Culture-independent methods for identifying microbial communities in cheese

Food Microbiology

Volumn 25, Issue 7, 2008, Pages 839-848

  Jany, Jean Luc ^a   Barbier, Georges ^a  

^a UNIVERSITÉ DE BREST   (France)

Author keywords

Cheese; Culture independent methods; Fungi; Microbial communities

Indexed keywords

BACTERIAL DNA; FUNGAL DNA;

AGAR GEL ELECTROPHORESIS; BACTERIAL COUNT; BACTERIUM; CHEESE; CLASSIFICATION; DNA MICROARRAY; FOOD CONTROL; GENETICS; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; ISOLATION AND PURIFICATION; METHODOLOGY; MICROBIOLOGY; PHYLOGENY; POLYMERASE CHAIN REACTION; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; REVIEW; SINGLE STRAND CONFORMATION POLYMORPHISM;

BACTERIA; CHEESE; CHROMATOGRAPHY, HIGH PRESSURE LIQUID; COLONY COUNT, MICROBIAL; DNA, BACTERIAL; DNA, FUNGAL; ELECTROPHORESIS, AGAR GEL; FOOD MICROBIOLOGY; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PHYLOGENY; POLYMERASE CHAIN REACTION; POLYMORPHISM, RESTRICTION FRAGMENT LENGTH; POLYMORPHISM, SINGLE-STRANDED CONFORMATIONAL;

BACTERIA (MICROORGANISMS); FUNGI;

EID: 49449084992     PISSN: 07400020     EISSN: 10959998     Source Type: Journal    
DOI: 10.1016/j.fm.2008.06.003     Document Type: Review

References (110)

