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First description of bacterial and fungal communities in Colombian coffee beans fermentation analysed using Illumina-based amplicon sequencing

dc.rights.licensehttp://creativecommons.org/licenses/by-nc-nd/4.0/
dc.contributor.authorde Oliveira Junqueira A.C.
dc.contributor.authorde Melo Pereira G.V.
dc.contributor.authorCoral Medina J.D.
dc.contributor.authorAlvear M.C.R.
dc.contributor.authorRosero R.
dc.contributor.authorde Carvalho Neto D.P.
dc.contributor.authorEnríquez H.G.
dc.contributor.authorSoccol C.R.
dc.date.accessioned2024-12-02T20:15:59Z
dc.date.available2024-12-02T20:15:59Z
dc.date.issued2019
dc.identifier.issn20452322
dc.identifier.urihttps://hdl.handle.net/20.500.14112/28999
dc.description.abstractIn Colombia, coffee growers use a traditional method of fermentation to remove the cherry pulp surrounding the beans. This process has a great influence on sensory quality and prestige of Colombian coffee in international markets, but has never been studied. Here we use an Illumina-based amplicon sequencing to investigate bacterial and fungal communities associated with spontaneous coffee-bean fermentation in Colombia. Microbial-derived metabolites were further analysed by high–performance liquid chromatography and gas chromatography–mass spectrometry. Highly diverse bacterial groups, comprising 160 genera belonging to 10 phyla, were found. Lactic acid bacteria (LAB), mainly represented by the genera Leuconostoc and Lactobacillus, showed relative prevalence over 60% at all sampling times. The structure of the fungal community was more homogeneous, with Pichia nakasei dominating throughout the fermentation process. Lactic acid and acetaldehyde were the major end-metabolites produced by LAB and Pichia, respectively. In addition, 20 volatile compounds were produced, comprising alcohols, organic acids, aldehydes, esters, terpenes, phenols, and hydrocarbons. Interestingly, 56 microbial genera, associated with native soil, seawater, plants, insects, and human contact, were detected for the first time in coffee fermentation. These microbial groups harbour a remarkable phenotypic diversity and may impart flavours that yield clues to the terroir of Colombian coffees. © 2019, The Author(s).
dc.description.sponsorshipThe authors gratefully acknowledge the support provided by Brazilian Council for Scientific and Technological Development (Grant Number 303254/2017-3).
dc.format.mediumRecurso electrónico
dc.format.mimetypeapplication/pdf
dc.language.isoeng
dc.publisherNature Publishing Group
dc.rights.uriAttribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)
dc.sourceScientific Reports
dc.sourceSci. Rep.
dc.sourceScopus
dc.titleFirst description of bacterial and fungal communities in Colombian coffee beans fermentation analysed using Illumina-based amplicon sequencing
datacite.contributorDepartment of Bioprocess Engineering and Biotechnology, Federal University of Paraná (UFPR), 19011 Curitiba, Paraná, 81531-980, Brazil
datacite.contributorDepartment of Process and Biotechnology, Mariana University, Nariño, 520002, Pasto, Colombia
datacite.contributorde Oliveira Junqueira A.C., Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná (UFPR), 19011 Curitiba, Paraná, 81531-980, Brazil
datacite.contributorde Melo Pereira G.V., Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná (UFPR), 19011 Curitiba, Paraná, 81531-980, Brazil
datacite.contributorCoral Medina J.D., Department of Process and Biotechnology, Mariana University, Nariño, 520002, Pasto, Colombia
datacite.contributorAlvear M.C.R., Department of Process and Biotechnology, Mariana University, Nariño, 520002, Pasto, Colombia
datacite.contributorRosero R., Department of Process and Biotechnology, Mariana University, Nariño, 520002, Pasto, Colombia
