Detection, identification and enumeration methods for spoilage yeasts

Food spoilage microorganisms

Volumn , Issue , 2006, Pages 28-54

  Kurtzman, C P ^a  

^a NATIONAL CENTER FOR AGRICULTURAL UTILIZATION RESEARCH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 71849117809     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1533/9781845691417.1.28     Document Type: Chapter

References (107)

1. Baleiras Couto M.M., Hartog B.J., Huis In't Veld J.H.J., Hofstra H., Van Der Vossen J.M.B.M. Identification of spoilage yeasts in a food-production chain by microsatellite polymerase chain reaction fingerprinting. Food Microbiol 1996, 13:59-67.
2. Banno I. Studies on the sexuality of Rhodotorula. J Gen Appl Microbiol 1967, 13:167-196.
3. Barnett J.A., Payne R.W., Yarrow D. Yeasts: Characteristics and Identification 2000, Cambridge University Press, Cambridge. 3rd edn.
4. Belloch C., Querol A., Garcia M.D., Barrio E. Phylogeny of the genus Kluyveromyces inferred from the mitochondrial cytochrome-c oxidase II gene. Int J Syst Evol Microbiol 2000, 50:405-416.
5. Berbee M.L., Taylor J.W. Fungal molecular evolution: gene trees and geologic time. The Mycota 2001, 231-245. Springer-Verlag, Berlin, VII, Part B. D.J. Mclaughlin, E. Mclaughlin, P. Lemke (Eds.).
6. Betts R.P., Bankes P., Banks J.G. Rapid enumeration of viable microorganism by staining and direct microscopy. Lett Appl Microbiol 1989, 9:199-204.
7. Beuchat L.R., Cousin M.A. Yeasts and molds. Compendium of Methods for the Microbiological Examination of Foods 2001, 209-215. Amer. Public Health Assoc, Washington, DC. F.P. Downes, K. Ito (Eds.).
8. Beuchat L.R., FräNdberg E., Deák T., Alzamora S.M., Chen J., Guerrero S., Löpez-Malo A., Ohlsson I., Olsen M., Peinado J.M., Schnurer J., De Siloniz M.I., Tornai-Lehoczki J. Performance of mycological media in enumerating desiccated food spoilage yeasts: an interlaboratory study. Int J Food Microbiol 2001, 70:89-96.
9. Boekhout T., Fonseca A., Batenburg-Van Der Vegte W.H. Bulleromyces genus novum (Tremellales), a teleomorph for Bullera alba, and the occurrence of mating in Bullera variabilis. Antonie van Leeuwenhoek 1991, 59:81-93.
10. Bonner T.I., Brenner D.J., Neufeld B.R., Britten R.J. Reduction in the rate of DNA reassociation by sequence divergence. J Mol Biol 1973, 81:123-135.
11. Britten R.J., Graham D.E., Neufeld B.R. Analysis of repeating DNA sequences by reassociation. Methods in Enzymology 1974, Vol 29:363-418. Academic Press, New York. L. Grossman, K. Moldave (Eds.).
12. Brul S., Klis F.M., Oomes S.J.C.M., Montijn R.C., Schuren F.H.J., Coote P., Hellingwerf K.J. Detailed process design based on genomics of survivors of food preservation processes. Trends Food Sci Technol 2002, 13:325-333.
13. Cain R.F. Evolution of the fungi. Mycologia 1972, 64:1-14.
14. Casey G.C., Dobson D.W. Potential of using real-time PCR-based detection of spoilage yeast in fruit juice - a preliminary study. Int J Food Microbiol 2004, 91:327-335.
15. Chapman D.D., Abercrombie D.L., Douady C.J., Pikitch E.K., Stanhopen M.J., Shivji M.S. A streamlined, bi-organelle, multiplex PCR approach to species identification: Application to global conservation and trade monitoring of the great white shark. Cons Genet 2003, 4:415-425.
16. Cocolin L., Heisei A., Mills D.A. Direct identification of the indigenous yeasts in commercial wine fermentations. Amer J Enol Viti 2001, 52:49-53.
