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Ultrahigh Resolution Mass Spectrometry Based Non-targeted Microbial Metabolomics

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Genetics Meets Metabolomics

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Abstract

Microbial metabolomes gain more and more attention due to the fact that microorganisms are ubiquitous and important in environment and health. Some are involved in basic environmental processes and govern element cycles in the entire ecosystem; others have relevance for animals and human (as commensal or pathogens) and have the potential to be used in biotechnology. The tools of Metabolomics have been used for many years in microbial research and the paradigm is changing from studies on single species cultures to multispecies communities, like in biofilms or environmental and human microbiomes. These changes lead to a new variety of metabolomic tools (metametabolomics) adapted to the study of multiple organisms systems. In addition the needs in high-resolution instrumentation are changing to analytical platforms that enable to deal with the yet unknown compounds. ICR-FT/MS is a promising ultrahigh resolution mass spectrometry approach mastering the challenge in non-targeted metabolomics. This chapter presents an introduction to the current state of the art in microbial metabolomics, the importance of ICR-FT/MS in this field and is describing solutions for non-targeted metabolomics with a focus on bacterial samples.

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References

  1. Schopf JW (2006) Fossil evidence of Archaean life. Philos Trans R Soc B Biol Sci 361(1470):869–885

    Article  CAS  Google Scholar 

  2. Cavalier-Smith T (2006) Cell evolution and earth history: stasis and revolution. Philos Trans R Soc B Biol Sci 361(1470):969–1006

    Article  CAS  Google Scholar 

  3. Leewenhoeck A (1684) An abstract of a letter from Mr. Anthony Leewenhoeck at Delft, sated Sep. 17. 1683. Containing some microscopical observations, about animals in the scurf of the teeth, the substance call’d worms in the nose, the cuticula consisting of scales. Philos Trans 14(155–166):568–574

    Google Scholar 

  4. van Leeuwenhoek A (1700) Part of a letter from Mr Antony van Leeuwenhoek, concerning the worms in sheeps livers, gnats, and animalcula in the excrements of frogs. Philos Trans 22(260–276):509–518

    Google Scholar 

  5. van Leeuwenhoek A (1702) Part of a letter from Mr Antony van Leeuwenhoek, F. R. S. concerning green weeds growing in water, and some animalcula found about them. Philos Trans 23(277–288):1304–1311

    Google Scholar 

  6. Whitman WB, Coleman DC, Wiebe WJ (1998) Prokaryotes: the unseen majority. Proc Natl Acad Sci 95(12):6578–6583

    Article  PubMed  CAS  Google Scholar 

  7. Fredrickson JK, Zachara JM, Balkwill DL et al (2004) Geomicrobiology of high-level nuclear waste-contaminated vadose sediments at the Hanford site, Washington state. Appl Environ Microbiol 70(7):4230–4241

    Article  PubMed  CAS  Google Scholar 

  8. Steinhoff U (2005) Who controls the crowd? New findings and old questions about the intestinal microflora. Immunol Lett 99(1):12–16

    Article  PubMed  CAS  Google Scholar 

  9. O’Hara AM, Shanahan F (2006) The gut flora as a forgotten organ. EMBO Rep 7(7):688–693

    Article  PubMed  Google Scholar 

  10. Rappá MS, Giovannoni SJ (2003) The uncultured microbial majority. Annu Rev Microbiol 57(1):369–394

    Article  Google Scholar 

  11. Buchanan B, Arnon D (1990) A reverse KREBS cycle in photosynthesis: consensus at last. Photosynth Res 24(1):47–53

    Article  PubMed  CAS  Google Scholar 

  12. Villas-Bôas SG, Roessner-Tunali U, Hansen MAE, Smedsgaard J, Nielsen J (2007) Metabolome analysis: an introduction, 1st edn. Wiley, Indianapolis

    Google Scholar 

  13. Frimmersdorf E, Horatzek S, Pelnikevich A, Wiehlmann L, Schomburg D (2010) How pseudomonas aeruginosa adapts to various environments: a metabolomic approach. Environ Microbiol 12(6):1734–1747

    Article  PubMed  CAS  Google Scholar 

  14. Hertkorn N, Frommberger M, Witt M et al (2008) Natural organic matter and the event horizon of mass spectrometry. Anal Chem 80(23):8908–8919

    Article  PubMed  CAS  Google Scholar 

  15. Wikoff WR, Anfora AT, Liu J et al (2009) Metabolomics analysis reveals large effects of gut microflora on mammalian blood metabolites. Proc Natl Acad Sci 106(10):3698–3703

    Article  PubMed  CAS  Google Scholar 

  16. Soga T, Ohashi Y, Ueno Y et al (2003) Quantitative metabolome analysis using capillary electrophoresis mass spectrometry. J Proteome Res 2(5):488–494

    Article  PubMed  CAS  Google Scholar 

  17. van der Werf MJ, Overkamp KM, Muilwijk B, Coulier L, Hankemeier T (2007) Microbial metabolomics: toward a platform with full metabolome coverage. Anal Biochem 370(1):17–25

    Article  PubMed  Google Scholar 

  18. Garcia DE, Baidoo EE, Benke PI et al (2008) Separation and mass spectrometry in microbial metabolomics. Curr Opin Microbiol 11(3):233–239