1. Anderson I.C., and Cairney J.W.G. Diversity and ecology of soil fungal communities: increased understanding through the application of molecular techniques. Environ. Microbiol. 6 (2004) 769-779
2. Andrighetto C., De Dea P., Lombardi A., Neviani E., Rossetti L., and Giraffa G. Molecular identification and cluster analysis of homofermentative thermophilic lactobacilli isolated from dairy products. Res. Microbiol. 149 (1998) 631-643
3. Andrighetto C., Marcazzan G., and Lombardi A. Use of RAPD-PCR and TTGE for the evaluation of biodiversity of whey cultures for Grana Padano cheese. Lett. Appl. Microbiol. 38 (2004) 400-405
4. Avis P.G., Dickie I.A., and Mueller G.M. A 'dirty' business: testing the limitations of terminal restriction fragment length polymorphism (TRFLP) analysis of soil fungi. Mol. Ecol. 15 (2006) 873-882
5. Bae J.W., Rhee S.K., Park J.R., Chung W.H., Nam Y.D., Lee I., Kim H., and Park Y.H. Development and evaluation of genome-probing microarrays for monitoring lactic acid bacteria. Appl. Environ. Microbiol. 71 (2005) 8825-8835
6. Baker G.C., Smith J.J., and Cowan D.A. Review and re-analysis of domain-specifc 16S primers. J. Microbiol. Methods 55 (2003) 541-555
7. Barlaan E.A., Sugimori M., Furukawa S., and Takeuchi K. Profiling and monitoring of microbial populations by denaturing high-performance liquid chromatography. J. Microbiol. Methods 61 (2005) 399-412
8. Berbee M.L., Pirseyedi M., and Hubbard S. Cochliobolus phylogenetics and the origin of known, highly virulent pathogens, inferred from ITS and glyceraldehyde-3-phosphate dehydrogenase gene sequences. Mycologia 91 (1999) 964-977
9. Beresford T.P., Fitzsimmons N.A., Brennan N.L., and Cogan T.M. Recent advances in cheese microbiology. Int. Dairy J. 11 (2001) 259-274
10. Berthier F., Beuvier E., Dasen A., and Grappin R. Origin and diversity of mesophilic lactobacilli in Comté cheese, as revealed by PCR with repetitive and species-specific primers. Int. Dairy J. 11 (2001) 293-305
11. Blackwell M., Hibbett D.S., Taylor W., and Spatafora J.W. Research coordination networks: a phylogeny for kingdom fungi (Deep Hypha). Mycologia 98 (2006) 829-837
12. Bodrossy L., and Sessitch A. Oligonucleotide microarrays in microbial diagnostics. Curr. Opin. Microbiol. 7 (2004) 245-254
13. Bonaïti C., Parayre S., and Irlinger F. Novel extraction strategy of ribosomal RNA and genomic DNA from cheese for PCR-based investigations. Int. J. Food Microbiol. 107 (2006) 171-179
14. Brodie E., Edwards S., and Clipson N. Soil fungal community structure in a temperate upland grassland soil. FEMS Microbiol. Ecol. 45 (2003) 105-114
15. Callon C., Delbès C., Duthoit F., and Montel M. Application of SSCP-PCR fingerprinting to profile the yeast community in raw milk Salers cheeses. Syst. Appl. Microbiol. 29 (2006) 172-180
16. Chakravorty S., Helb D., Burday M., Connell N., and Aland D. A detailed analysis of 16S ribosomal RNA gene segments for the diagnosis of pathogenic bacteria. J. Microbiol. Methods 69 (2007) 330-339
17. Cihlar R.L., and Sypherd P.S. The organization of the ribosomal RNA genes in the fungus Mucor racemosus. Nucleic Acid Res. 25 (1980) 793-804
18. Cocolin L., Innocente N., Biasutti M., and Comi G. The late blowing in cheese: a new molecular approach based on PCR and DGGE to study the microbial ecology of the alteration process. Int. J. Food Microbiol. 90 (2004) 83-91
19. Cocolin L., Diez A., Urso R., Rantsiou K., Comi G., Bergmaier I., and Beimfohr C. Optimization of conditions for profiling bacterial populations in food by culture-independent methods. Int. J. Food Microbiol. 120 (2007) 100-109
20. Coppola S., Blaiotta G., Ercolini D., and Moschetti G. Molecular evaluation of microbial diversity occurring in different types of Mozzarella cheese. J. Appl. Microbiol. 90 (2001) 414-420
21. Coppola S., Fusco V., Andolfi R., Aponte M., Blaiotta G., Ercolini D., and Moschetti G. Evaluation of microbial diversity during the manufacture of Fior di Latte di Agerola, a traditional raw milk pasta-filata cheese of the Naples area. J. Dairy Res. 73 (2006) 264-272