17. Daniel H.-M., Meyer W. Evaluation of ribosomal RNA and actin gene sequences for the identification of ascomycetous yeasts. Int J Food Microbiol 2003, 86:71-78.
18. Daniel H.-M., Sorrell T.C., Meyer W. Partial sequence analysis of the actin gene and its potential for studying the phylogeny of Candida species and their teleomorphs. Int J Syst Evol Microbiol 2001, 51:1593-1606.
19. Deák T. Detection, enumeration and isolation of yeasts. Yeasts in Food - Beneficial and Detrimental Aspects 2003, 39-68. Behr's Verlag, Hamburg. T. Boekhout, V. Robert (Eds.).
20. Deák T., Beuchat L.R. Identification of foodborne yeasts. J Food Prot 1987, 50:243-264.
21. De Barros Lopes M., Rainiere S., Henschje P.A., Langridge P. AFLP fingerprinting for analysis of yeast genetic variation. Int J Syst Bacteriol 1999, 49:915-924.
22. Diaz M.R., Fell J.W. Molecular analysis of ITS and IGS rDNA regions of the psychrophilic yeasts in the genus Mrakia. Antonie van Leeuwenhoek 2000, 77:7-12.
23. Diaz M.R., Fell J.W. High-throughput detection of pathogenic yeasts of the genus Trichosporon. J Clin Microbiol 2004, 42:3696-3706.
24. Diaz M.R., Boekhout T., Theelen B., Fell J.W. Molecular sequence analysis of the intergenic spacer (IGS) associated with rDNA of the two varieties of the pathogenic yeast Cryptococcus neoformans. Syst Appl. Microbiol 2000, 23:535-545.
25. Dobzhansky T. Organismic and molecular aspects of species formation. Molecular Evolution 1976, 95-105. Sinauer Assoc, Sunderland, Massachusetts. F.J. Ayala (Ed.).
26. Fan M., Chen L.C., Ragan M.A., Gutell R., Warner J.R., Currie B.P., Casadevall A. The 5S rRNA and the RNA intergenic spacer of the two varieties of Cryptococcus neoformans. J Med Vet Mycol 1995, 33:215-221.
27. Fell J.W. Rapid identification of yeast species using three primers in a polymerase chain reaction. Mol Mar Biol Biotechnol 1993, 1:175-186.
28. Fell J.W., Blatt G. Separation of strains of the yeasts Xanthophyllomyces dendrorhous and Phaffia rhodozyma based on rDNA, IGS and ITS sequence analysis,. J Ind Microbiol Biotechnol 1999, 21:677-681.
29. Fell J.W., Statzell A., Hunter I.L., Phaff H.J. Leucosporidium gen. nov. The heterobasidiomycetous stage of several yeasts of the genus Candida. Antonie van Leeuwenhoek 1969, 35:433-462.
30. Fell J.W., Boekhout T., Fonseca A., Scorzetti G., Statzell-Tallman A. Biodiversity and systematics of basidiomycetous yeasts as determined by large-subunit rDNA D1/D2 domain sequence analysis. Int J Syst Evol Microbiol 2000, 50:1351-1371.
31. Fleet G.H. Food spoilage yeasts. Yeast Technology 1990, 124-166. Springer-Verlag, Heidelberg. J.F.T. Spencer, D.M. Spencer (Eds.).
32. Fleet G.H. Spoilage yeasts. Crit Rev Biotechnol 1992, 12:1-44.
33. Gadanho M., Almeida J.M., Sampaio J.P. Assessment of yeast diversity in a marine environment in the south of Portugal by microsatellite-primed PCR. Antonie van Leeuwenhoek 2003, 84:217-227.
34. Geiser D.M., Pitt J.I., Taylor J.W. Cryptic speciation and recombination in the aflatoxin-producing fungus Aspergillus flavus. Proc Natl Acad Sci USA 1998, 95:388-393.
35. Gould G.W. Methods for preservation and extension of shelf life. Int J Food Microbiol 1996, 33:51-64.
36. Groth C., Hansen J., Piškur J. A natural chimeric yeast containing genetic material from three species. Int J Syst Bacteriol 1999, 49:1933-1938.
