PCR-SSCP-based reconstruction of the original fungal flora of heat-processed meat products

International Journal of Food Microbiology

Volumn 162, Issue 1, 2013, Pages 71-81

  Dorn In, Samart ^a   Hölzel, Christina S ^a   Janke, Tobias ^a   Schwaiger, Karin ^a   Balsliemke, Joachim ^b   Bauer, Johann ^a  

^a TECHNICAL UNIVERSITY OF MUNICH   (Germany)

^b Bavarian Health and Food Safety Authority   (Germany)

Author keywords

Fungi; Heat processed meat; PCR; Plant; Primer; SSCP

Indexed keywords

FUNGAL DNA; POLYACRYLAMIDE GEL;

ALTERNARIA ALTERNATA; ANIMAL TISSUE; ARTICLE; AUREOBASIDIUM PULLULANS; BOTRYTIS; BOTRYTIS ACLADA; CANDIDA RUGOSA; CANDIDA TROPICALIS; CANDIDA ZEYLANOIDES; CONTROLLED STUDY; EUROTIUM AMSTELODAMI; FOOD PROCESSING; FUNGAL CONTAMINATION; FUNGUS; GENE AMPLIFICATION; GUIGNARDIA; GUIGNARDIA MANGIFERAE; HIGH TEMPERATURE PROCEDURES; ITERSONILIA; ITERSONILIA PERPLEXANS; LASIODIPLODIA; LASIODIPLODIA THEOBROMAE; LEWIA; LEWIA INFECTORIA; NEOFUSICOCCUM; NEOFUSICOCCUM PARVUM; NONHUMAN; PICHIA; PICHIA MEMBRANIFACIENS; PLEOSPORA; PLEOSPORA HERBARUM; POLYMERASE CHAIN REACTION; SENSITIVITY AND SPECIFICITY; SINGLE STRAND CONFORMATION POLYMORPHISM;

EID: 84872918076     PISSN: 01681605     EISSN: 18793460     Source Type: Journal    
DOI: 10.1016/j.ijfoodmicro.2012.12.022     Document Type: Article

References (60)