22. Coppola S., Blaiotta G., and Ercolini D. Dairy products. In: Cocolin L., and Ercolini D. (Eds). Molecular Techniques in the Microbial Ecology of Fermented Foods (2007), Springer, New York, USA 31-90
23. Dasen A., Berthier F., Grappin R., Williams A.G., and Banks J. Genotypic and phenotypic characterization of the dynamics of the lactic acid bacterial population of adjunct-containing Cheddar cheese manufactured from raw and microfiltered pasteurized milk. J. Appl. Microbiol. 94 (2003) 595-607
24. Delbès C., and Montel M.C. Design and application of Staphylococcus-specific single strand conformation polymorphism-PCR analysis to monitor Staphylococcus populations diversity and dynamics during production of raw milk cheese. Lett. Appl. Microbiol. 41 (2005) 169-174
25. Delbès C., Ali-Mandjee L., and Montel M.C. Monitoring bacterial communities in raw milk and cheese by culture-dependent and -independent 16S rRNA gene-based analyses. Appl. Environ. Microbiol. 73 (2007) 1882-1891
26. Dickie I.A., Xu B., and Koide R.T. Vertical niche differentiation of ectomycorrhizal hyphae in soil as shown by T-RFLP analysis. New Phytol. 156 (2002) 527-535
27. Doaré-Lebrun E., El Arbi A., Charlet M., Guérin L., Pernelle J.J., Ogier J.C.C., and Bouix M. Analysis of fungal diversity of grapes by application of temporal temperature gradient gel electrophoresis-potentialities and limits of the method. J. Appl. Microbiol. 101 (2006) 1340-1350
28. Drake M., Small C., Spence K.D., and Swanson B.G. Rapid detection and identification of Lactobacillus spp. in dairy products by using the polymerase chain reaction. J. Food Prot. 59 (1996) 1031-1036
29. Duggan D.J., Bittner M., Chen Y., Meltzer P., and Trent J.M. Expression profiling using cDNA microarrays. Nat. Genet. 21 (1999) 10-14
30. Duthoit F., Godon J., and Montel M. Bacterial community dynamics during production of registered designation of origin Salers cheese as evaluated by 16S rRNA single-strand conformation polymorphism analysis. Appl. Environ. Microbiol. 69 (2003) 3840-3848
31. Duthoit F., Tessier L., and Montel M.C. Diversity, dynamics and activity of bacterial populations in 'Registered Designation of Origin' Salers cheese by single-strand conformation polymorphism analysis of 16S rRNA genes. J. Appl. Microbiol. 98 (2005) 1198-1208
32. Duthoit F., Callon C., Tessier L., and Montel M.C. Relationships between sensorial characteristics and microbial dynamics in 'Registered Designation of Origin' Salers cheese. Int. J. Food Microbiol. 103 (2005) 259-270
33. Einax E., and Voigt K. Oligonucleotide primers for the universal amplification of beta-tubulin genes facilitate phylogenetic analyses in the regnum Fungi. Org. Divers. Evol. 3 (2003) 185-194
34. El Baradei G., Delacroix-Buchet A., and Ogier J.C. Biodiversity of bacterial ecosystems in traditional Egyptian Domiati cheese. Appl. Environ. Microbiol. 73 (2007) 1248-1255
35. Elder Jr. J.F., and Turner B.J. Concerted evolution of repetitive DNA sequences in Eukaryotes. Q. Rev. Biol. 70 (1995) 297-320
36. Ercolini D. PCR-DGGE fingerprinting: novel strategies for detection of microbes in food. J. Microbiol. Methods 56 (2004) 297-314
37. Ercolini D., Moschetti G., Blaiotta G., and Coppola S. The potential of a polyphasic PCR-DGGE approach in evaluating microbial diversity of natural whey cultures for water-buffalo Mozzarella cheese production: bias of culture-dependent and culture-independent analyses. Syst. Appl. Microbiol. 24 (2001) 610-617
38. Ercolini D., Hill P.J., and Dodd C.E.R. Bacterial community structure and location in Stilton cheese. Appl. Environ. Microbiol. 69 (2003) 3540-3548
39. Ercolini D., Mauriello G., Blaiotta G., Moschetti G., and Coppola S. PCR-DGGE fingerprints of microbial succession during a manufacture of traditional water buffalo mozzarella cheese. J. Appl. Microbiol. 96 (2004) 263-270
40. Ercolini D., Frisso G., Mauriello G., Salvatore F., and Coppola S. Microbial diversity in natural whey cultures used for the production of Caciocavallo Silano PDO cheese. Int. J. Food Microbiol. (2008) 10.1016/j.ijfoodmicro.2008.03.007