37. Hausner G., Reid J., Klassen G.R. Do galeate-ascospore members of the Cephaloascaceae, Endomycetaceae and Ophiostomataceae share a common phylogeny?. Mycologia 1992, 84:870-881.
38. Heard G.M., Fleet G.H. Evaluation of selective media for enumeration of yeasts during wine fermentation. J Appl Bacteriol 1986, 60:477-481.
39. Heard G.M., Fleet G.H. A convenient microtitre tray procedure for yeast identification. J Appl Bacteriol 1990, 68:447-451.
40. Hendriks L., Goris A., Van De Peer Y., Neefs J.-M., Vancanneyt M., Kersters K., Berny J.-F., Hennebert G.L., De Wachter R. Phylogenetic relationships among ascomycetes and ascomycete-like yeasts as deduced from small ribosomal subunit RNA sequences. Syst Appl Microbiol 1992, 15:98-104.
41. Henschke P.A., Thomas D.S. Detection of wine-spoiling yeasts by electronic methods. J Appl Bacteriol 1988, 64:123-133.
42. Hocking A.D. Media for preservative resistant yeasts: a collaborative study. Int J Food Microbiol 1996, 29:167-175.
43. James S.A., Collins M.D., Roberts I.N. Use of an rRNA internal transcribed spacer region to distinguish phylogenetically closely related species of the genera Zygosaccharomyces and Torulaspora. Int J Syst Bacteriol 1996, 46:189-194.
44. Kluyver A.J., Van Niel C.B. über Spiegelbilder erzeugende Hefenarten und die neue Hefengattung Sporobolomyces'. Zentralbl Bakteriol Parasitenkd 1924, 63:1-20. Abt. II.
45. Kluyver A.J., Van Niel C.B. Sporobolomyces: ein Basidiomyzet?. Ann Mycol 1927, 25:389-394.
46. Koburger J.A., Marth E.H. Yeasts and molds. Compendium of Methods for the Microbiological Examination of Foods 1984, 197-202. Amer Public Health Assoc, Washington, DC. 2nd edn. M.L. Speck (Ed.).
47. Kurtzman C.P. Synonymy of the yeast genera Hansenula and Pichia demonstrated through comparisons of deoxyribonucleic acid relatedness. Antonie van Leeuwenhoek 1984, 50:209-217.
48. Kurtzman C.P. Resolution of varietal relationships within the species Hansenula anomala, Hansenula bimundalis, and Pichia nakazawae through comparisons of DNA relatedness. Mycotaxon 1984, 19:271-279.
49. Kurtzman C.P. Prediction of biological relatedness among yeasts from comparisons of nuclear DNA complementarity. The Expanding Realm of Yeast-like Fungi 1987, 459-468. Elsevier, Amsterdam. G.S. De Hoog, T. Smith M, A.C.M. Weijman (Eds.).
50. Kurtzman C.P. Candida shehatae - genetic diversity and phylogenetic relationships with other xylose-fermenting yeasts. Antonie van Leeuwenhoek 1990, 57:215-222.
51. Kurtzman C.P. DNA-DNA hybridization approaches to species identification in small genome organisms. Methods in Enzymology 1993, Vol 224:335-348. Academic Press, New York. E.A. Zimmer, T.J. White, R.L. Cann, A.C. Wilson (Eds.).
52. Kurtzman C.P. Systematics of the ascomycetous yeasts assessed from ribosomal RNA sequence divergence. Antonie van Leeuwenhoek 1993, 63:165-174.
53. Kurtzman C.P. Phylogenetic circumscription of Saccharomyces, Kluyveromyces and other members of the Saccharomycetaceae, and the proposal of the new genera Lachancea, Nakaseomyces, Naumovia, Vanderwaltozyma and, Zygotorulaspora. FEMS Yeast Res 2003, 4:233-245.