1. Aldaoud R., Salib A S., Cunnington J.H. First record of Itersonilia perplexans on Anethum graveolens (dill) in Australia. Australasian Plant Disease Notes 2009, 4:60-61.
2. Anderson I.C., Campbell C.D., Prosser J.I. Potential bias of fungal 18S rDNA and internal transcribed spacer polymerase chain reaction primers for estimating fungal biodiversity in soil. Environmental Microbiology 2003, 5:36-47.
3. Bockelmann W., Heller M., Heller K.J. Identification of yeasts of dairy origin by amplified ribosomal DNA restriction analysis (ARDRA). International Dairy Journal 2008, 18:1066-1071.
4. Borneman J., Hartin R.J. PCR primers that amplify fungal rRNA genes from environmental samples. Applied and Environmental Microbiology 2000, 66:4356-4360.
5. Bundesgesundheitsblatt -Gesundheitsforschung-Gesundheitsschutz Empfehlung des Robert Koch-Instituts; Schimmelpilzbelastung in Innenräumen-Befunderhebung, gesundheitliche Bewertung und Maßnahmen Mitteilung der Kommission "Methoden und Qualitätssicherung in der Umweltmedizin" 2007, 50:1308-1323. 10.1007/s00103-007-0339-y.
6. Burgess T.I., Barber P.A., Mohali S., Pegg G., de Beer W., Wingfield M.J. Three new Lasiodiplodia spp. from the tropics, recognized based on DNA sequence comparisons and morphology. Mycologia 2006, 98:423-435.
7. Chilvers M.I., Du Toit L.J. Detection and identification of Botrytis species associated with neck rot, scape blight, and umbel blight of onion. Plant Health Progress 2006, Online. 10.1094/PHP-2006-1127-01-DG.
8. Comi G., Orlic S., Rezepovic S., Urso R., Iacumin L. Moulds isolated from Istrian dried ham at the pre-ripening and ripening level. International Journal of Food Microbiology 2004, 96:29-34.
9. Deak T., Beuchat L.R. Handbook of Food Spoilage Yeasts 1996, CRC Press, New York.
10. Ege M.J., Mayer M., Normand A.-C., Genuneit J., Cookson W.O.C.M., Braun-Fahrländer C., Heederik D., Piarroux R., von Mutius E. Exposure to environmental microorganisms and childhood asthma. The New England Journal of Medicine 2011, 364:701-709.
11. Einsele H., Hebart H., Roller G., Löffler J., Rothenhöfer I., Müller C., Bowden R., van Burik J.A., Engelhard D., Kanz L., Schumacher U. Detection and identification of fungal pathogens in blood by using molecular probes. Journal of Clinical Microbiology 1997, 35:1353-1360.
12. FAO: Food and Agriculture Organization of the United Nations, 2010. How to feed the world in 2050, available at:; Medium term projections for meat and dairy products to 2010, Available at: .; Change in the livestock sector, available at:; Global and regional food consumption patterns and trends, available at:. Last access: January 16, 2012. http://www.fao.org/DOCREP/005/AC911E/ac911e05.htm.
13. Fávaro L.C.L., Melo F.L., Aguilar-Vildoso C.I., Araújo W.L. Polyphasic analysis of intraspecific diversity in Epicoccum nigrum warrants reclassification into separate species. PloS One 2011, 6(8):e14828. 10.1371/journal.pone.0014828.
14. Fredricks D.N., Smith C., Meier A. Comparison of six DNA extraction methods for recovery of fungal DNA as assessed by quantitative PCR. Journal of Clinical Microbiology 2005, 43:5122-5128.
15. Gabrio T. Schimmelpilze in Innenräumen Available at, (Last access: November 16, 2011). http://www.analytik-news.de/Fachartikel/Volltext/lga1.pdf.
16. Gardes M., Bruns T.D. ITS primers with enhanced specificity for basidiomycetes-application to the identification of mycorrhizae and rusts. Molecular Ecology 1993, 2:113-118.
17. Gill C.O., Lowry P.D. Growth at sub-zero temperatures of black spot fungi from meat. The Journal of Applied Bacteriology 1982, 52:245-250.
18. Gill C.O., Lowry P.D., Di Menna M.E. A note on the identities of organisms causing black spot spoilage of meat. International Journal of Applied Bacteriology 1981, 51:183-187.
19. Hagn A., Pritsch K., Ludwig W., Schloter M. Theoretical and practical approaches to evaluate suitable primer sets for the analysis of soil fungal communities. Acta Biotechnologica 2003, 23:373-381.
20. Haugland R.A., Heckman J.L., Wymer L.J. Evaluation of different methods for the extraction of DNA from fungal conidia by quantitative competitive PCR analysis. Journal of Microbiological Methods 1999, 37:165-176.
