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

Altschul, 1990, Basic local alignment search tool, J. Mol. Biol., 215, 403, 10.1016/S0022-2836(05)80360-2 Avallone, 2001, Microbiological and biochemical study of coffee fermentation, Curr. Microbiol., 42, 252, 10.1007/s002840110213 Avallone, 2002, Involvement of pectinolytic micro-organisms in coffee fermentation, Int. J. Food Sci. Technol., 37, 191, 10.1046/j.1365-2621.2002.00556.x Bastian, M., Heymann S. & Jacomy M. Gephi: an open source software for exploring and manipulating networks. International AAAI Conference on Weblogs and Social Media (2009). URL https://gephi.org/. Batista, L.R. & Chalfoun, S.M. Quality of coffee beans in Cocoa and Coffee Fermentations (eds. Schwan, R.F. & Fleet, G.H) 477–508 (CRC Press, 2014). Batista, 2009, Ochratoxin A in coffee beans (Coffea arabica L.) processed by dry and wet methods, Food Control, 20, 784, 10.1016/j.foodcont.2008.10.003 Bertsch, 2013, An electron-bifurcating caffeyl-CoA reductase, J. Biol. Chem., 288, 11304, 10.1074/jbc.M112.444919 Bolger, 2014, Trimmomatic: a flexible trimmer for Illumina sequence data, Bioinformatics, 30, 1, 10.1093/bioinformatics/btu170 Brando, C.H.J. & Brando, M.F. Methods of coffee fermentation and drying in Cocoa and Coffee Fermentations (eds. Schwan, R.F. & Fleet, G.H) 367–396 (CRC Press, 2014). Buchfink, 2015, Fast and sensitive protein alignment using DIAMOND, Nature Meth., 12, 59, 10.1038/nmeth.3176 Carvalho Neto, 2017, Yeast diversity and physicochemical characteristics associated with coffee bean fermentation from the Brazilian Cerrado Mineiro region, Fermentation, 3, 11, 10.3390/fermentation3010011 Carvalho Neto, 2018, Efficient coffee beans mucilage layer removal using lactic acid fermentation in a stirred-tank bioreactor: kinetic, metabolic and sensorial studies. Food Biosci., 26, 80 Carvalho, 2018, High-throughput rRNA gene sequencing reveals high and complex bacterial diversity associated with Brazilian coffee bean fermentation, Food Technol. Biotechnol., 56, 90 De Bruyn, 2017, Exploring the impacts of postharvest processing on the microbiota and metabolite profiles during green coffee bean production, Appl. Environ. Microbiol., 83, 10.1128/AEM.02398-16 de Oliveira Junqueira, A.C., Pereira, G.V.M., Coral Medina, J.D., Alvear, M.C.R., Rosero, R., Carvalho Neto, D.P., Enriquez, H.G., Soccol, C.R. First description of bacterial and fungal communities in Colombian coffee beans fermentation analysed using Illumina-based amplicon sequencing. Sci. Rep. 9, 8794 (2019). De Vuyst, 2016, The cocoa bean fermentation process: from ecosystem analysis to starter culture development, J. Appl. Microbiol., 121, 5, 10.1111/jam.13045 Denoeud, 2014, The coffee genome provides insight into the convergent evolution of caffeine biosynthesis, Science, 345, 1181, 10.1126/science.1255274 Di Cagno, 2013, Exploitation of vegetables and fruits through lactic acid fermentation, Food Microbiol., 33, 1, 10.1016/j.fm.2012.09.003 Evangelista, 2014, Improvement of coffee beverage quality by using selected yeast strains during the fermentation in dry process, Food Res. Int., 61, 183, 10.1016/j.foodres.2013.11.033 Feng, 2016, Culture-dependent and -independent methods to investigate the predominant microorganisms associated with wet processed coffee, Curr. Microbiol., 73, 190, 10.1007/s00284-016-1047-3 Field, 2006, Open software for biologists: from famine to feast, Nat. Biotechnol., 24, 801, 10.1038/nbt0706-801 Filannino, 2014, Metabolic responses of Lactobacillus plantarum strains during fermentation and storage of vegetable and fruit juices, Appl. Environ. Microbiol., 80, 2206, 10.1128/AEM.03885-13 Filannino, 2015, Metabolism of phenolic compounds by Lactobacillus spp. during fermentation of cherry juice and broccoli puree, Food Microbiol., 4, 272, 10.1016/j.fm.2014.08.018 Gänzle, 2015, Lactic metabolism revisited: metabolism of lactic acid bacteria in food fermentations and food