54. Kurtzman C.P., Fell J.W. The Yeasts, A Taxonomic Study 1998, Elsevier, Amsterdam. 4th edn.
55. Kurtzman C.P., Fell J.W. Yeast systematics and phylogeny-implications of molecular identification methods for studies in ecology. Biodiversity and Ecophysiology of Yeasts 2005, 11-30. Springer-Verlag, Heidelberg. C. Rosa, G. Péter (Eds.).
56. Kurtzman C.P., Phaff H.J. Molecular taxonomy. The Yeasts 1987, Vol 1:63-94. Academic Press, London. 2nd edn. A.H. Rose, J.S. Harrison (Eds.).
57. Kurtzman C.P., Robnett C.J. Orders and families of ascosporgenous yeasts and yeast-like taxa compared from ribosomal RNA sequence similarities. Ascomycete Systematics, Problems and Perspectives in the Nineties 1994, 249-258. Plenum Press, New York. D.L. Hawksworth (Ed.).
58. Kurtzman C.P., Robnett C.J. Molecular relationships among hyphal ascomycetous yeasts and yeastlike taxa. Can J Bot 1995, 73(Suppl 1):S824-S830.
59. Kurtzman C.P., Robnett C.J. Identification and phylogeny of ascomycetous yeasts from analysis of nuclear large subunit (26S) ribosomal DNA partial sequences. Antonie van Leeuwenhoek 1998, 73:331-371.
60. Kurtzman C.P., Robnett C.J. Phylogenetic relationships among yeasts of the "Saccharomyces complex" determined from multigene sequence analyses. FEMS Yeast Res 2003, 3:417-432.
61. Kurtzman C.P., Smittle R.B. Salad dressings. Compendium of Methods for the Microbiological Examination of Foods 1984, 682-689. Amer Public Health Assoc, Washington, DC. 2nd edn. M.L. Speck (Ed.).
62. Kurtzman C.P., Sugiyama J. Ascomycetous yeasts and yeastlike taxa. The Mycota VII 2001, 179-200. Springer-Verlag, Berlin, Part A. D.J. Mclaughlin, E. Mclaughlin, P. Lemke (Eds.).
63. Kurtzman C.P., Smiley M.J., Johnson C.J., Wickerham L.J., Fuson G.B. Two new and closely related heterothallic species, Pichia amylophila and Pichia mississippiensis: characterization by hybridization and deoxyribonucleic acid reassociation. Int J Syst Bacteriol 1980, 30:208-216.
64. Kurtzman C.P., Smiley M.J., Johnson C.J. Emendation of the genus Issatchenkia Kudriavsev and comparison of species by deoxyribonucleic acid reassociation, mating reaction, and ascospore ultrastructure. Int J Syst Bacteriol 1980, 30:503-513.
65. Kurtzman C.P., Robnett C.J., Ward J.N., Brayton C., Gorelick P., Walsh T.J. Multigene phylogenetic analysis of pathogenic Candida species in the Kazachstania (Arxiozyma) telluris complex and description of their ascosporic states as Kazachstania bovina sp. nov., K. heterogenica sp. nov., K. pintolopesii sp. nov., and K. slooffiae sp. nov. J Clin Microbiol 2005, 43:101-111.
66. Kwon-Chung K.J. A new genus, Filobasidiella, the perfect state of Cryptococcus neoformans. Mycologia 1975, 67:1197-1200.
67. Lachance M.A., Daniel H.M., Meyer W., Prasad G.S., Gautam S.P., Boundy-Mills K. The D1/D2 domain of the large-subunit rDNA of the yeast species Clavispora lusitaniae is unusually polymorphic. FEMS Yeast Res 2003, 4:253-258.
68. Landvik S. Neolecta, a fruit-body producing genus of the basal ascomycetes, as shown by SSU and LSU rDNA sequences. Mycol Res 1996, 100:199-202.
69. Loureiro V., Malfeito-Ferreira M. Spoilage yeasts in the wine industry. Int J Food Microbiol 2003, 86:23-50.
70. Mannarelli B.M., Kurtzman C.P. Rapid identification of Candida albicans and other human pathogenic yeasts by using short oligonucleotides in a PCR. J Clin Microbiol 1998, 36:1634-1641.