41. Ercolini D., Blaiotta G., Moschetti G., and Coppola S. Evaluation of PCR-DGGE analysis for molecular typing cheeses. Ann. Microbiol. 52 (2002) 81-87
42. Feurer C., Vallaeys T., Corrieu G., and Irlinger F. Does smearing inoculum reflect the bacterial composition of the smear at the end of the ripening of a French soft, red-smear cheese?. J. Dairy Sci. 87 (2004) 3189-3197
43. Feurer C., Irlinger F., Spinnler H.E., Glaser P., and Vallaeys T. Assessment of the rind microbial diversity in a farmhouse-produced vs a pasteurized industrially produced soft red-smear cheese using both cultivation and rDNA-based methods. J. Appl. Microbiol. 97 (2004) 546-556
44. Fitzsimmons N.A., Cogan T.M., Condon S., and Beresford T. Phenotypic and genotypic characterization of non-starter lactic acid bacteria in mature Cheddar cheese. Appl. Environ. Microbiol. 65 (1999) 3418-3426
45. Florez A., and Mayo B. Fungal diversity and succession during the manufacture and ripening of traditional, Spanish, blue-veined Cabrales cheese, as determined by PCR-DGGE. Int. J. Food Microbiol. 10 (2006) 165-171
46. Fox, P.F., Guinee, T.P., Cogan, T.M., McSweeney, P.L.H., 2000. In: Fox, P., Guinee, T., Cogan, T.M. (Eds.), Fundamentals of Cheese Science. Aspen Publications, Gaithersburg, MD, USA.
47. Frueh F.W., and Noyer-Weidner M. Use of denaturing high-performance liquid chromatography for rapid detection and identification of seven Candida species. J. Clin. Microbiol. 43 (2005) 5912-5915
48. Garbeva P., van Veen J.A., and van Elsas J.D. Microbial diversity in soil: selection of microbial populations by plant and soil type and implications for disease suppressiveness. Annu. Rev. Phytopathol. 1 (2004) 243-270
49. Gente S., Larpin S., Cholet O., Gueguen M., Vernoux J., and Demasures N. Development of primers for detecting dominant yeasts in smear-ripened cheeses. J. Dairy Res. 74 (2007) 137-145
50. Goldenberg O., Herrmann S., Marjoram G., Noyer-Weidner M., Hong G., Bereswill S., and Göbel U.B. Molecular monitoring of the intestinal flora by denaturing high performance liquid chromatography. J. Microbiol. Methods 68 (2007) 94-105
51. Guschin D.Y., Mobarry B.K., Proudnikov D., Stahl D.A., Rittmann B.E., and Mirzabekov A.D. Oligonucleotide microchips as genosensors for determinative and environmental studies in microbiology. Appl. Environ. Microbiol. 63 (1997) 2397-2402
52. Hansen M.C., Tolker-Nielsen T., Givskov M., and Molin S. Biased 16S rDNA PCR amplification caused by interference from DNA flanking the template region. FEMS Microbiol. Ecol. 26 (1998) 141-149
53. Head I.M., Saunders J.R., and Pickup R.W. Microbial evolution, diversity, and ecology: a decade of ribosomal RNA analysis of uncultivated microorganisms. Microb. Ecol. 35 (1998) 1-21
54. Hibbet D., Binder M., Bischoff J., Blackwell M., Cannon P., Eriksson O., Huhndorf S., James T., Kirk P., Lucking R., Thorsten H., Lumbsch T., Lutzoni F., Matheny P., McLaughlin D., Powell M., Redhead S., Schoch C., Spatafora J., Stalpers J., Vilgalys R., Aime M., Aptroot A., Bauer R., Begerow D., Benny G., Castlebury L., Crous P., Dai Y., Gams W., Geiser D., Griffith G., Gueidan C., Hawcksworth D., Hestmark G., Hosaka K., Humber R., Hyde K., Ironside J., Koljalg U., Kurtzman C., Larsson K., Lichtwardt R., Longcore J., Miadlikowska J., Miller A., Moncalvo J.M., Mozley-Standridge S., Oberwrinkler F., Parmasto E., Reeb V., Rogers J., Roux C., Ryvarden L., Sampaio J., Schussler A., Sugiyama J., Thorn R., Tibell L., Untereiner W., Wlaker C., Wang Z., Weir A., Weiss M., White M., Winka K., Yao Y., and Zhang N. A higher-level phylogenetic classification of the Fungi. Mycol. Res. 111 (2007) 509-547
55. Hugenholtz P., Goebel B.M., and Pace N.R. Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J. Bacteriol. 180 (1998) 4765-4774