spoilage, Curr. Opin. Food Sci., 2, 106, 10.1016/j.cofs.2015.03.001 Geiser, 2005, Gibberella xylarioides (anamorph: Fusarium xylarioides), a causative agent of coffee wilt disease in Africa, is a previously unrecognized member of the G. fujikuroi species complex, Mycologia, 97, 191, 10.1080/15572536.2006.11832853 Goecks, 2010, Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences, Genome Biol., 11, R86, 10.1186/gb-2010-11-8-r86 Götz, 2010, Glucose and glucose 6-phosphate as carbon sources in extra- and intracellular growth of enteroinvasive Escherichia coli and Salmonella enterica, Microbiol., 156, 1176, 10.1099/mic.0.034744-0 Gueule, 2015, Pantoea coffeiphila sp. nov., cause of the ‘potato taste’ of Arabica coffee from the African great lakes region, Int. J. Syst. Evol. Microbiol., 65, 23, 10.1099/ijs.0.063545-0 Huson, 2007, MEGAN analysis of metagenome data, Genome Res., 17, 377, 10.1101/gr.5969107 ICO Illeghems, 2012, Phylogenetic analysis of a spontaneous cocoa bean fermentation metagenome reveals new insights into its bacterial and fungal community diversity, PLoS One, 7, 10.1371/journal.pone.0038040 Illeghems, 2015, Applying meta-pathway analyses through metagenomics to identify the functional properties of the major bacterial communities of a single spontaneous cocoa bean fermentation process sample, Food Microbiol., 50, 54, 10.1016/j.fm.2015.03.005 Itoh, 2008, Roles of pgaABCD genes in synthesis, modification and export of the Escherichia coli biofilm adhesin poly-beta-1,6-N-acetyl-D-glucosamine, J. Bacteriol., 190, 3670, 10.1128/JB.01920-07 Jackson, 2015, Emerging perspectives on the natural microbiome of fresh produce vegetables, Agriculture, 5, 170, 10.3390/agriculture5020170 Jung, 2011, Metagenomic analysis of kimchi, a traditional Korean fermented food. Appl. Environ. Microbiol., 77, 2264 Kadner, R. Expression of the uhp sugar-phosphate transport system of Escherichia coli in Two-Component Signal Transduction (eds. Hoch, J. & Silhavy, T.) 263–274 (ASM Press, 1995). Kanehisa, 2016, KEGG as a reference resource for gene and protein annotation. Nucleic Acids Res, 4, 44, D457 Kang, 2015, MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities, Peer J., 3, 10.7717/peerj.1165 Kim, 2009, Production of γ-aminobutyric acid in black raspberry juice during fermentation by Lactobacillus brevis GABA100, Int. J. Food Microbiol., 130, 12, 10.1016/j.ijfoodmicro.2008.12.028 Laroute, 2016, GABA production in Lactococcus lactis is enhanced by arginine and co-addition of malate, Front. Microbiol., 7, 1, 10.3389/fmicb.2016.01050 Lee, L. W., Cheong, M. W., Curran, P., Yu, B., Liu, S. Q. (2015). Coffee fermentation and flavor - an intricate and delicate relationship. Food Chem. 185, 182–191 (2015). Li, 2013, Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM, arXiv Li, 2010, Fast and accurate long-read alignment with burrows-wheeler transform, Bioinformatics, 26, 589, 10.1093/bioinformatics/btp698 Li, 2014, MEGAHIT: an ultra-fast single-node solution for large and complex metagenomic assembly via succinct de Bruijn graph, Bioinformatics, 31, 1674, 10.1093/bioinformatics/btv033 Masella, 2012, PANDAseq: paired-end assembler for Illumina sequences, BMC Bioinformatics, 13, 31, 10.1186/1471-2105-13-31 Masoud, 2004, Yeast involved in fermentation of Coffea arabica in East Africa determined by genotyping and by direct denaturating gradient gel electrophoresis, Yeast, 21, 549, 10.1002/yea.1124 McMurdie, 2013, Phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data, PLoS One, 8, 10.1371/journal.pone.0061217 McNew, 2015, Evaluating species richness: biased ecological inference results from spatial heterogeneity in detection probabilities, Ecol. Appl., 25, 1669, 10.1890/14-1248.1 Menzel, 2015, Kaiju: fast and sensitive taxonomic classification for metagenomics, Nat. Commun., 7 Oksanen Pereira, 2014, Isolation, selection and evaluation of yeasts for use in fermentation of coffee beans by the