71. Martini A., Phaff H.J. The optical determination of DNA-DNA homologies in yeasts. Ann Microbiol 1973, 23:59-68.
72. Masoud W., Cesar L.B., Jespersen L., Jakobsen M. Yeast involved in fermentation of Coffea arabica in East Africa determined by genotyping and by direct denaturing gradient gel electrophoresis. Yeast 2004, 21:549-556.
73. Meroth C.B., Hammes W.P., Hertel C. Identification and population dynamics of yeasts in sourdough fermentation processes by PCR-denaturing gradient gel electrophoresis. Appl Environ Microbiol 2003, 69:7453-7461.
74. Miller R., Galston G. Rapid methods for detection of yeast and Lactobacillus by ATP bioluminescence. J Inst Brew 1989, 95:317-321.
75. Muyzer G., Smalla K. Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology. Antonie van Leeuwenhoek 1998, 73127-73141.
76. Nilsson-Tillgren T., Gjermansen C., Kielland-Brandt M.C., Petersen J.G.L., Holmberg S. Genetic differences between Saccharomyces carlsbergensis and S. cerevisiae. Analysis of chromosome III by single chromosome transfer. Carlsberg Res Commun 1981, 46:65-76.
77. Nishida H., Sugiyama J. Phylogenetic relationships among Taphrina, Saitoella, and other fungi. Mol Biol Evol 1993, 12:883-886.
78. Nishida H., Sugiyama J. Archiascomycetes: detection of a major new lineage within the Ascomycota. Mycoscience 1994, 35:361-366.
79. Nyland G. Studies on some unusual Heterobasidiomycetes from Washington State. Mycologia 1949, 41:686-701.
80. Oberwinkler F., Bandoni R.J., Blanz P., Kisimova-Horovitz L. Cystofilobasidium: a new genus in the Filobasidiaceae. Syst Appl Microbiol 1983, 4:114-122.
81. O'donnell K., Kistler H.C., Tacke B.K., Casper H.H. Gene genealogies reveal global phylogeographic structure and reproductive isolation among lineages of Fusarium graminearum, the fungus causing wheat scab. Proc Natl Acad Sci USA 2000, 97:7905-7910.
82. Olive L.S. An unusual Heterobasidiomycete with Tilletia-like basidia. J Elisha Mitchell Sci Soc 1968, 84:261-266.
83. Page B.T., Kurtzman C.P. Rapid identification of Candida and other clinically important yeast species by flow cytometry. J Clin Microbiol 2005, 43:4507-4514.
84. Peterson S.W., Kurtzman C.P. Ribosomal RNA sequence divergence among sibling species of yeasts. Syst Appl Microbiol 1991, 14:124-129.
85. Pitt J.I., Hocking A.D. Fungi and Food Spoilage 1997, Blackie Academic &Professional, Sydney. 2nd edn.
86. Prakitchaiwattana C.J., Fleet G.H., Heard G.M. Application and evaluation of denaturing gradient gel electrophoresis to analyse the yeast ecology of wine grapes. FEMS Yeast Res 2004, 4:865-877.
87. Price C.W., Fuson G.B., Phaff H.J. Genome comparison in yeast systematics: delimitation of species within the genera Schwanniomyces, Saccharomyces, Debaryomyces, and Pichia. Microbio. Rev 1978, 42:161-193.
88. Raso J., Barbosa-Canovas G.V. Nonthermal preservation of foods using combined processing techniques. Crit Rev Food Sci Nutr 2003, 43:265-285.
89. Redhead S.A., Malloch D.W. The Endomycetaceae: new concepts, new taxa. Can J Bot 1977, 55:1701-1711.
90. Reyns K.M.F.A., Soontjens C.C.F., Cornelis K., Weemaes C.A., Hendrickx M.E., Michiels C.W. Kinetic analysis and modelling of combined high-pressure-temperature inactivation of the yeast Zygosaccharomyces bailii. Int J Food Microbiol 2000, 56:199-210.