datacite.contributorde Carvalho Neto D.P., Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná (UFPR), 19011 Curitiba, Paraná, 81531-980, Brazil
datacite.contributorEnríquez H.G., Department of Process and Biotechnology, Mariana University, Nariño, 520002, Pasto, Colombia
datacite.contributorSoccol C.R., Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná (UFPR), 19011 Curitiba, Paraná, 81531-980, Brazil
datacite.rightshttp://purl.org/coar/access_right/c_abf2
oaire.resourcetypehttp://purl.org/coar/resource_type/c_6501
oaire.versionhttp://purl.org/coar/version/c_ab4af688f83e57aa
dc.contributor.contactpersonC.R. Soccol
dc.contributor.contactpersonDepartment of Bioprocess Engineering and Biotechnology, Federal University of Paraná (UFPR), Paraná, 19011 Curitiba, 81531-980, Brazil
dc.contributor.contactpersonemail: soccol@ufpr.br
dc.contributor.sponsorConselho Nacional de Desenvolvimento Científico e Tecnológico, CNPq, (303254/2017-3)
dc.identifier.doi10.1038/s41598-019-45002-8
dc.identifier.instnameUniversidad Mariana
dc.identifier.local8794
dc.identifier.pissn31217528
dc.identifier.reponameRepositorio Clara de Asis
dc.identifier.urlhttps://www.scopus.com/inward/record.uri?eid=2-s2.0-85067809964&doi=10.1038%2fs41598-019-45002-8&partnerID=40&md5=cb91fba981dd220db8d543c880e4fba7
dc.relation.citationvolume9
dc.relation.iscitedby80
dc.relation.referencesReport on Coffee Total Production by All Exporting Countries in Thousand 60 Kg Bags, 1, (2018)
dc.relation.referencesLara-Estrada L., Vaast P., Effects of altitude, shade, yield and fertilization on coffee quality (Coffea arabica L. var. Caturra) produced in agroforestry systems of the Northern Central Zones of Nicaragua, In 2nd International Symposium on Multi-Strata Agroforestry Systems with Perennial Crops, 68, pp. 17-21, (2007)
dc.relation.referencesPereira G.V.M., Et al., Exploring the impacts of postharvest processing on the aroma formation of co ff ee beans – A review, Food Chem., 272, pp. 441-452, (2019)
dc.relation.referencesPereira G.V., Et al., Microbial ecology and starter culture technology in coffee processing, Crit. Rev. Food Sci. Nutr., 57, pp. 2775-2788, (2017)
dc.relation.referencesLee L.W., Cheong M.W., Curran P., Yu B., Liu S.Q., Coffee fermentation and flavor - An intricate and delicate relationship, Food Chem., 185, pp. 182-191, (2015)
dc.relation.referencesAvallone S., Guyot B., Brillouet J.M., Olguin E., Guiraud J.P., Microbiological and biochemical study of coffee fermentation, Curr. Microbiol., 42, pp. 252-256, (2001)
dc.relation.referencesMasoud W., Cesar L.B., Jespersen L., Jakobsen M., Yeast involved in fermentation of Coffea arabica in East Africa determined by genotyping and by direct denaturating gradient gel electrophoresis, Yeast, 21, pp. 549-556, (2004)
dc.relation.referencesPereira G.V.M., Et al., Isolation, selection and evaluation of yeasts for use in fermentation of coffee beans by the wet process, Int. J. Food Microbiol., 188, pp. 60-66, (2014)
dc.relation.referencesCarvalho D.P.D., Pereira G.V.M., Soccol C.R., High-Throughput rRNA Gene Sequencing Reveals High and Complex Bacterial Diversity Associated with Brazilian Coffee Bean Fermentation, Food Technol. Biotechnol., 56, (2018)
dc.relation.referencesDe Bruyn F., Et al., Exploring the Impacts of Postharvest Processing on the Microbiota and Metabolite Profiles during Green Coffee Bean Production, Appl. Environ. Microbiol., 83, pp. e02398-e2316, (2017)
dc.relation.referencesPereira G.V.M., Et al., Conducting starter culture-controlled fermentations of coffee beans during on-farm wet processing: Growth, metabolic analyses and sensorial effects, Food Res. Int., 75, pp. 348-356, (2015)
