Optimization of a sample preparation method for the metabolomic analysis of clinically relevant bacteria

Journal of Microbiological Methods

Volumn 87, Issue 1, 2011, Pages 24-31

  Marcinowska, Renata ^a   Trygg, Johan ^a   Wolf Watz, Hans ^a   Mortiz, Thomas ^b   Surowiec, Izabella ^a  

^a UMEÅ UNIVERSITY   (Sweden)

^b SWEDISH UNIVERSITY OF AGRICULTURAL SCIENCES   (Sweden)

Author keywords

Bacteria metabolomics; Extraction method optimization; GC MS TOF profiling; Multivariate data analysis

Indexed keywords

METHANOL; SODIUM CHLORIDE;

ARTICLE; BACTERIAL METABOLISM; BACTERIUM CULTURE; CELL GROWTH; CENTRIFUGATION; CONCENTRATION (PARAMETERS); CONTROLLED STUDY; ESCHERICHIA COLI; MASS FRAGMENTOGRAPHY; METABOLITE; METABOLOMICS; METHICILLIN RESISTANT STAPHYLOCOCCUS AUREUS; NONHUMAN; OPTICAL DENSITY; PRIORITY JOURNAL; PROCESS OPTIMIZATION; PSEUDOMONAS AERUGINOSA; REPRODUCIBILITY; SALMONELLA TYPHIMURIUM; SPECIES DIFFERENTIATION; TIME OF FLIGHT MASS SPECTROMETRY; YERSINIA PSEUDOTUBERCULOSIS;

CELL FRACTIONATION; ESCHERICHIA COLI; GAS CHROMATOGRAPHY-MASS SPECTROMETRY; HUMANS; METABOLOME; METHICILLIN-RESISTANT STAPHYLOCOCCUS AUREUS; MULTIVARIATE ANALYSIS; PRINCIPAL COMPONENT ANALYSIS; PSEUDOMONAS AERUGINOSA; SALMONELLA TYPHIMURIUM; YERSINIA PSEUDOTUBERCULOSIS;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; PSEUDOMONAS AERUGINOSA; SALMONELLA TYPHIMURIUM; STAPHYLOCOCCUS AUREUS; YERSINIA PSEUDOTUBERCULOSIS;

EID: 80052372759     PISSN: 01677012     EISSN: 18728359     Source Type: Journal    
DOI: 10.1016/j.mimet.2011.07.001     Document Type: Article

References (32)