56. James T.Y., Kauff F., Schoch C.L., Matheny P.B., Hofstetter V., Cox C.J., Celio G., Gueidan C., Fraker E., Miadlikowska J., Lumbsch H.T., Rauhut A., Reeb V., Arnold A.E., Amtoft A., Stajich J.E., Hosaka K., Sung G., Johnson D., O'Rourke B., Crockett M., Binder M., Curtis J.M., Slot J.C., Wang Z., Wilson A.W., Schussler A., Longcore J.E., O'Donnel K., Mozley-Standridge S., Porter D., Letcher P.M., Powell M.J., Taylor J.W., White M.M., Griffith G.W., Davies D.R., Humber R.A., Morton J.B., Sugiyama J., Rossman A.Y., Rogers J.D., Pfister D.H., Hewitt D., Hansen K., Hambleton S., Shoemaker R.A., Kohlmeyer J., Volkmann-Kohlmeyer B., Spotts R.A., Serdani M., Crous P.W., Hugues K.W., Matsuura K., Langer E., Langer G., Untereiner W.A., Lucking R., Budel B., Geiser D.M., Aptroot A., Diederich P., Schmitt I., Schultz M., Yahr R., Hibbett D.S., Lutzoni F., McLaughlin D.J., Spatafora J., and Vilgalys R. Reconstructing the early evolution of Fungi using a six-gene phylogeny. Nature 443 (2006) 818-822
57. Joseph N., Krauskopf E., Vera M., and Michot B. Ribosomal internal transcribed spacer 2 (ITS2) exhibits a common core of secondary structure in vertebrate and yeast. Nucleic Acid Res. 27 (1999) 4533-4540
58. Kanagawa T. Bias and artifacts in multitemplate polymerase chain reaction (PCR). J. Biosci. Bioeng. 96 (2003) 317-323
59. Kellogg E.A., and Appels R. Intraspecific and interspecific variation in 5S RNA genes are decoupled in diploid wheat relatives. Genetics 140 (1995) 325-343
60. Klappenbach J.A., Dunbar J.M., and Schmidt T.M. rRNA operon copy number reflects ecological strategies of bacteria. Appl. Environ. Microbiol. 66 (2000) 1328-1333
61. Lafarge V., Ogier J.C., Girard V., Maladen V., Leveau J., and Delacroix-Buchet A. Le potentiel de la TTGE pour l'étude bactérienne de quelques laits crus. Le Lait 84 (2004) 169-178
62. Le Bourhis A., Saunier K., Doré J., Carlier J., Chamba J., Popoff M., and Tholozan J. Development and validation of PCR primers to assess the diversity of Clostridium spp. in cheese by temporal temperature gradient gel electrophoresis. Appl. Environ. Microbiol. 71 (2005) 29-38
63. Le Bourhis A., Doré J., Carlier J., Chamba J., Popoff M., and Tholozan J. Contribution of C. beijerinckii and C. sporogenes in association to C. tyrobutyricum to the butyric fermentation in Emmental type cheese. Int. J. Food Microbiol. 113 (2007) 154-163
64. Liao D. Concerted evolution: molecular mechanism and biological implications. Am. J. Hum. Genet. 64 (1999) 24-30
65. Liao D. Gene conversion drives within genic sequences: concerted evolution of ribosomal RNA genes in bacteria and archaea. J. Mol. Evol. 51 (2000) 305-317
66. Liu J., and Schardl C. A conserved sequence in internal transcribed spacer 1 of plant nuclear genes. Plant Mol. Biol. 26 (1994) 775-778
67. Liu W.T., Marsh T.L., Cheng H., and Forney L.J. Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA. Appl. Environ. Microbiol. 63 (1997) 4516-4522
68. Liu W.T., Marsh T.L., and Forney L.J. Determination of the microbial diversity of anaerobic-aerobic activated sludge by a novel molecular biological technique. Water Sci. Technol. 37 (1998) 417-422
69. Lutzoni F., Kauff F., Cox C.J., McLaughlin D., Celio G., Dentinger B., Padamsee M., Hibbet M., James T.Y., Baloch E., Grube M., Reeb V., Hofstetter V., Schoch C., Arnold A.E., Miadlikowska J., Spatafora J., Johnson D., Hambleton S., Crockett M., Shoemaker R., Sung J., Lucking R., Lumbsch T., O'Donnell K., Binder M., Diederich P., Ertz D., Gueidan C., Hansen K., Harris R.C., Hosaka K., Lim Y., Matheny B., Nishida H., Pfister D., Rogers J., Rossman A., Schmitt I., Sipman H., Stone J., Sugiyama J., Yahr R., and Vilgalys R. Assembling the fungal tree of life: progress, classification and evolution of subcellular traits. Am. J. Bot. 91 (2004) 1446-1480
70. Mannu L., Comunian R., and Maria M.F. Mesophilic lactobacilli in Fiore Sardo cheese: PCR identification and evolution during ripening. Int. Dairy J. 10 (2000) 383-389
71. Mauriello G., Moio L., Genovese A., and Ercolini D. Relationships between flavoring capabilities, bacterial composition, and geographical origin of natural whey cultures used for traditional water-buffalo Mozzarella cheese manufacture. J. Dairy Sci. 86 (2003) 486-497
