Characterization of the cultivable microbial community in a spinach-processing plant using MALDI-TOF MS

Food Microbiology

Volumn 34, Issue 2, 2013, Pages 406-411

  Hausdorf, Lena ^a   Mundt, Kerstin ^a   Winzer, Michaela ^b   Cordes, Christiana ^b   Fröhling, Antje ^a   Schlüter, Oliver ^a   Klocke, Michael ^a  

^a LEIBNIZ INSTITUTE FOR AGRICULTURAL ENGINEERING AND BIOECONOMY ATB   (Germany)

^b ANHALT UNIVERSITY OF APPLIED SCIENCES   (Germany)

Author keywords

16S rRNA gene nucleotide sequence analysis; Bacteria; Identification; Post harvest processing; Vegetables; Whole cell MALDI TOF mass spectra

Indexed keywords

ARCOBACTER; BACTERIA (MICROORGANISMS); FIRMICUTES; GAMMAPROTEOBACTERIA; SPINACIA OLERACEA;

EID: 84875640686     PISSN: 07400020     EISSN: 10959998     Source Type: Journal    
DOI: 10.1016/j.fm.2012.10.008     Document Type: Article

References (41)

1. Amann R., Ludwig W. Ribosomal RNA-targeted nucleic acid probes for studies in microbial ecology. FEMS Microbiology Reviews 2000, 24(5):555-565.
2. Arnold R.J., Reilly J.P. Fingerprint matching of E coli strains with matrix-assisted laser desorption ionization time-of-flight mass spectrometry of whole cells using a modified correlation approach. Rapid Communications In Mass Spectrometry 1998, 12(10):630-636.
3. Ashelford K.E., Chuzhanova N.A., Fry J.C., Jones A.J., Weightman A.J. New screening software shows that most recent large 16S rRNA gene clone libraries contain chimeras. Applied and Environmental Microbiology 2006, 72(9):5734-5741.
4. Baggerman W.I., Koster T. A comparison of enrichment and membrane filtration methods for the isolation of Campylobacter from fresh and frozen foods. Food Microbiology 1992, 9(2):87-94.
5. Bernardet J.F., Bowman J.P. The prokaryotes: a handbook on the biology of bacteria. Proteobacteria: Delta and Epsilon Subclasses. Deeply Rooted Bacteria 2006, vol. 7:481-532. Springer, Berlin. third ed.
6. Bielaszewska M., Mellmann A., Zhang W., Köck R., Fruth A., Bauwens A., Peters G., et al. Characterisation of the Escherichia coli strain associated with an outbreak of haemolytic uraemic syndrome in Germany, 2011: a microbiological study. The Lancet Infectious Diseases 2011, 11(9):671-676. 10.1016/S1473-3099(11)70165-7.
7. Böhme K., Fernández-No I., Gallardo J., Cañas B., Calo-Mata P. Safety assessment of fresh and processed seafood products by MALDI-TOF mass fingerprinting. Food and Bioprocess Technology 2011, 4(6):907-918.
8. D'Antuono L.F., Elementi S., Neri R. Post harvest patterns of deltamethrine and nitrates in industrial spinach. Acta Horticulturae 2007, Produzioni Vegetali Dipartimento di Scienze e Technologie Agroambientali, University of Bologna, Via Fanin 44, 40127 Bologna, Italy. A.N. Fardous, W. Schnitzler, M. Qaryouti (Eds.).
9. De Bruyne K., Slabbinck B., Waegeman W., Vauterin P., De Baets B., Vandamme P. Bacterial species identification from MALDI-TOF mass spectra through data analysis and machine learning. Systematic and Applied Microbiology 2011, 34(1):20-29.
10. Dieckmann R., Malorny B. Rapid screening of epidemiologically important Salmonella enterica subsp. enterica serovars by whole-cell matrix-assisted laser desorption ionization-time of flight mass spectrometry. Applied and Environmental Microbiology 2011, 77(12):4136-4146.
11. Dieckmann R., von Dohren H. Rapid screening and dereplication of bacterial isolates from marine sponges of the Sula Ridge by Intact-Cell-MALDI-TOF mass spectrometry (ICM-MS). Applied Microbiology and Biotechnology 2005, 67(4):539-548.
12. Doyle M.P., Erickson M.C. Summer meeting 2007 - the problems with fresh produce: an overview. Journal of Applied Microbiology 2008, 105(2):317-330.
13. Ferreira L., Sanchez-Juanes F., Munoz-Bellido J.L., Gonzalez-Buitrago J.M. Rapid method for direct identification of bacteria in urine and blood culture samples by matrix-assisted laser desorption ionization time-of-flight mass spectrometry: intact cell vs. extraction method. Clinical Microbiology and Infection 2011, 17(7):1007-1012.
14. Good I.J. The population frequencies of species and the estimation of population parameters. Biometrika 1953, 40(3-4):237-264.
15. Hammer O., Harper D.A.T., Ryan P.D. PAST: palaeontological statistics software package for education and data analysis. Palaeontologia Electronica 2001, 4:9-11.
16. Hausdorf L., Fröhling A., Schlüter O., Klocke M. Analysis of the bacterial community within carrot wash water. Canadian Journal of Microbiology 2011, 57(5):447-452.
17. Holland S.M. Analytical Rarefaction 2003, Retrieved from:. http://www.uga.edu/strata/software.
