INF at 15%. C. canephora brews exhibited higher levels of soluble solids, CGA, caffeine, and melanoidins than C. arabica brews. Based on these results, it can be concluded that in the absence of thermal processing as in hot brews, more concentrated cold brews, such as 15%, produced at 25 °C by dripping and immersion methods, are preferable for later dilution due to the higher content of soluble solids and bioactive compounds that contribute reducing the number of microorganisms in the beverage.

Microbiomes associated with Coffea arabica and Coffea canephora in four different floristic domains of Brazil

Brazilian coffee production relies on the cultivation of Coffea arabica and Coffea canephora. Climate change has been responsible for the decreasing yield of the crops in the country yet the associated microbial community can mitigate these effects by improving plant growth and defense. Although some studies have tried to describe the microorganisms associated with these Coffea species, a study that compares the microbiome on a wider spatial scale is needed for a better understanding of the terroir of each coffee planting region. Therefore, our aim was to evaluate the microbial communities harbored in soils and fruits of these Coffea species in four Brazilian floristic domains (Amazon, Atlantic Forest Caatinga, and Cerrado). One hundred and eight samples (90 of soil and 90 of fruits) were used in the extraction and sequencing of the fungal and bacterial DNA. We detected more than 1000 and 500 bacterial and fungal genera, respectively. Some soil microbial taxa were more closely related to one coffee species than the other species. Bacillus bataviensis tends to occur more in arid soils from the Caatinga, while the fungus Saitozyma sp. was more related to soils cultivated with C. arabica. Thus, the species and the planting region (floristic domain) of coffee affect the microbial composition associated with this crop. This study is the first to report microbial communities associated with coffee produced in four floristic domains that include sites in eight Brazilian states. Data generated by DNA sequencing provides new insights into microbial roles and their potential for the developing more sustainable coffee management, such as the production of biofertilizers and starter culture for fermentation of coffee cherries.

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.

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.

Comprehensive Review of Fungi on Coffee

Coffee is grown in more than 80 countries as a cash crop and consumed worldwide as a beverage and food additive. It is susceptible to fungal infection during growth, processing and storage. Fungal infections, in particular, can seriously affect the quality of coffee and threaten human health. The data for this comprehensive review were collected from the United States Department of Agriculture, Agricultural Research Service (USDA ARS) website and published papers. This review lists the fungal species reported on coffee based on taxonomy, life mode, host, affected plant part and region. Five major fungal diseases and mycotoxin-producing species (post-harvest diseases of coffee) are also discussed. Furthermore, we address why coffee yield and quality are affected by fungi and propose methods to control fungal infections to increase coffee yield and improve quality. Endophytic fungi and their potential as biological control agents of coffee disease are also discussed.

The Rhizosphere Microbiomes of Five Species of Coffee Trees

Coffee is one of the most important commodities in the global market. Of the 130 species of Coffea, only Coffea arabica and Coffea canephora are actually cultivated on a large scale. Despite the economic and social importance of coffee, little research has been done on the coffee tree microbiome. To assess the structure and function of the rhizosphere microbiome, we performed a deep shotgun metagenomic sequencing of the rhizospheres of five different species, C. arabica, C. canephora, Coffea stenophylla, Coffea racemosa, and Coffea liberica. Our findings indicated that C. arabica and C. stenophylla have different microbiomes, while no differences were detected between the other Coffea species. The core rhizosphere microbiome comprises genera such as Streptomyces, Mycobacterium, Bradyrhizobium, Burkholderia, Sphingomonas, Penicillium, Trichoderma, and Rhizophagus, several of which are potential plant-beneficial microbes. Streptomyces and mycorrhizal fungi dominate the microbial communities. The concentration of sucrose in the rhizosphere seems to influence fungal communities, and the concentration of caffeine/theobromine has little effect on the microbiome. We also detected a possible relationship between drought tolerance in Coffea and known growth-promoting microorganisms. The results provide important information to guide future studies of the coffee tree microbiome to improve plant production and health.

IMPORTANCE The microbiome has been identified as a fundamental factor for the maintenance of plant health, helping plants to fight diseases and the deleterious effects of abiotic stresses. Despite this, in-depth studies of the microbiome have been limited to a few species, generally with a short life cycle, and perennial species have mostly been neglected. The coffee tree microbiome, on the other hand, has gained interest in recent years as Coffea trees are perennial tropical species of enormous importance, especially for developing countries. A better understanding of the microorganisms associated with coffee trees can help to mitigate the deleterious effects of climate change on the crop, improving plant health and making the system more sustainable.