91. Rigby S., Procop G.W., Haase G., Wilson D., Hall G., Kurtzman C., Oliveira K., Von Oy S., Hyldig-Nielsen J.J., Coull J., Stender H. Fluorescence in situ hybridization with peptide nucleic acid probes for rapid identification of Candida albicans directly from blood culture bottles. J Clin Microbiol 2002, 40:2182-2186.
92. Rohm H., Lechner F. Evaluation and reliability of a simplified method for identification of foodborne yeasts. Appl Environ Microbiol 1990, 56:1290-1295.
93. Rokas A., Williams B.L., King N., Carroll S.B. Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature 2003, 425:798-804.
94. Sampaio J.P. Diversity, phylogeny and classification of basidiomycetous yeasts. Frontiers in Basidiomycete Mycology 2004, 49-80. Springer-Verlag, Heidelburg. R. Agerer, P. Blanz, F. Peipenbring (Eds.).
95. Scorzetti G., Fell J.W., Fonseca A., Statzell-Tallman A. Systematics of basidiomycetous yeasts: a comparison of large subunit D1/D2 and internal transcribed spacer rDNA regions. FEMS Yeast Res 2002, 2:495-517.
96. Sjamsuridzal W., Tajiri Y., Nishida H., Thuan T.B., Kawasaki H., Hirata A., Yakota A., Sugiyama J. Evolutionary relationships of members of the genera Taphrina, Protomyces, Schizosaccharomyces, and related taxa within the archiascomycetes: integrated analysis of genotypic and phenotypic characters. Mycoscience 1997, 38:267-280.
97. ŠpíPek M., Yang J., Groth C., Petersen R.F., LangkjR R.B., Naumova E.S., Sulo P., Naumov G.I., PiKur J. Saccharomyces sensu lato chromosomes are highly dynamic. FEMS Yeast Res 2003, 3:363-373.
98. Stender H., Kurtzman C., Hyldig-Nielsen J.J., SØRensen D., Broomer A., Oliveira K., Perry-O'keefe H., Sage A., Young B., Coull J. Identification of Dekkera bruxellensis (Brettanomyces) from wine by fluorescence in situ hybridization using peptide nucleic acid probes. Appl Environ Microbiol 2001, 67:938-941.
99. Sugiyama J. Relatedness, phylogeny and evolution of the fungi. Mycoscience 1998, 39:487-511.
100. Swann E.C., Taylor J.W. Phylogenetic perspectives on basidiomycete systematics: evidence from the 18S rRNA gene. Can J Bot 1995, 73(Suppl 1):S862-S868.
101. Van Der Vossen J.M.B.M., Hofstra H. DNA based typing, identification and detection systems for food spoilage microorganisms: development and implementation. Int J Food Microbiol 1996, 3:35-49.
102. Vaughan-Martini A., Kurtzman C.P. Deoxyribonucleic acid relatedness among species of the genus Saccharomyces sensu stricto. Int J Syst Bacteriol 1985, 35:508-511.
103. Vos P., Hogers R., Bleeker M., Reijans M., Vandelee T., Hornes M., Frijters A., Pot J., Peleman J., Kuiper M., Zabeau M. AFLP - a new technique for DNA-fingerprinting. Nucleic Acids Res 1995, 23:4407-4414.
104. Walker H.W., Ayres J.C. Yeasts as spoilage organisms. The Yeasts 1970, vol 3:463-527. Academic Press, New York. A.H. Rose, J.S. Harrison (Eds.).
105. Williams J.G.K., Kubelik A.E., Levak K.J., Rafalski J.A., Tingey S.C. DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acid Res 1990, 18:6335-6531.
106. Wilmotte A., Van De Peer Y., Goris A., Chapelle S., De Baere R., Nelissen B., Neefs J.-M., Hennebert G.L., De Wachter R. Evolutionary relationships among higher fungi inferred from small ribosomal subunit RNA sequence analysis. Syst Appl Microbiol 1993, 16:436-444.
107. Yarrow D. Methods for the isolation, maintenance and identification of yeasts. A Taxonomic Study 1998, 77-100. Elsevier, Amsterdam. 4th edn. C.P. Kurtzman, J.W. Fell, Y. The (Eds.).