Temporal shotgun metagenomics of an Ecuadorian coffee fermentation process highlights the predominance of lactic acid bacteria

Pothakos, Vasileios; Vuyst, Luc De; Zhang, Sophia Jiyuan; Bruyn, Florac De; Verce, Marko; Torres, Julio Montero; Callanan, Michael; Moccand, Cyril; Weckx, Stefan

doi:10.1016/j.crbiot.2020.02.001

Cited by 45 publications

(32 citation statements)

References 58 publications

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“…Up until the present, ten works have been published using next generation sequencing approaches to evaluate the impact of post-harvesting methods on coffee bean microbial community profiles ( Table 2 ). These studies were all conducted with arabica coffee, yet they were dispersed across 3 continents including three studies in Ecuador [ 69 , 70 , 71 ], one in Brazil [ 72 ], one in Honduras [ 73 ], one in Mexico [ 74 ], one in Colombia [ 75 ], two in Australia [ 76 , 77 ] and one in China [ 60 ]. Of the 10, only two studies depended on shotgun metagenomic sequencing and for the targeted amplicon studies authors chose different variable regions of the 16S rRNA gene, and either ITS or 18S to probe fungi.…”

Section: Post-harvest Microbial Ecology Of Coffee Beansmentioning

confidence: 99%

“…Eight of the ten studies went on to evaluate microbial community structure during wet fermentation over time [ 60 , 69 , 71 , 72 , 75 , 76 , 77 , 78 ]. All of these works demonstrated strong adaptation of lactic acid bacteria to the coffee fermentation environment.…”

Section: Post-harvest Microbial Ecology Of Coffee Beansmentioning

confidence: 99%

“…In wet fermentation, most studies found limited fungal diversity, with Pichia governing the process. The Pichia species identified included P. kluyveri [ 69 , 78 ], P. nakasei [ 75 ] and P. kudriavzevii [ 71 , 76 , 77 ]. Both common and region-specific species have been found during wet fermentation of coffee beans [ 76 ].…”

Section: Post-harvest Microbial Ecology Of Coffee Beansmentioning

confidence: 99%

“…Just a year later, De Oliveira Junqueira [ 75 ] identified over 157 genera using a similar approach. Both Zhang et al [ 60 , 78 ] and Pothakos et al [ 71 ] were the only ones to apply a shotgun metagenomics approach to the coffee post harvesting process and showed the strength of the technique to identify genes, predict functions and build networks, besides taxonomic classification of microorganisms. While only true metatranscriptomics can elucidate actual gene expression, the functional prediction based on genes has underlined the contributions of the different microbial groups to wet coffee processing.…”

Section: Post-harvest Microbial Ecology Of Coffee Beansmentioning

confidence: 99%

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

et al. 2021

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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.

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Section: Post-harvest Microbial Ecology Of Coffee Beansmentioning

confidence: 99%

Section: Post-harvest Microbial Ecology Of Coffee Beansmentioning

confidence: 99%

Section: Post-harvest Microbial Ecology Of Coffee Beansmentioning

confidence: 99%

Section: Post-harvest Microbial Ecology Of Coffee Beansmentioning

confidence: 99%

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

et al. 2021

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“…In contrast to amplicon sequencing, shotgun metagenomic studies of fermented food ecosystems with a concomitant functional analysis based on gene prediction are much less applied (Escobar-Zepeda et al, 2016;Wu et al, 2017;Pothakos et al, 2020). However, it seems to be a robust tool for assessing both the species diversity and functionality of microorganisms in various fermented foods and beverages.…”

Section: Introductionmentioning

confidence: 99%

Temporal Shotgun Metagenomics Revealed the Potential Metabolic Capabilities of Specific Microorganisms During Lambic Beer Production

et al. 2020

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Lambic beer production processes are characterized by a temporal succession of well-adapted microbial species. Temporal metagenomic analysis of a Belgian, traditional, lambic beer production process, which was examined microbiologically and metabolomically before, confirmed that the microbial diversity is limited. Moreover, it allowed to link the consumption and production of certain compounds to specific microbial groups or species. Fermentation characteristics, such as the conversion of malic acid into lactic acid and acetoin production, were retrieved and could be attributed to specific microorganisms, namely Pediococcus damnosus and Acetobacter species, respectively. Traits previously ascribed to brewery-specific Dekkera bruxellensis strains were confirmed during the lambic beer production process examined multiphasically; in particular, the higher production of 4-ethylguaiacol compared to 4-ethylphenol was further shown by mass spectrometric analysis. Moreover, the absence of phenolic acid decarboxylase in Brettanomyces custersianus was shown culture-independently and could explain its late occurrence during the maturation phase. Furthermore, the potential of maltooligosaccharide degradation could be ascribed metagenomically to not only Brettanomyces species but also Saccharomyces kudriavzevii, possibly explaining their degradation early in the lambic beer production process. Also, acetic acid bacteria (AAB) seemed to be able to consume maltooligosaccharides via their conversion into trehalose. Furthermore, these AAB possessed esterase genes, potentially capable of forming ethyl acetate, which may contribute to the flavor of lambic beer. Improved knowledge on the reasons behind certain community dynamics and the role of the different microorganisms in terms of potential functionality could improve brewery practices to assure to produce more quality-stable end-products.

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The use of mesophilic and lactic acid bacteria strains as starter cultures for improvement of coffee beans wet fermentation

Ribeiro

Miguel

Martinez

et al. 2020

World J Microbiol Biotechnol

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Temporal shotgun metagenomics of an Ecuadorian coffee fermentation process highlights the predominance of lactic acid bacteria

Cited by 45 publications

References 58 publications

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

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

Temporal Shotgun Metagenomics Revealed the Potential Metabolic Capabilities of Specific Microorganisms During Lambic Beer Production

The use of mesophilic and lactic acid bacteria strains as starter cultures for improvement of coffee beans wet fermentation

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