1. Barsch A., Patschkowski T., Niehaus K. Comprehensive metabolite profiling of Sinorhizobium meliloti using gas chromatography-mass spectrometry. Funct. Integr. Genomics 2004, 4:219-230.
2. Bolten C.J., Kiefer P., Letisse F., Portais J.C., Wittmann C. Sampling for metabolome analysis of microorganisms. Anal. Chem. 2007, 79(10):3843-3849.
3. Fiehn O. Metabolomics-the link between genotypes and phenotypes. Plant Mol. Biol. 2002, 48:155-171.
4. Gullberg J., Jonsson P., Nordström A., Sjöström M., Moritz T. Design of experiments: an efficient strategy to identify factors influencing extraction and derivatization of Arabidopsis thaliana samples in metabolomic studies with gas chromatography/mass spectrometry. Anal. Biochem. 2004, 331(2):283-295.
5. Jaki B.U., Franzblau S.G., Cho S.H., Pauli G.F. Development of an extraction method for mycobacterial metabolome analysis. J. Pharm. Biomed. 2006, 41(1):196-200.
6. Jensen N.B., Jokumsen K.V., Villadsen J. Determination of the phosphorylated sugars of the Embden-Meyerhoff-Parnas pathway in Lactococcus lactis using a fast sampling technique and solid phase extraction. Biotechnol. Bioeng. 1999, 63:357-362.
7. Jiye A., Trygg J., Gullberg J., Johansson A.I., Jonsson P., Antti H., et al. Extraction and GC/MS analysis of the human blood plasma metabolome. Anal. Chem. 2005, 77:8086-8094.
8. Jonsson P., Gullberg J., Nordstrom A., Kusano M., Kowalczyk M., Sjostrom M., et al. A strategy for identifying differences in large series of metabolomic samples analyzed by GC/MS. Anal. Chem. 2004, 76:1738-1745.
9. Jonsson P., Johansson A., Gullberg J., Trygg J., Grund B., Marklund S., et al. High-throughput data analysis for detecting and identifying differences between samples in GC/MS-based metabolomic analyses. Anal. Chem. 2005, 77:5635-5642.
10. Jonsson P., Stenlund H., Moritz T., Trygg J., Sjostrom M., Verheij E.R., et al. A strategy for modeling dynamic responses in metabolic samples characterized by GC/MS. Metabolomics 2006, 2(3):135-143.
11. Koek M.M., Muilwijk B., Van der Werf M.J., Hankemeier T. Microbial metabolomics with gas chromatography mass spectrometry. Anal. Chem. 2006, 78:1272-1281.
12. Lee D.Y., Fiehn O. High quality metabolomic data for Chlamydomonas reinhardtii. Plant Meth. 2008, 4:7.
13. Maharjan R.P., Ferenci T. Global metabolite analysis: the influence of extraction methodology on metabolome profiles of Escherichia coli. Anal. Biochem. 2003, 313:145-154.
14. Park S.J., Lee S.Y., Cho J., Kim T.Y., Lee J.W., Park J.H., et al. Global physiological understanding and metabolic engineering of microorganisms based on omics studies. Appl. Microbiol. Biotechnol. 2005, 68:567-579.
15. Plassmeier J., Barsch A., Persicke M., Niehaus K., Kalinowski J. Investigation of central carbon metabolism and the 2-methylcitrate cycle in Corynebacterium glutamicum by metabolic profiling using gas chromatography-mass spectrometry. J. Biotechnol. 2007, 130:354-363.
16. Pohjanen E., Thysell E., Jonsson P., Eklund C., Silfver A., Carlsson I.B., et al. A multivariate screening strategy for investigating metabolic effects of strenuous physical exercise in human serum. J. Proteome Res. 2007, 6:2113-2120.
17. Sellick Ch.A., Hansen R., Maqsood A.R., Dunn W.B., Stephens G.M., Goodacre R., et al. Effective quenching processes for physiologically valid metabolite profiling of suspension cultured mammalian cells. Anal. Chem. 2009, 81(1):174-183.
18. Shin M.H., Lee D.Y., Liu K.-H., Fiehn O., Kim K.H. Evaluation of sampling and extraction methodologies for the global metabolic profiling of Saccharophagus degradans. Anal. Chem. 2010, 82:6660-6666.
19. Smart K.F., Aggio R.B.M., Van Houtte J.R., Villas-Boas S.G. Analytical platform for metabolome analysis of microbial cells using methyl chloroformate derivatization followed by gas chromatography-mass spectrometry. Nat. Protoc. 2010, 5(10):1709-1729.
20. Sprott G.D., Koval S.F., Schnaitman C.A. Methods for General and Molecular Bacteriology 1994, Washington, ACM. P. Gerhardt, P.R.G.E. Murray, W.A. Wood, N.R. Krieg (Eds.).
21. Tang H., Wang Y., Nicholson J.K., Lindon J.C. Use of Relaxation-Edited one-dimensional and two-dimensional nuclear magnetic resonance spectroscopy to improve detection of small metabolites in blood plasma. Anal. Biochem. 2004, 325:260-272.
22. Tweeddale H., Notley-Mcrobb L., Ferenci T. Effect of slow growth on metabolism of Escherichia coli, as revealed by global metabolite pool ("metabolome") analysis. J. Bacteriol. 1998, 180:5109-5116.
23. Van der Werf M.J., Overkamp K.M., Muilwijk B., Coulier L., Hankemeier T. Microbial metabolomics: toward a platform with full metabolome coverage. Anal. Biochem. 2007, 370:17-25.
24. Van der Werf M.J., Overkamp K.M., Muilwijk B., Koek M.M., der Werff-van Van, der Vat B.J.C., et al. Comprehensive analysis of the metabolome of Pseudomonas putida S12 grown on different carbon sources. Mol. Biosyst. 2008, 4:315-327.
25. Villas-Boas S.G., Bruheim P. Cold glycerol-saline: the promising quenching solution for accurate intracellular metabolite analysis of microbial cells. Anal. Biochem. 2007, 370:87-97.
26. Villas-Boas S.G., Højer-Pedersen J., Akesson M., Smedsgaard J., Nielsen J. Global metabolite analysis of yeast: evaluation of sample preparation methods. Yeast 2005, 22:1155-1169.
27. Want E.J., O'Maille G., Smith C.A., Brandon T.R., Uritboonthai W., Qin Ch., et al. Solvent-dependent metabolite distribution, clustering, and protein extraction for serum profiling with mass spectrometry. Anal. Chem. 2006, 78(3):743-752.
28. Weibel K.E., Mor J.R., Fiechter A. Rapid sampling of yeast cells and automated assays of adenylate, citrate, pyruvate and glucose-6-phosphate pools. Anal. Biochem. 1974, 58:208-216.
29. Wenyun L., Kimball E., Rabinowitz J.D. A high-performance liquid chromatography-tandem mass spectrometry method for quantitation of nitrogen-containing intracellular metabolites. J. Am. Soc. Mass Spectrom. 2006, 17:37-50.
30. Winder C.L., Dunn W.B., Schuler S., Broadhurst D., Jarvis R., Stephens G.M., et al. Global metabolic profiling of Escherichia coli cultures: an evaluation of methods for quenching and extraction of intracellular metabolites. Anal. Chem. 2008, 80:2939-2948.
31. Wittmann C., Kromer J.O., Kiefer P., Binz T., Heinzle E. Impact of the cold shock phenomenon on quantification of intracellular metabolites in bacteria. Anal. Biochem. 2004, 327(1):135-139.
32. Wuolikainen A., Hedenstrom A., Moritz T., Marklund S.L., Antti H., Andersen P.M. Optimization of procedures for collecting and storing of CSF for studying the metabolome in ALS. Amyotroph. Lateral Scler. 2009, 10(4):229-236.