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

Vaughan, Michael J.; Mitchell, Thomas K.; Gardener, Brian B. McSpadden

doi:10.1128/aem.01933-15

Cited by 41 publications

(22 citation statements)

References 89 publications

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“…The digested beans present a specific flavour and characteristics. Novel production methods require new approaches to exploit the coffee microbiome and novel associations of gut-microbiome strains in the development of desired flavours [39].…”

Section: Coffee Bean Microbiota In Fermentation Processesmentioning

confidence: 99%

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Challenges in Specialty Coffee Processing and Quality Assurance

Poltronieri¹,

Rossi

2016

Challenges

128

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Coffee is an important crop that assures a sustainable economy to farmers in tropical regions. A dramatic concern for coffee production is currently represented by climate change, which threatens the survival of Coffea arabica cultivation worldwide and imposes modifications of the agronomic practices to prevent this risk. The quality of coffee beans depends on optimized protocols of cultivation, ripe berries collection, and removal of the outer fruit layers by dry or wet processes and moisture reduction. Storage and shipment represent two steps where bean quality needs to be preserved by preventing fungal contamination that may impact the final product and form mycotoxins, mainly ochratoxin A. In this review, we describe the challenges faced by the coffee industry to guarantee quality from production to roasting and brewing. An overview of novel technologies, such as the application of starter cultures in fermentation and the exploitation of industrial enzymes in accelerating the process of flavour development in coffee beans, is given. Moreover, the results of studies on microbial populations on coffee and the differences found in fungi, yeasts and bacteria composition among the investigations, are summarized. In particular, this review describes new attempts to contain the development of mycotoxigenic fungi, through the application of antagonistic microorganisms such as S. cerevisiae. The new wave of specialty coffees, i.e., those with a cupping score higher than 85/100, is also presented. It is shown how, through careful coffee production methods and controlled fermentation processes, coffee producers may increase their income by assuring high standards of quality and high added value for the coffee experience sector.

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Section: Coffee Bean Microbiota In Fermentation Processesmentioning

confidence: 99%

“…Different types of microorganisms interact with natural coffee mucilage in very diverse ways, some simultaneously and others in succession [39]. The main aim is to control the process in order to avoid over-fermentation linked flavours [40,41].…”

Section: Bacteria and Yeasts Associated To Coffee Fermentation Processesmentioning

confidence: 99%

Challenges in Specialty Coffee Processing and Quality Assurance

Poltronieri¹,

Rossi

2016

Challenges

128

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“…Microorganisms are ubiquitous during the different stages of postharvest coffee processing (2,(19)(20)(21)(22). Enterobacteriaceae and other Gram-negative bacteria, including acetic acid bacteria (AAB), bacilli, lactic acid bacteria (LAB), yeasts, and filamentous fungi have been found through culture-dependent and -independent methods during coffee fermentation processes (5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15)(16)(17)(18)22).…”

mentioning

confidence: 99%

“…Despite the complexity of coffee processing and the numerous factors contributing to the quality traits of the green coffee beans, all studies conducted so far only targeted specific steps of the processing (2,19,21). Their primary goal has been the identification of the microbiota associated with the fermentation part of the processing and the chemical profiling of the green coffee beans and/or bean germination process.…”

mentioning

confidence: 99%

Exploring the Impacts of Postharvest Processing on the Microbiota and Metabolite Profiles during Green Coffee Bean Production