dc.relation.referencesEvangelista S.R., Et al., Improvement of coffee beverage quality by using selected yeasts strains during the fermentation in dry process, Food Res. Int., 61, pp. 183-195, (2014)
dc.relation.referencesPereira G.V.M., Soccol V.T., Soccol C.R., Current state of research on cocoa and coffee fermentations, Curr. Opin. Food Sci., 7, pp. 50-57, (2016)
dc.relation.referencesLee L.W., Cheong M.W., Curran P., Yu B., Liu S.Q., Modulation of coffee aroma via the fermentation of green coffee beans with Rhizopus oligosporus: II. Effects of different roast levels, Food Chem., 211, pp. 925-936, (2016)
dc.relation.referencesLee L.W., Et al., Modulation of the volatile and non-volatile profiles of coffee fermented with Yarrowia lipolytica: II. Roasted coffee, LWT, 80, pp. 32-42, (2017)
dc.relation.referencesFleet G.H., Yeast interactions and wine flavour, Int. J. Food Microbiol., 86, pp. 11-22, (2003)
dc.relation.referencesViljoen B.C., Yeast ecological interactions. Yeast-yeast, yeast-bacteria, yeast-fungi and yeasts as biocontrol agents, Yeast in Food and Beverages, pp. 83-110, (2006)
dc.relation.referencesJouhten P., Ponomarova O., Gonzalez R., Patil K.R., Saccharomyces cerevisiae metabolism in ecological context, FEMS Yeast Res., 16, pp. 1-8, (2016)
dc.relation.referencesAlexandre H., Guilloux-Benatier M., Yeast autolysis in sparkling wine - A review, Aust. J. Grape Wine Res., 12, pp. 119-127, (2006)
dc.relation.referencesCrotti E., Et al., Acetic acid bacteria, newly emergin symbionts of insects, Appl. Environ. Microbiol., 76, pp. 6963-6970, (2010)
dc.relation.referencesAnderson K.E., Et al., Highly similar microbial communities are shared among related and trophically similar ant species, Mol. Ecol., 21, pp. 2282-2296, (2012)
dc.relation.referencesLakshmanan V., Selvaraj G., Bais H.P., Functional soil microbiome: Belowground solutions to an aboveground problem, Plant Physiol., 166, pp. 689-700, (2014)
dc.relation.referencesFindley K., Et al., Topographic diversity of fungal and bacterial communities in human skin, Nature, 498, pp. 367-370, (2013)
dc.relation.referencesKreisinger J., Cizkova D., Kropackova L., Albrecht T., Cloacal microbiome structure in a long-distance migratory bird assessed using deep 16sRNA pyrosequencing, PLoS One, 10, (2015)
dc.relation.referencesRenganath Rao R., Et al., Alkaline Protease Production from Brevibacterium luteolum (MTCC 5982) Under Solid-State Fermentation and Its Application for Sulfide-Free Unhairing of Cowhides, Appl. Biochem. Biotechnol., 182, pp. 511-528, (2017)
dc.relation.referencesLiu M., Et al., Kineococcus xinjiangensis sp. nov., isolated from desert sand, Int. J. Syst. Evol. Microbiol., 61, pp. 1865-1869, (2011)
dc.relation.referencesGueule D., Et al., Pantoea coffeiphila sp. nov., cause of the ‘potato taste’ of Arabica coffee from the African great lakes region, Int. J. Syst. Evol. Microbiol., 65, pp. 23-29, (2015)
dc.relation.referencesJiayang Q., Zijun X., Cuiqing M., Nengzhong X., Peihai L., Production of 2,3-Butanediol by, Chinese J. Chem. Eng., 14, pp. 132-136, (2006)
dc.relation.referencesDahl S., Tavaria F.K., Malcata F.X., Relationships between flavour and microbiological profiles in Serra da Estrela cheese throughout ripening, Int. Dairy J., 10, pp. 255-262, (2000)
dc.relation.referencesBrown B.P., Wernegreen J.J., Deep divergence and rapid evolutionary rates in gut-associated Acetobacteraceae of ants, BMC Microbiol., 16, (2016)
dc.relation.referencesDouglas A.E., Multiorganismal Insects: Diversity and Function of Resident Microorganisms, Annu. Rev. Entomol., 60, pp. 17-34, (2015)
dc.relation.referencesPereira G.V.M., Et al., Potential of lactic acid bacteria to improve the fermentation and quality of coffee during on-farm processing, Int. J. Food Sci. Technol., 51, pp. 1689-1695, (2016)