18. Houf K., Devriese L.A., De Zutter L., Van Hoof J., Vandamme P. Development of a new protocol for the isolation and quantification of Arcobacter species from poultry products. International Journal of Food Microbiology 2001, 71(2-3):189-196.
19. Hughes J.B., Hellmann J.J., Ricketts T.H., Bohannan B.J.M. Counting the uncountable: statistical approaches to estimating microbial diversity. Applied and Environmental Microbiology 2001, 67(10):4399-4406.
20. ISO/DIS 4833-1 Microbiology of Food and Animal Feed - Horizontal Method for the Enumeration of Microorganisms - Part 1: Colony-count Technique at 30 °C by the Pour Plate Technique (ISO/DIS 4833-1:2003) 2003, Beuth Verlag.
21. Jasson V., Jacxsens L., Luning P., Rajkovic A., Uyttendaele M. Alternative microbial methods: an overview and selection criteria. Food Microbiology 2010, 27(6):710-730.
22. Jooste P.J., Britz T.J., Haast J.D. A numerical taxonomic study of Flavobacterium-Cytophaga strains from dairy sources. Journal of Applied Microbiology 1985, 59(4):311-323.
23. Kim H.M..H., Cho B.C. Arcobacter marinus sp. nov. International Journal of Systematic and Evolutionary Microbiology 2010, 60:531-536.
24. Kolaczkowski B., Thornton J.W. Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous. Nature 2004, 431(7011):980-984.
25. Kroumova V., Gobbato E., Basso E., Mucedola L., Giani T., Fortina G. Direct identification of bacteria in blood culture by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry: a new methodological approach. Rapid Communications in Mass Spectrometry: RCM 2011, 25(15):2247-2249.
26. Lane D.J. Nucleic Acid Techniques in Bacterial Systematics 1991, 115-175. Wiley and Sons. E. Stackebrandt, M. Goodfellow (Eds.).
27. Lewis K. Persisters, biofilms, and the problem of cultivability. Microbiology Monographs 2009, vol. 10:181-194. Springer, Berlin/Heidelberg, Retrieved from:. http://www.springerlink.com/content/0vv5640168795640/abstract/, S.S. Epstein (Ed.).
28. Little C.L., Gillespie I.A. Prepared salads and public health. Journal of Applied Microbiology 2008, 105(6):1729-1743.
29. Ludwig W. ARB: a software environment for sequence data. Nucleic Acids Research 2004, 32(4):1363-1371.
30. Matte-Tailliez O., Brochier C., Forterre P., Philippe H. Archaeal phylogeny based on ribosomal proteins. Molecular Biology and Evolution 2002, 19(5):631-639.
31. Munoz R., López-López A., Urdiain M., Moore E.R.B., Rosselló-Móra R. Evaluation of matrix-assisted laser desorption ionization-time of flight whole cell profiles for assessing the cultivable diversity of aerobic and moderately halophilic prokaryotes thriving in solar saltern sediments. Systematic and Applied Microbiology 2011, 34(1):69-75.
32. Rosmini M. Evaluation of two alternative techniques for counting mesophilic aerobic bacteria in raw milk. Food Control 2004, 15(1):39-44.
33. Ruelle V., Moualij B.E., Zorzi W., Ledent P., Pauw E.D. Rapid identification of environmental bacterial strains by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Rapid Communications in Mass Spectrometry 2004, 18(18):2013-2019.
34. Sauer S., Kliem M. Mass spectrometry tools for the classification and identification of bacteria. Nature Reviews Microbiology 2010, 8(1):74-82.
35. Scullion R.H., Madden R.H. A comparison of three methods for the isolation of Arcobacter spp. from retail raw poultry in Northern Ireland. Journal of Food Protection 2004, 67(4):799-804.
36. Valentine N., Wunschel S., Wunschel D., Petersen C., Wahl K. Effect of culture conditions on microorganism identification by matrix-assisted laser desorption ionization mass spectrometry. Applied and Environmental Microbiology 2005, 71(1):58-64.
37. von Wintzingerode F., Göbel U.B., Stackebrandt E. Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiology Reviews 1997, 21(3):213-229.
38. Wang M., Ahrné S., Jeppsson B., Molin G. Comparison of bacterial diversity along the human intestinal tract by direct cloning and sequencing of 16S rRNA genes. FEMS Microbiology Ecology 2005, 54(2):219-231.
39. Welham K.J., Domin M.A., Scannell D.E., Cohen E., Ashton D.S. The characterization of micro-organisms by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Rapid Communications in Mass Spectrometry 1998, 12(4):176-180.
40. Yarza P., Ludwig W., Euzéby J., Amann R., Schleifer K.-H., Glöckner F.O., Rosselló-Móra R. Update of the All-Species Living Tree Project based on 16S and 23S rRNA sequence analyses. Systematic and Applied Microbiology 2010, 33(6):291-299.
41. Zagory D. Effects of post-processing handling and packaging on microbial populations. Postharvest Biology and Technology 1999, 15(3):313-321.