Assessment of microbial population dynamics during yoghurt and hard cheese fermentation and ripening by DNA population fingerprinting

International Dairy Journal

Volumn 16, Issue 5, 2006, Pages 457-466

  Rademaker, J L W ^a   Hoolwerf, J D ^a   Wagendorp, A A ^a   Te Giffel, M C ^a  

^a NIZO FOOD RESEARCH   (Netherlands)

Author keywords

Cheese; Microflora; Population dynamics; Population structure; T RFLP; Yoghurt

Indexed keywords

CELLS; DAIRY PRODUCTS; DNA; FERMENTATION; FOOD PRESERVATION; POPULATION STATISTICS;

CHEESE; MICROFLORA; POPULATION DYNAMICS; POPULATION STRUCTURE; T-RFLP; YOGHURT;

MICROORGANISMS;

BACTERIA (MICROORGANISMS); LACTOBACILLUS; LACTOCOCCUS; STREPTOCOCCUS;

EID: 30844433319     PISSN: 09586946     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.idairyj.2005.05.009     Document Type: Article

References (28)

1. E. Avaniss-Aghajani, K. Jones, D. Chapman, and C. Brunk A molecular technique for identification of bacteria using small subunit ribosomal RNA sequences Biotechniques 17 1994 144 149
2. C.B. Blackwood, T. Marsh, S-H. Kim, and E.A. Paul Terminal restriction fragment length polymorphism data analysis for quantitative comparison of microbial communities Applied and Environmental Microbiology 69 2003 926 932
3. B.G. Clement, L.E. Kehl, K.L. DeBord, and C.L. Kitts Terminal restriction fragment patterns [TRFPs], a rapid, PCR-based method for the comparison of complex bacterial communities Journal of Microbiological Methods 31 1998 135 142
4. J.R. Cole, B. Chai, T.L. Marsh, R.J. Farris, Q. Wang, S.A. Kulam, S. Chandra, D.M. McGarrell, T.M. Schmidt, G.M. Garrity, and J.M. Tiedje The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy Nucleic Acids Research 31 1 2003 442 443
5. J.J. Engebretson, and C.L. Moyer Fidelity of select restriction endonucleases in determining microbial diversity by Terminal-Restriction Fragment Length Polymorphism Applied and Environmental Microbiology 69 8 2003 4823 4829
6. G. Giraffa, and E. Neviani DNA-based, culture-independent strategies for evaluating microbial communities in food-associated ecosystems International Journal of Food Microbiology 67 1-2 2001 19 34
7. P. Hugenholtz, B.M. Goebel, and N.R. Pace Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity Journal of Bacteriology 180 1999 4765 4774
8. J.A. Klappenbach, P.R. Saxman, J.R. Cole, and T.M. Schmidt rrndb: the Ribosomal RNA Operon Copy Number Database Nucleic Acids Research 29 1 2001 181 184
9. T.D. Leser, R.H. Lindecrona, T.K. Jensen, B.B. Jensen, and K. Moller Changes in bacterial community structure in the colon of pigs fed different experimental diets and after infection with Brachyspira hyodysenteriae Applied and Environmental Microbiology 66 8 2000 3290 3296
10. W.T. Liu, T.L. Marsh, H. Cheng, and L.J. Forney Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA Applied and Environmental Microbiology 63 11 1997 4516 4522
11. W.T. Liu, T.L. Marsh, and L.J. Forney Determination of the microbial diversity of anaerobic-aerobic activated sludge by a novel molecular biological technique Water Science and Technology 37 3 1998 417 422
12. H. Lüdemann, I. Arth, and W. Liesack Spatial changes in the bacterial community structure along a vertical oxygen gradient in flooded paddy soil cores Applied and Environmental Microbiology 66 2000 754 762
13. T. Lueders, and M. Friedrich Archaeal population dynamics during sequential reduction processes in rice field soil Applied and Environmental Microbiology 66 2000 2732 2742