21. Iacumin L., Chiesa L., Boscolo D., Manzano M., Cantoni C., Orlic S., Comi G. Moulds and orchratoxin A on surfaces of artisanal and industrial dry sausages. Food Microbiology 2009, 26:65-70.
22. Jayakumar V., Rajalakshmi S., Amaresan N. Leaf spot caused by Neofusicoccum parvum reported on nutmeg in India. New Disease Report 2011, 23:19. 10.5197/j.2044-0588.2011.023.019.
23. Karakousis A., Tan L., Ellis D., Alexiou H., Wormald P.J. An assessment of the efficiency of fungal DNA extraction methods for maximizing the detection of medically important fungi using PCR. Journal of Microbiological Methods 2006, 65:38-48.
24. Köhl J., Haas B.G., de Geijn H.G., Speksnijder A., Kastelein P., de Hoog S., van den Ende B.G. Pathogenicity of Stemphylium vesicarium from different hosts causing brown spot in pear. European Journal of Plant Pathology 2009, 124:151-162.
25. Kumar M., Shukla P.K. Use of PCR targeting of internal transcribed spacer regions and single-stranded conformation polymorphism analysis of sequence variation in different regions of rRNA genes in fungi for rapid diagnosis of mycotic keratitis. Journal of Clinical Microbiology 2005, 43:662-668.
26. Lee D.-H., Zo Y.-G., Kim S.-J. Nonradioactive method to study profiles of natural bacterial communities by PCR-single-strand-conformation polymorphism. Applied and Environmental Microbiology 1996, 62:3112-3120.
27. Leong S.L., Pettersson O.V., Rice T., Hocking A.D., Schnürer J. The extreme xerophilic mould Xeromyces bisporus-growth and competition at various water activities. International Journal of Food Microbiology 2011, 145:57-63.
28. Magalhães P.O., Lopes A.M., Mazzola P.G., Rangel-Yagui C., Penna T.C.V., Pessoa A. Methods of endotoxin removal from biological preparations: a review. Journal of Pharmacy & Pharmaceutical Sciences 2007, 10:388-404.
29. Mahmoud A.-L.E., Sayed A.M., Abou El-Alla A.A. Mycoflora and natural occurrence of mycotoxins in some meat products and livers of poultry and imported bulls. Pakistan Journal of Biological Sciences 2001, 4:611-613.
30. Manter D.K., Vivanco J.M. Use of the ITS primers, ITS1F and ITS4, to characterize fungal abundance and diversity in mixed-template samples by qPCR and length heterogeneity analysis. Journal of Microbiological Methods 2007, 71:7-14.
31. Martin K.J., Rygiewicz P.T. Fungal-specific PCR primers developed for analysis of the ITS region of environmental DNA extracts. BMC Microbiology 2005, 5.
32. Martin C., Roberts D., van der Weide M., Rossau R., Jannes G., Smith T., Maher M. Development of a PCR-based line probe assay for identification of fungal pathogens. Journal of Clinical Microbiology 2000, 38:3735-3742.
33. Matos T.J., Jensen B.B., Bernado F.M., Barreto A.H., Hojberg O. Mycoflora of two types of Portuguese dry-smoked sausages and inhibitory effect of sodium benzoate, potassium sorbate, and methyl p-hydroxybenzoate on mould growth rate. Journal of Food Protection 2007, 70:1468-1474.
34. Mirhendi H., Makimura K., Khoramizadeh M., Yamaguchi H. A one-enzyme PCR-RFLP assay for identification of six medically important Candida species. Nihon Ishinkin Gakkai Zasshi=Japanese Journal of Medical Mycology 2006, 47:225-229.
35. Miźáková A., Pipová M., Turek P. The occurrence of moulds in fermented raw meat products. Czech Journal of Food Science 2002, 20:89-94.
36. Nova M.X.V., Schuler A.R.P., Brasileiro B.T.R.V., Morais J.M.A. Yeast species involved in artisanal cachaca fermentation in three stills with different technological levels in Pernambuco, Brazil. Food Microbiology 2009, 26:460-466.
37. Okubo A., Sugiyama S. Comparison of molecular fingerprinting methods for analysis of soil microbial community structure. Ecological Research 2009, 24:1399-1405.
38. Perelló A., Sisterna M. Formation of Lewia infectoria, the teleomorph of Alternaria infectoria, on wheat in Argentina. Australasian Plant Pathology 2008, 37:589-591.
39. Peters S., Koschinsky S., Schwieger F., Tebbe C.C. Succession of microbial communities during hot composting as detected by PCR-single strand conformation polymorphism based genetic profiles of small-subunit rRNA genes. Applied and Environmental Microbiology 2000, 66:930-936.