72. Muyzer G., Teske A., Wirsen C.O., and Jannasch H.W. Phylogenetic relationships of Thiomicrospora species and their identification in deep-sea hydrothermal vent samples by denaturing gradient gel electrophoresis of 16S rDNA fragments. Arch. Microbiol. 164 (1995) 165-172
73. Myers R.M., Fischer S.G., Maniatis T., and Lerman L.S. Modification of the melting properties of duplex DNA by attachment of a GC-rich DNA sequence as determined by denaturing gradient gel electrophoresis. Nucleic Acid Res. 13 (1985) 3111-3129
74. Myers R.M., Fischer S.G., Lerman L.S., and Maniatis T. Nearly all single base substitutions in DNA fragments joined to a GC-clamp can be detected by denaturing gradient gel electrophoresis. Nucleic Acid Res. 13 (1985) 3131-3145
75. Myers R.M., Maniatis T., and Lerman L.S. Detection and localization of single base changes by denaturing gradient gel electrophoresis. Method. Enzymol. 155 (1987) 501-527
76. Oefner P.J., and Underhill P.A. Comparative DNA sequencing by denaturing high-performance liquid chromatography (DHPLC). Am. J. Hum. Genet. 57 (1995) A266
77. Ogier J.C., Son O., Gruss A., Tailliez P., and Delacroix-Buchet A. Identification of the bacterial microflora in dairy products by temporal temperature gradient gel-electrophoresis. Appl. Environ. Microbiol. 68 (2002) 3691-3701
78. Ogier J.C., Lafarge V., Girard V., Rault A., Maladen V., Gruss A., Leveau J., and Delacroix-Buchet A. Molecular fingerprinting of dairy microbial ecosystems by use of temporal temperature and denaturing gradient gel electrophoresis. Appl. Environ. Microbiol. 70 (2004) 5628-5643
79. Orita M., Iwahana H., Kanazawa H., Hayashi K., and Sekiya T. Detection of polymorphisms of human DNA by gel electrophoresis as single-strand conformation polymorphisms. Proc. Natl. Acad. Sci. USA 86 (1989) 2766-2770
80. Parayre S., Falentin H., Madec M., Sivieri K., Le Dizes A., Sohier D., and Lortal S. Easy DNA extraction and optimisation of PCR-temporal temperature gel electrophoresis to identify the predominant high and low GC-content bacteria from dairy products. J. Microbiol. Methods 69 (2007) 431-441
81. Peplies J., Glockner F.O., and Amann R. Optimization strategies for DNA microarrays-based detection of bacteria with 16S rRNA-targeting oligonucleotide probes. Appl. Environ. Microbiol. 69 (2003) 1397-1407
82. Rademaker J.L.W., Peinhopf M., Rijnen L., Bockelmann W., and Noordman W.H. The surface microflora dynamics of bacterial smear-ripened Tilsit cheese determined by T-RFLP DNA population fingerprint analysis. Int. Dairy J. 15 (2005) 785-794
83. Randazzo C.L., Torriani S., Akkermans A.D.L., de Vos W.M., and Vaughan E.E. Diversity, dynamics, and activity of bacterial communities during production of an artisanal Sicilian cheese as evaluated by 16S rRNA analysis. Appl. Environ. Microbiol. 68 (2002) 1882-1892
84. Randazzo C.L., Vaughan E.E., and Caggia C. Artisanal and experimental Pecorino Siciliano cheese: microbial dynamics during manufacture assessed by culturing and PCR-DGGE analyses. Int. J. Food Microbiol. 109 (2006) 1-8
85. Ravnik-Glavac M., Glavac D., and Dean M. Sensitivity of single-strand conformation polymorphism and heteroduplex method for mutation detection on the cystic fibrosis gene. Hum. Mol. Genet. 3 (1994) 801-807
86. Reysenbach A.L., Giver L.J., Wickham G.S., and Pace N.R. Differential amplification of rRNA genes by polymerase chain reaction. Appl. Environ. Microbiol. 58 (1992) 3417-3418
87. Samson R.A., Seifert K.A., Kuijpers A., Houbraken J., and Frisvad C. Phylogenetic analysis of Penicillium subgenus Penicillium using partial β-tubulin sequences. Stud. Mycol. 49 (2004) 175-200
88. Sandine W.E., and Elliker P.R. Microbially induced flavors and fermented foods: flavor in fermented dairy products. J. Agric. Food Chem. 18 (1970) 557-566
89. Saubusse M., Millet L., Delbès C., Callon C., and Montel M.C. Application of single strand conformation polymorphism-PCR method for distinguishing cheese bacterial communities that inhibit Listeria monocytogenes. Int. J. Food Microbiol. 116 (2007) 126-135