14. T. Lueders, and M.W. Friedrich Evaluation of PCR amplification bias by terminal restriction fragment length polymorphism analysis of small-subunit rRNA and mcrA genes by using defined template mixtures of methanogenic pure cultures and soil DNA extracts Applied and Environmental Microbiology 69 1 2003 320 326
15. T.L. Marsh Terminal restriction fragment length polymorphism (T-RFLP): an emerging method for characterizing diversity among homologous populations of amplification products Current Opinion in Microbiology 2 1999 323 327
16. T.L. Marsh, P. Saxman, J. Cole, and J. Tiedje Terminal restriction fragment length polymorphism analysis program, a Web-based research tool for microbial community analysis Applied and Environmental Microbiology 66 8 2000 3616 3620
17. A. Mengoni, E. Grassi, and M. Bazzicalupo A cloning method for the taxonomic interpretation of T-RFLP patterns Biotechniques 33 2002 990 992
18. M.M. Moeseneder, J.M. Arrieta, G. Muyzer, C. Winter, and G.J. Herndl Optimization of terminal-restriction fragment length polymorphism analysis for complex marine bacterioplankton communities and comparison with denaturing gradient gel electrophoresis Applied and Environmental Microbiology 65 8 1999 3518 3525
19. J. Ogier, O. Son, A. Gruss, P. Tailliez, and A. Delacroix-Buchet Identification of the bacterial microflora in dairy products by temporal temperature gradient gel electrophoresis Applied and Environmental Microbiology 68 2002 3691 3701
20. A.M. Osborn, E.R.B. Moore, and K.N. Timmis An evaluation of terminal-restriction fragment length polymorphism (T-RFLP) analysis for the study of microbial community structure and dynamics Environmental Microbiology 2 1 2000 39 50
21. Pette, J. W., Lolkema, H., 1950. De bereiding van yoghurt (preparation of yoghurt). N.I.Z.O. mededeling no. 1 (32pp.). Ede, The Netherlands: Nederlands Instituut voor Zuivelonderzoek, Hoorn, currently NIZO Food Research.
22. J.L.W. Rademaker, and P.H.M. Savelkoul PCR amplification-based microbial typing D.H. Pershing F.C. Tenover J. Versalovic Y.W. Tang E.R. Unger D.A. Relman T.J. White Molecular Microbiology Diagnostic Principles and Practice 2004 ASM Press Washington, DC, USA 197 221
23. J.LW. Rademaker, F. Driehuis, M.C. te Giffel, P.G. van Wikselaar, and P.M. Becker Measurement of microbial population dynamics of silages by T-RFLP DNA fingerprints L.M. Gechie C. Thomas Proceedings of the XIIIth International Silage Conference, September 11-13, 2002 2002 The Scottish Agricultural College (SAC) Ayr, Scotland, UK 376 377
24. J.L.W. Rademaker, W. Noordman, and M.C. te Giffel Vingerafdrukken van micro-organismen (Fingerprints of microorganism) Voedingsmiddelentechnologie 9 2003 10 12
25. J.L.W. Rademaker, M. Peinhopf, L. Rijnen, W. Bockelmann, and W.H. Noordman The surface microflora dynamics of bacterial smear-ripened Tilsit cheese determined by T-RFLP DNA population fingerprint analysis International Dairy Journal 15 2005 785 794
26. T.M. Schmidt Multiplicity of ribosomal RNA operons in prokaryotic genomes F.J. de Bruijn J.R. Lupski G.M. Weinstock Bacterial genomes: Physical structure and analysis 1997 Chapman & Hall New York, NY, USA 221 229
27. P.H.A. Sneath N.S. Mair M.E. Sharpe J.G. Holt Bergey's Manual of Systematic Bacteriology vol. 2 1986 Williams & Wilkins Baltimore, MD, USA 1069
28. P. Walstra, A. Noomen, and T.J. Geurts Dutch type varieties P.F. Fox Cheese: Chemistry, physics and microbiology vol. 2 1987 Elsevier Applied Science Publishers London, UK 45 92