Ochratoxin a levels in fermented specialty coffees from Caparaó, Brazil: Is it a cause of concern for coffee drinkers?

Although postharvest coffee fruit fermentation can improve coffee flavour and quality, the mycotoxin ochratoxin A (OTA) can also be a result of microbiological activity, albeit in the later drying step of coffee processing. To evaluate the possible occurrence of OTA contamination in postharvest fruit fermentation, fourteen coffees that entailed two different postharvest fruit fermentation times were evaluated. These coffees originated in the surroundings of the village of Pedra Menina in the qualified Denomination of Origin and coffee producer region of Caparaó on the border between Minas Gerais and Espírito Santo states in Brazil. All coffees were classified according to the Specialty Coffee Association (SCA) protocol and 12 achieved specialty level. OTA was determined in all 14 coffees using immunoaffinity for sample clean-up and high-performance liquid chromatography with fluorescence detection for quantification. One sample presented an OTA concentration of 0.75 µg kg^-1 and two samples showed OTA concentrations of 0.87 µg kg^-1. The other samples had concentrations of OTA below the limit of quantification obtained in this work (0.64 µg kg^-1). Thus, all samples showed OTA concentrations far below the most stringent maximum residue limit (MRL) of 5 µg kg^-1 established for roasted coffees by European legislation. These low levels were similar to most of the previous results for Brazilian coffees listed and tabled in this work. This comparison showed that OTA contamination due to this kind of postharvest process - fruit fermentation - should not be a concern for producers and consumers of these fermented coffees.

Facility-specific 'house' microbiome ensures the maintenance of functional microbial communities into coffee beans fermentation: implications for source tracking

This work aimed at studying the unconfirmed hypothesis predicting the existence of a connection between coffee farm microbiome and the resulting spontaneous fermentation process. Using Illumina-based amplicon sequencing, 360 prokaryotes and 397 eukaryotes were identified from coffee fruits and leaves, over-ripe fruits, water used for coffee de-pulping, depulped coffee beans, soil, and temporal fermentation samples at an experimental farm in Honduras. Coffee fruits and leaves were mainly associated with high incidence of Enterobacteriaceae, Pseudomonas, Colletotrichum, and Cladosporium. The proportion of Enterobacteriaceae was increased when leaves and fruits were collected on the ground compared to those from the coffee tree. Coffee farm soil showed the richest microbial diversity with marked presence of Bacillus. Following the fermentation process, microorganisms present in depulped coffee beans (Leuconostoc, Gluconobater, Pichia, Hanseniaspora, and Candida) represented more than 90% of the total microbial community, which produced lactic acid, ethanol, and several volatile compounds. The community ecology connections described in this study showed that coffee fruit provides beneficial microorganisms for the fermentation process. Enterobacteria, Colletotrichum, and other microbial groups present in leaves, fruit surface, over-ripe fruits, and soil may transfer unwanted aromas to coffee beans, so they should be avoided from having access to the fermentation tank.

Brazilian Coffee Production and the Future Microbiome and Mycotoxin Profile Considering the Climate Change Scenario

Brazil holds a series of favorable climatic conditions for agricultural production including the hours and intensity of sunlight, the availability of agricultural land and water resources, as well as diverse climates, soils and biomes. Amidst such diversity, Brazilian coffee producers have obtained various standards of qualities and aromas, between the arabica and robusta species, which each present a wide variety of lineages. However, temperatures in coffee producing municipalities in Brazil have increased by about 0.25 °C per decade and annual precipitation has decreased. Therefore, the agricultural sector may face serious challenges in the upcoming decades due to crop sensitivity to water shortages and thermal stress. Furthermore, higher temperatures may reduce the quality of the culture and increase pressure from pests and diseases, reducing worldwide agricultural production. The impacts of climate change directly affect the coffee microbiota. Within the climate change scenario, aflatoxins, which are more toxic than OTA, may become dominant, promoting greater food insecurity surrounding coffee production. Thus, closer attention on the part of authorities is fundamental to stimulate replacement of areas that are apt for coffee production, in line with changes in climate zoning, in order to avoid scarcity of coffee in the world market.