dc.relation.referencesLeong K.-H., Et al., Diversity of Lactic Acid Bacteria Associated with Fresh Coffee Cherries in Taiwan, Curr. Microbiol., 68, pp. 440-447, (2014)
dc.relation.referencesVelmourougane K., Impact of natural fermentation on physicochemical, microbiological and cup quality characteristics of Arabica and Robusta coffee, Proc. Natl. Acad. Sci. India Sect. B - Biol. Sci., 83, pp. 233-239, (2013)
dc.relation.referencesDjossou O., Et al., Robusta coffee beans post-harvest microflora: Lactobacillus plantarum sp. as potential antagonist of Aspergillus carbonarius, Anaerobe, 17, pp. 267-272, (2011)
dc.relation.referencesCarvalho Neto D.P., Et al., Efficient coffee beans mucilage layer removal using lactic acid fermentation in a stirred-tank bioreactor: Kinetic, metabolic and sensorial studies, Food Biosci., 26, pp. 80-87, (2018)
dc.relation.referencesEndo A., Dicks L.M.T., Pgysiology of the LAB. in Lactic Acid Bacteria: Biodiversity and Taxonomy, pp. 13-30, (2014)
dc.relation.referencesSilva C.F., Batista L.R., Abreu L.M., Dias E.S., Schwan R.F., Succession of bacterial and fungal communities during natural coffee (Coffea arabica) fermentation, Food Microbiol., 25, pp. 951-957, (2008)
dc.relation.referencesFeng X., Et al., Culture-Dependent and -Independent Methods to Investigate the Predominant Microorganisms Associated with Wet Processed Coffee, Curr. Microbiol., 73, pp. 190-195, (2016)
dc.relation.referencesThe Yeasts - a Taxonomic Study, (2011)
dc.relation.referencesGueho E., Et al., The role of Malassezia species in the ecology of human skin and as pathogens, Med. Mycol., 36, pp. 220-229, (1998)
dc.relation.referencesTakashima M., Suh S.-O., Nakase T., Bensingtonia musae sp. nov. isolated from a dead leaf of Musa paradisiaca and its phylogenetic relationship among basidiomycetous yeasts, J. Gen. Appl. Microbiol., 41, pp. 143-151, (1995)
dc.relation.referencesNagahama T., Et al., Dipodascus tetrasporeus sp. nov., an ascosporogenous yeast isolated from deep-sea sediments in the Japan Trench, Int. J. Syst. Evol. Microbiol., 58, pp. 1040-1046, (2008)
dc.relation.referencesSimmons D.R., James T.Y., Meyer A.F., Longcore J.E., Lobulomycetales, a new order in the Chytridiomycota, Mycol. Res., 113, pp. 450-460, (2009)
dc.relation.referencesFreeman K.R., Et al., Evidence that chytrids dominate fungal communities in high-elevation soils, Proc. Natl. Acad. Sci., 106, pp. 18315-18320, (2009)
dc.relation.referencesMurthy P.S., Madhava Naidu M., Improvement of Robusta Coffee Fermentation with Microbial Enzymes, Eur. J. Appl. Sci., 3, pp. 130-139, (2011)
dc.relation.referencesCarvalho Neto D.P., Et al., Yeast Diversity and Physicochemical Characteristics Associated with Coffee Bean Fermentation from the Brazilian Cerrado Mineiro Region, Fermentation, 3, (2017)
dc.relation.referencesVelmourougane K., Shanmukhappa D.R., Venkatesh K., Prakasan C.B., & Jayarama. Use of starter culture in coffee fermentation - effect on demucilisation and cup quality, Indian Coffee, 72, pp. 31-34, (2008)
dc.relation.referencesAvallone S., Brillouet J.M., Guyot B., Olguin E., Guiraud J.P., Involvement of pectolytic micro-organisms in coffee fermentation, Int. J. Food Sci. Technol., 37, pp. 191-198, (2002)
dc.relation.referencesWang C., Sun J., Lassabliere B., Yu B., Zhao F., Zhao F., Chen Y., Liu S.Q., Potential of lactic acid bacteria to modulate coffee volatiles and effect of glucose supplementation: fermentation of green coffee beans and impact of coffee roasting, Journal of the Science of Food and Agriculture, 99, 1, pp. 409-420, (2018)
dc.relation.referencesCiani M., Ferraro L., Fatichenti F., Influence of glycerol production on the aerobic and anaerobic growth of the wine yeast Candida stellata, Enzyme Microb. Technol., 27, pp. 698-703, (2000)
