Avallone S, Guyot B, Brillouet JM, Olguin E, Guiraud JP (2001) Microbiological and biochemical study of coffee fermentation. Curr Microbiol 42:252–256
Avallone S, Brillouet JM, Guyot B, Olguin E, Guiraud JP (2002) Involvement of pectolytic micro-organisms in coffee fermentation. Int J Food Sci Technol 37:191–198
Batista LR, Chalfoun SM, Prado G, Schwan RF, Wheals AE (2003) Toxigenic fungi associated with processed (green) coffee beans (Coffea arabica L.). Int J Food Microbiol 85:293–300
Chen YS, Wu HC, Pan SF, Lin BG, Lin YH, Tung WC, Li YL, Chiang CM, Yanagida F (2013) Isolation and characterization of lactic acid bacteria from yan-taozih (pickled peaches) in Taiwan. Ann Microbiol 63:607–614
Crowley S, Mahony J, van Sinderen D (2013) Broad-spectrum antifungal-producing lactic acid bacteria and their application in fruit models. Folia Microbiol 58:291–299
De Bruyne K, Schillinger U, Caroline L, Boehringer B, Cleenwerck I, Vancanneyt M, De Vuyst L, Franz CM, Vandamme P (2007) Leuconostoc holzapfelii sp. nov., isolated from Ethiopian coffee fermentation and assessment of sequence analysis of housekeeping genes for delineation of Leuconostoc species. Int J Syst Evol Microbiol 57:2952–2959
Djossou O, Perraud-Gaime I, Mirleau FL, Rodriguez-Serrano G, Karou G, Niamke S, Ouzari I, Boudabous A, Roussos S (2011) Robusta coffee beans post-harvest microflora: Lactobacillus plantarum sp. as potential antagonist of Aspergillus carbonarius. Anaerobe 17:267–272
Gamboa-Gaitán MÁ (2012) Presence of Aspergillus and other fungal symbionts in coffee beans from Colombia. Acta Biol Colomb 17:39–50
Guzmán-López O, Loera O, Parada JL, Castillo-Morales A, Martínez-Ramírez C, Augur C, Gaime-Perraud I, Saucedo-Castañeda G (2009) Microcultures of lactic acid bacteria: characterization and selection of strains, optimization of nutrients and gallic acid concentration. J Ind Microbiol Biotechnol 36:11–20
Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120
Kozaki M, Uchimura T, Okada S (1992) Experimental manual of lactic acid bacteria. Asakurasyoten, Tokyo, pp 29–72
Kumar S, Kunwar A, Gautam S, Sharma A (2012) Inactivation of A. ochraceus spores and detoxification of ochratoxin A in coffee beans by gamma irradiation. J Food Sci 77:T44–T51
Lan WT, Chen YS, Wu HC, Yanagida F (2012) Bio-protective potential of lactic acid bacteria isolated from fermented wax gourd. Folia Microbiol 57:99–105
Magnani M, Fernandes T, Prete CEC, Homechim M, Ono EYS, Vilas-Boas LA, Sartori D, Furlaneto MC, Fungaro MHP (2005) Molecular identification of Aspergillus spp. isolated from coffee beans. Sci Agric 62:45–49
Naser SM, Thompson FL, Hoste B, Gevers D, Dawyndt P, Vancanneyt M, Swings J (2005) Application of multilocus sequence analysis (MLSA) for rapid identification of Enterococcus species based on rpoA and pheS genes. Microbiology 151:2141–2150
Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425
Schillinger U, Boehringer B, Wallbaum S, Caroline L, Gonfa A, Kostinek MHN, Holzapfel WH, Franz CM (2008) A genus-specific PCR method for differentiation between Leuconostoc and Weissella and its application in identification of heterofermentative lactic acid bacteria from coffee fermentation. FEMS Microbiol Lett 286:222–226
Sheu DS, Wang YT, Lee CY (2000) Rapid detection of polyhydroxyalkanoate-accumulating bacteria isolated from the environment by colony PCR. Microbiology 146:2019–2025
Silva CF, Batista LR, Abreu LM, Dias ES, Schwan RF (2008) Succession of bacterial and fungal communities during natural coffee (Coffea arabica) fermentation. Food Microbiol 25:951–957
Su SW (2007) Tea or coffee: a study of the beverage choice pattern and its affecting factors at teatime in Kaohsiung, Taiwan. Asia Pac Manag Rev 12:245–257
Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739
Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The Clustal X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 24:4876–4882
Torriani S, Felis GE, Dellaglio F (2001) Differentiation of Lactobacillus plantarum, Lactobacillus pentosus, and Lactobacillus paraplantarum by recA gene sequence analysis and multiplex PCR assay with recA gene-derived primers. Appl Environ Microbiol 67:3450–3454
Yanagida F, Chen Y, Onda T, Shinohara T (2005) Durancin L28-1A, a new bacteriocin from Enterococcus durans L28-1, isolated from soil. Lett Appl Microbiol 40:430–435