wet process, Int. J. Food Microbiol., 188, 60, 10.1016/j.ijfoodmicro.2014.07.008 Pereira, 2015, Conducting starter culture-controlled fermentations of coffee beans during on-farm wet processing: growth, metabolic analyses and sensorial effects. Food Res. Int., 75, 348 Pereira, 2016, Potential of lactic acid bacteria to improve the fermentation and quality of coffee during on-farm processing, Int. J. Food Sci. Technol., 51, 1689, 10.1111/ijfs.13142 Pereira, 2017, Microbial ecology and starter culture technology in coffee processing, Crit. Rev. Food Sci., 57, 2775, 10.1080/10408398.2015.1067759 Pereira, 2019, Exploring the impacts of post-harvest processing on the aroma formation of coffee beans: a review, Food Chem., 272, 441, 10.1016/j.foodchem.2018.08.061 Pothakos, 2016, Acetic acid bacteria in fermented food and beverage ecosystems, 73 Pruitt, 2007, Maglott, D.R. NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins, Nucleic Acids Res., 35, 501, 10.1093/nar/gkl842 R Core Team, 2016 Sakiyama, N.S. & Ferrão, M.A. Botany and production of coffee in Cocoa and Coffee Fermentations (eds. Schwan, R.F. & Fleet, G.H) 341–365 (CRC Press, 2014). Salvetti, 2016, Whole-metagenome-sequencing-based community profiles of Vitis vinifera L. cv. Corvina berries withered in two post-harvest conditions, Front. Microbiol., 7, 1, 10.3389/fmicb.2016.00937 Sanchez Seemann, 2014, Prokka: rapid prokaryotic genome annotation, Bioinformatics, 30, 2068, 10.1093/bioinformatics/btu153 Selmar, 2006, Germination of coffee seeds and its significance for coffee quality, Plant Biol., 8, 260, 10.1055/s-2006-923845 Silva, C.F. Microbial activity during coffee fermentation in Cocoa and Coffee Fermentations (eds. Schwan, R.F. & Fleet, G.H.) 398–423 (CRC Press, 2014). Silva, 2000, Microbial diversity during maturation and natural processing of coffee cherries of Coffea arabica in Brazil, Int. J. Food Microbiol., 60, 251, 10.1016/S0168-1605(00)00315-9 Silva, 2008, Succession of bacterial and fungal communities during natural coffee (Coffea arabica) fermentation, Food Microbiol., 25, 951, 10.1016/j.fm.2008.07.003 Silva, 2013, Evaluation of a potential starter culture for enhance quality of coffee fermentation, World J. Microbiol. Biotechnol., 29, 235, 10.1007/s11274-012-1175-2 Toth, 2006, Comparative genomics reveals what makes an enterobacterial plant pathogen, Annu. Rev. Phytopathol., 44, 305, 10.1146/annurev.phyto.44.070505.143444 Vaughan, 2015, What’s inside that seed we brew? A new approach to mining the coffee microbiome, Appl. Environ. Microbiol., 81, 6518, 10.1128/AEM.01933-15 Velmourougane, 2013, 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, 233, 10.1007/s40011-012-0130-1 Velmourougane, 2008, Venkatesh, K. & Prakasan, C. B. & Jayarama. Use of starter culture in coffee fermentation – effect on demucilisation and cup quality, Indian Coffee, 72, 31 Verce, M., De Vuyst, L. & Weckx, S. Shotgun metagenomics of a water kefir fermentation ecosystem reveals a novel Oenococcus species. Front. Microbiol. 10, 479. Vermote, 2018, Amplicon and shotgun metagenomic sequencing indicates that microbial ecosystems present in cheese brines reflect environmental inoculation during the cheese production process, Int. Dairy J., 87, 44, 10.1016/j.idairyj.2018.07.010 Waters, 2017, Overview on the mechanisms of coffee germination and fermentation and their significance for coffee and coffee beverage quality, Crit. Rev. Food Sci. Nutr., 57, 259, 10.1080/10408398.2014.902804 Wolfe, 2014, Cheese rind communities provide tractable systems for in situ and in vitro studies of microbial diversity, Cell, 158, 422, 10.1016/j.cell.2014.05.041 Wood, 2014, Kraken: ultrafast metagenomic sequence classification using exact alignments, Genome Biol., 15, R46, 10.1186/gb-2014-15-3-r46 Zhang, 2019, Following coffee production from cherries to cup: microbiological and metabolomic analysis of wet processing of Coffea arabica. Appl. Environ. Microbiol 85