40. Pitkäranta M., Meklin T., Hyvärinen A., Paulin L., Auvinen P., Nevalainen A., Rintala H. Analysis of fungal flora in indoor dust by ribosomal DNA sequence analysis, quantitative PCR and culture. Applied and Environmental Microbiology 2008, 74:233-244.
41. Pollmer U. Zusatzstoff-Lexikon: Hefeextrakt. Europäisches Institut für Lebensmittel- und Ernährungs-wissenschaften e.V. Deutsches Zusatzstoff-Museum Available at:, (Last access: December 8, 2011). http://www.zusatzstoffmuseum.de/lexikon-der-zusatzstoffe/begriff/hefeextrakt.html.
42. Redecker D. Specific PCR primers to identify arbuscular mycorrhizal fungi within colonized roots. Mycorrhiza 2000, 10:73-80.
43. Reiß J. Schimmelpilze-Lebensweise, Nutzen, Schaden, Bekämpfung 1986, Springer-Verlag, Berlin.
44. Robinson C.H., Szaro T.M., Izzo A.D., Anderson I.C., Parkin P.I., Bruns T.D. Spatial distribution of fungal communities in a coastal grassland soil. Soil Biology and Biochemistry 2009, 41:414-416.
45. Rodeva R., Gabler J., Stoyanova Z. First evidence of Itersonilia perplexans on dill (Anethum graveolens) in Bulgaria. Scientific works of the Lithuanian institute of horticulture and Lithuanian university of agriculture. Sodininkyste ir daržininkyste 2009, 28:193-198.
46. Romão A.S., Spósito M.B., Andreote F.D., Azevedo J.L., Araújo W.L. Enzymatic differences between the endophyte Guignardia mangiferae (Botryosphaeriaceae) and the citrus pathogen G. citricarpa. Genetics and Molecular Research 2011, 10:243-252.
47. Samson R.A., Hoekstra E.S., Frisvad J.C., Filtenborg O. Introduction to food- and airborne fungi 2000, Ponsen & Looyen, Wageningen. sixth ed.
48. Sandhu G.S., Kline B.C., Stockman L., Roberts G.D. Molecular probes for diagnosis of fungal infections. Journal of Clinical Microbiology 1995, 33:2913-2919.
49. Smit E., Leeflang P., Glandorf B., van Elsas J.D., Wernars K. Analysis of fungal diversity in the wheat rhizosphere by sequencing of cloned PCR-amplified genes encoding 18S rRNA and temperature gradient gel electrophoresis. Applied and Environmental Microbiology 1999, 65:2614-2621.
50. Suezawa Y., Suzuki M. Bioconversion of Ferulic Acid to 4-Vinylguaiacol and 4-Ethylguaiacol and of 4-Vinylguaiacol to 4-Ethylguaiacol by halotolerant feasts belonging to the genus Candida. Bioscience, Biotechnology, and Biochemistry 2007, 71:1058-1062.
51. Tagesspiegel online Problemzone Gammelfleisch (Last access: November 9, 2012). http://www.tagesspiegel.de/politik/deutschland/fleischskandal-in-lohne-problemzone-gammelfleisch/1147582.html.
52. Tagesspiegel online Gammelige Schweineköpfe zu Wurst verarbeitet (Last access: November 9, 2012). http://www.tagesspiegel.de/weltspiegel/lebensmittel-gammelige-schweinekoepfe-zu-wurst-verarbeitet/1147950.html.
53. Mille-Lindblom C., von Wachenfeldt E., Tranvik L.J. Ergosterol as a measure of living fungal biomass: persistence in environmental samples after fungal death. Journal of Microbiological Methods 2004, 59:253-262.
54. Weber H. Mikrobiologie der Lebensmittel, Fleisch-Fisch-Feinkost 2003, Behr's Verlag, Hamburg.
55. Weidenbörner M. Lebensmittel-Mykologie 1999, Behr's Verlag, Hamburg.
56. White T.J., Bruns T., Lee S., Taylor J. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. PCR Protocols: A Guide to Methods and Applications 1990, 315-322.
57. Wijnands L.M., van der Meij-Florijn A., Delfgou-van Asch E.H.M., van Leusden F.M. Heat sensitivity of Clostridium perfringens. RIVM Report 330371004 Available at:, (Last access: December 12, 2011). http://www.rivm.nl/bibliotheek/rapporten/330371004.pdf.
58. Wu Z., Wang X.-R., Blomquist G. Evaluation of PCR primers and PCR conditions for specific detection of common airborne fungi. Journal of Environmental Monitoring 2002, 4:377-382.
59. Yohalem D.S., Nielsen K., Green H., Jensen D.F. Biocontrol agents efficiently inhibit sporulation of Botrytis aclada on necrotic leaf tips but spread to adjacent living tissue is not prevented. FEMS Microbiology Ecology 2004, 47:279-303.
60. Zhou G., Whong W.-Z., Ong T., Chen B. Development of a fungus-specific PCR assay for detecting low-level fungi in an indoor environment. Molecular and Cellular Probes 2000, 14:339-348.