dc.relation.referencesMoreno J.A., Zea L., Moyano L., Medina M., Aroma compounds as markers of the changes in sherry wines subjected to biological ageing, Food Control, 16, pp. 333-338, (2005)
dc.relation.referencesRoutray W., Mishra H.N., Scientific and Technical Aspects of Yogurt Aroma and Taste: A Review, Compr. Rev. Food Sci. Food Saf., 10, pp. 208-220, (2011)
dc.relation.referencesSwiegers J.H., Bartowsky E.J., Henschke P.A., Pretorius I.S., Yeast and bacterial modulation of wine aroma and flavour, Aust. J. Grape Wine Res., 11, pp. 139-173, (2005)
dc.relation.referencesKieronczyk A., Skeie S., Langsrud T., Yvon M., Cooperation between Lactococcus lactis and nonstarter lactobacilli in the formation of cheese aroma from amino acids, Appl. Environ. Microbiol., 69, pp. 734-739, (2003)
dc.relation.referencesAnnan N.T., Poll L., Sefa-Dedeh S., Plahar W.A., Jakobsen M., Influence of starter culture combinations of Lactobacillus fermentum, Saccharomyces cerevisiae and Candida krusei on aroma in Ghanaian maize dough fermentation, Eur. Food Res. Technol., 216, pp. 377-384, (2003)
dc.relation.referencesBasso R.F., Alcarde A.R., Portugal C.B., Could non-Saccharomyces yeasts contribute on innovative brewing fermentations?, Food Res. Int., 86, pp. 112-120, (2016)
dc.relation.referencesVallet A., Lucas P., Lonvaud-Funel A., De Revel G., Pathways that produce volatile sulphur compounds from methionine in Oenococcus oeni, J. Appl. Microbiol., 104, pp. 1833-1840, (2008)
dc.relation.referencesWaters D.M., Arendt E.K., Moroni A.V., Overview on the mechanisms of coffee germination and fermentation and their significance for coffee and coffee beverage quality, Crit. Rev. Food Sci. Nutr., 57, pp. 259-274, (2017)
dc.relation.referencesCaporaso J.G., Et al., Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms, ISME J., 6, pp. 1621-1624, (2012)
dc.relation.referencesCaporaso J.G., Et al., QIIME allows analysis of high-throughput community sequencing data, Nat. Methods., 7, pp. 335-336, (2010)
dc.relation.referencesQuast C., Et al., The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools, Nucleic Acids Res., 41, pp. D590-D596, (2013)
dc.relation.referencesEdgar R.C., Search and clustering orders of magnitude faster than BLAST, Bioinformatics, 26, pp. 2460-2461, (2010)
dc.rights.accessrightsinfo:eu-repo/semantics/openAccess
dc.subject.keywordsBacteria
dc.subject.keywordsCoffee
dc.subject.keywordsColombia
dc.subject.keywordsFermentation
dc.subject.keywordsFungi
dc.subject.keywordsHigh-Throughput Nucleotide Sequencing
dc.subject.keywordsHydrogen-Ion Concentration
dc.subject.keywordsMetabolome
dc.subject.keywordsPhylogeny
dc.subject.keywordsRNA, Ribosomal, 16S
dc.subject.keywordsRNA, Ribosomal, 18S
dc.subject.keywordsSugars
dc.subject.keywordsTemperature
dc.subject.keywordsVolatile Organic Compounds
dc.subject.keywordscarbohydrate
dc.subject.keywordsRNA 16S
dc.subject.keywordsRNA 18S
dc.subject.keywordsvolatile organic compound
dc.subject.keywordsbacterium
dc.subject.keywordscoffee
dc.subject.keywordsColombia
dc.subject.keywordsfermentation
dc.subject.keywordsfungus
dc.subject.keywordsgenetics
dc.subject.keywordsgrowth, development and aging
dc.subject.keywordshigh throughput sequencing
dc.subject.keywordsmetabolome
dc.subject.keywordsmicrobiology
dc.subject.keywordspH
dc.subject.keywordsphylogeny
dc.subject.keywordstemperature
dc.subject.keywordsCoffee,
dc.subject.keywordsRNA, Ribosomal, 16S,
dc.subject.keywordsRNA, Ribosomal, 18S,
dc.subject.keywordsSugars,
dc.subject.keywordsVolatile Organic Compounds,
dc.type.driverinfo:eu-repo/semantics/article
dc.type.hasversioninfo:eu-repo/semantics/acceptedVersion
dc.type.redcolhttp://purl.org/redcol/resource_type/ART
dc.type.spaArtículo científico
dc.relation.citationissue1


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