Bruyn

Zhang

Pothakos

et al. 2017

Appl Environ Microbiol

191

164

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The postharvest treatment and processing of fresh coffee cherries can impact the quality of the unroasted green coffee beans. In the present case study, freshly harvested Arabica coffee cherries were processed through two different wet and dry methods to monitor differences in the microbial community structure and in substrate and metabolite profiles. The changes were followed throughout the postharvest processing chain, from harvest to drying, by implementing up-to-date techniques, encompassing multiple-step metagenomic DNA extraction, highthroughput sequencing, and multiphasic metabolite target analysis. During wet processing, a cohort of lactic acid bacteria (i.e., Leuconostoc, Lactococcus, and Lactobacillus) was the most commonly identified microbial group, along with enterobacteria and yeasts (Pichia and Starmerella). Several of the metabolites associated with lactic acid bacterial metabolism (e.g., lactic acid, acetic acid, and mannitol) produced in the mucilage were also found in the endosperm. During dry processing, acetic acid bacteria (i.e., Acetobacter and Gluconobacter) were most abundant, along with Pichia and non-Pichia (Candida, Starmerella, and Saccharomycopsis) yeasts. Accumulation of associated metabolites (e.g., gluconic acid and sugar alcohols) took place in the drying outer layers of the coffee cherries. Consequently, both wet and dry processing methods significantly influenced the microbial community structures and hence the composition of the final green coffee beans. This systematic approach to dissecting the coffee ecosystem contributes to a deeper understanding of coffee processing and might constitute a state-of-the-art framework for the further analysis and subsequent control of this complex biotechnological process.IMPORTANCE Coffee production is a long process, starting with the harvest of coffee cherries and the on-farm drying of their beans. In a later stage, the dried green coffee beans are roasted and ground in order to brew a cup of coffee. The on-farm, postharvest processing method applied can impact the quality of the green coffee beans. In the present case study, freshly harvested Arabica coffee cherries were processed through wet and dry processing in four distinct variations. The microorganisms present and the chemical profiles of the coffee beans were analyzed throughout the postharvest processing chain. The up-to-date techniques implemented facilitated the investigation of differences related to the method applied. For instance, different microbial groups were associated with wet and dry processing methods. Additionally, metabolites associated with the respective microorganisms accumulated on the final green coffee beans.

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“…The consumption of these products is increasing as the production, is exported to several other world countries in addition to Brazil. Characteristics, such as taste and flavor, have been modified in coffee using selected microorganisms that inhabit the coffee seeds as epi or endophytes [36,37], demonstrating the importance of studies of microbial communities from seeds.…”

Section: Discussionmentioning

confidence: 99%

Endophytic cultivable bacterial community obtained from the Paullinia cupana seed in Amazonas and Bahia regions and its antagonistic effects against Colletotrichum gloeosporioides

Silva¹,

Polônio

Quecine³

et al. 2016

Microbial Pathogenesis

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Guarana (Paullinia cupana var. sorbilis) is a plant from the Amazonas region with socio-economic importance. However, guarana production has been increasingly affected by unfavorable conditions resulting from anthracnose, caused by the Colletotrichum fungal genus, which primarily affects mainly the Amazonas region. The aim of the present study was to isolate bacterial endophytes from the seeds of guarana plants obtained from Amazonas region and the Northeast state of Bahia, a region where this disease is not a problem for guarana plantations. The number of bacterial Colony Forming Units (CFU/g seeds) was 2.4 × 10(4) from the Bahia and 2.9 × 10(4) from the Amazonas region. One hundred and two isolated bacteria were evaluated in vitro against the phytopathogenic strain Colletotrichum gloeosporioides L1. These isolates were also analyzed for the enzymatic production of amylase, cellulase, protease, pectinase, lipase and esterase. Approximately 15% of isolates, showing high antagonistic activity, and the production of at least one enzyme were identified through the partial sequencing of 16S rDNA. The genus Bacillus was the most frequently observed, followed by Paenibacillus, Ochrobactrum, Microbacterium and Stenotrophomonas. Proteolytic activity was observed in 24 isolates followed by amylolytic, pectinolytic and cellulolytic activities. No esterase and lipase production was detected. Most of the isolates, showing antagonistic effects against C. gloeosporioides and high enzymatic activities, were isolated from the anthracnose-affected region. A biocontrol method using the endophytes from guarana seeds could be applied in the future, as these bacteria are vertically transferred to guarana seedlings.

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

Cited by 41 publications

References 89 publications

Challenges in Specialty Coffee Processing and Quality Assurance

Challenges in Specialty Coffee Processing and Quality Assurance

Exploring the Impacts of Postharvest Processing on the Microbiota and Metabolite Profiles during Green Coffee Bean Production

Endophytic cultivable bacterial community obtained from the Paullinia cupana seed in Amazonas and Bahia regions and its antagonistic effects against Colletotrichum gloeosporioides

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