90. Seifert K.A., Samson R.A., Dewaard J.R., Houbraken J., Levesque C.A., Moncalvo J.M., Louis-Seize G., and Hebert P.D.N. Prospects for fungus identification using COI DNA barcodes, with Penicillium as a test case. Proc. Natl. Acad. Sci. USA 104 (2007) 3901-3906
91. Sheffield V.C., Beck J.S., Stone E.M., and Myers R.M. Attachment of a 40 bp G+C rich sequence (GC-clamp) to genomic DNA fragments by polymerase chain reaction results in improved detection of single-base changes. Proc. Natl. Acad. Sci. USA 86 (1989) 232-236
92. Skouboe P., Taylor J.W., Frisvad J.C., Lauritsen D., Larsen L., Alboek C., Boysen M., and Rossen L. Molecular methods for differentiation of closely related Penicillium species. In: Samson R.A., and Pitt J.I. (Eds). Integration of Modern Taxonomic Methods for Penicillium and Aspergillus Classification (2000), Harwood Academic Publishers, Amsterdam 179-188
93. Small J., Call D.R., Brockman F.J., Staub T.M., and Chandler D.P. Direct detection of 16S rRNA in soil extracts by using oligonucleotide microarrays. Appl. Environ. Microbiol. 67 (2001) 4708-4716
94. Stackebrandt E., Frederiksen W., Garrity G., Grimont P.A.D., Kämpfer P., Maiden M.C.J., Nesme X., Rosselo-Mora R., Swings J., Trüper H.G., Vauterin L., Ward A.C., and Whitman W.B. Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int. J. Syst. Evol. Biol. 52 (2002) 1043-1047
95. Suzuki M.T., and Giovannoni S.J. Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl. Environ. Microbiol. 62 (1996) 625-630
96. Tao, F., Li, C., Smejkal, G., Lazarev, A., Lawrence, N., Schumacher, R.T., 2007. Pressure cycling technology (PCT) applications in extraction of biomolecules from challenging biological samples. High Pressure Bioscience and biotechnology. In: Proceedings of the 4th International Conference on High Pressure and Biotechnology, vol. 1, pp. 166-173.
97. Throbäck I.N., Enwall K., Jarvis A., and Hallin S. Reassessing PCR primers targeting nirS, nirK and nosZ genes for community surveys of denitrifying bacteria with DGGE. FEMS Microbiol. Ecol. 49 (2004) 401-417
98. Valinsky L., Della Vedova G., Scupham A.J., Alvey S., Figueroa A., Yin B., Hartin R.J., Chrobak M., Crowley D.E., Jiang T., and Borneman J. Analysis of bacterial community composition by oligonucleotide fingerprinting of rRNA genes. Appl. Environ. Microbiol. 68 (2002) 3243-3250
99. Van de Peer Y., Chapelle S., and De Wachter R. A quantitative map of nucleotide substitution rates in bacterial rRNA. Nucleic Acid Res. 24 (1996) 3381-3391
100. Wagner M., Smidt H., Loy A., and Zhou J. Unravelling microbial communities with DNA-microarrays: challenges and future directions. Microb. Ecol. 53 (2007) 498-506
101. Walsh P.S., Erlich H.A., and Higuchi R. Preferential PCR amplification of alleles: mechanisms and solutions. PCR Methods Appl. 1 (1992) 241-250
102. Ward D.M., Weller R., and Bateson M.M. 16S rRNA sequences reveal uncultured inhabitants of a well-studied thermal community. FEMS Microbiol. Rev. 75 (1990) 105-116
103. Ward D.M., Bateson M.M., Weller R., and Ruff-Roberts A.L. Ribosomal RNA analysis of microorganisms as they occur in nature. Adv. Microb. Ecol. 12 (1992) 219-286
104. Weissensteiner T., and Lanchbury J.S. Strategy for controlling preferential amplification and avoiding false negatives in PCR typing. Biotechniques 21 (1996) 1102-1108
105. Wilson I.G. Inhibition and facilitation of nucleic acid amplification. Appl. Environ. Microbiol. 63 (1997) 3741-3751
106. Wintzingerode V.F., Göbel U.B., and Stackebrandt E. Determination of microbial diversity in environmental samples: pitfalls of PCR-based analysis. FEMS Microbiol. Rev. 21 (1997) 213-229
107. Woese C.R., and Fox G.E. Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc. Natl. Acad. Sci. USA 74 (1977) 5088-5090
108. Xiao W., and Oefner P.J. Denaturing high-performance liquid chromatography: a review. Hum. Mutat. 17 (2001) 439-474
109. Yoshino K., Nishigaki K., and Husimi Y. Temperature sweep gel electrophoresis: a simple method to detect point mutations. Nucleic Acid Res. 19 (1991) 3153
110. Zhou J. Microarrays for bacterial detection and microbial community analysis. Curr. Opin. Microbiol. 6 (2003) 288-294