    Article  PubMed  CAS  Google Scholar 

  19. van der Werf MJ, Jellema RH, Hankemeier T (2005) Microbial metabolomics: replacing trial-and-error by the unbiased selection and ranking of targets. J Ind Microbiol Biotechnol 32(6):234–252

    Article  PubMed  Google Scholar 

  20. Mashego M, Rumbold K, De Mey M et al (2007) Microbial metabolomics: past, present and future methodologies. Biotechnol Lett 29(1):1–16

    Article  PubMed  CAS  Google Scholar 

  21. Gougeon RD, Lucio M, Frommberger M et al (2009) The chemodiversity of wines can reveal a metabologeography expression of cooperage oak wood. Proc Natl Acad Sci 106(23):9174–9179

    Article  PubMed  CAS  Google Scholar 

  22. Liger-Belair G, Cilindre C, Gougeon RD et al (2009) Unraveling different chemical fingerprints between a champagne wine and its aerosols. Proc Natl Acad Sci 106(39):16545–16549

    Article  PubMed  CAS  Google Scholar 

  23. Aharoni A, Ric de Vos CH, Verhoeven HA et al (2002) Nontargeted metabolome analysis by use of Fourier transform ion cyclotron mass spectrometry. OMICS J Integr Biol 6(3):217–234

    Article  CAS  Google Scholar 

  24. Brown SC, Kruppa G, Dasseux JL (2005) Metabolomics applications of FT-ICR mass spectrometry. Mass Spectrom Rev 24(2):223–231

    Article  PubMed  CAS  Google Scholar 

  25. Ohta D, Kanaya S, Suzuki H (2010) Application of Fourier-transform ion cyclotron resonance mass spectrometry to metabolic profiling and metabolite identification. Curr Opin Biotechnol 21(1):35–44

    Article  PubMed  CAS  Google Scholar 

  26. Huang N, Siegel MM, Kruppa GH, Laukien FH (1999) Automation of a Fourier transform ion cyclotron resonance mass spectrometer for acquisition, analysis, and e-mailing of high-­resolution exact-mass electrospray ionization mass spectral data. J Am Soc Mass Spectrom 10(11):1166–1173

    Article  CAS  Google Scholar 

  27. Han J, Danell R, Patel J et al (2008) Towards high-throughput metabolomics using ultrahigh-field Fourier transform ion cyclotron resonance mass spectrometry. Metabolomics 4(2):128–140

    Article  PubMed  CAS  Google Scholar 

  28. Li X, Fekete A, Englmann M et al (2007) At-line coupling of UPLC to chip-electrospray-FTICR-MS. Anal Bioanal Chem 389(5):1439–1446

    Article  PubMed  CAS  Google Scholar 

  29. Suhre K, Schmitt-Kopplin P (2008) MassTRIX: mass translator into pathways. Nucleic Acids Res 36(suppl 2):W481–W484

    Article  PubMed  CAS  Google Scholar 

  30. Bondy JA MUSR (2007) Graduate text in mathematics: graph theory, 1st edn. Springer, New York

    Google Scholar 

  31. Breitling R, Ritchie S, Goodenowe D, Stewart ML, Barrett MP (2006) Ab initio prediction of metabolic networks using Fourier transform mass spectrometry data. Metabolomics 2(3):155–164

    Article  CAS  Google Scholar 

  32. Kind T, Fiehn O (2007) Seven golden rules for heuristic filtering of molecular formulas obtained by accurate mass spectrometry. BMC Bioinformatics 8(1):105

    Article  PubMed  Google Scholar 

  33. Hughey CA, Hendrickson CL, Rodgers RP, Marshall AG, Qian K (2001) Kendrick mass defect spectrum: a compact visual analysis for ultrahigh-resolution broadband mass spectra. Anal Chem 73(19):4676–4681

    Article  PubMed  CAS  Google Scholar 

  34. Rossello-Mora R, Lucio M, Pena A et al (2008) Metabolic evidence for biogeographic isolation of the extremophilic bacterium Salinibacter ruber. ISME J 2(3):242–253

    Article  PubMed  CAS  Google Scholar 

  35. Pena A, Teeling H, Huerta-Cepas J et al (2010) Fine-scale evolution: genomic, phenotypic and ecological differentiation in two coexisting Salinibacter ruber strains. ISME J 4(7):882–895

    Article  PubMed  CAS  Google Scholar 

  36. Brito-Echeverría J, Lucio M, López-López A et al (2011) Response to adverse conditions in two strains of the extremely halophilic species Salinibacter ruber. Extremophiles 15(3):379–389

    Article  PubMed  Google Scholar 

  37. Jansson J, Willing B, Lucio M et al (2009) Metabolomics reveals metabolic biomarkers of Crohn’s disease. PLoS One 4(7):e6386

    Article  PubMed  Google Scholar 

  38. Fekete A, Frommberger M, Rothballer M et al (2007) Identification of bacterial N-acylhomoserine lactones (AHLs) with a combination of ultra-performance liquid chromatography (UPLC), ultra-high-resolution mass spectrometry, and in-situ biosensors. Anal Bioanal Chem 387(2):455–467

    Article  PubMed  CAS  Google Scholar 

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Author information

Authors and Affiliations

  1. Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, Ingolstädter Landstraße 1, Neuherberg, Bavaria, 85764, Germany

    Michael Witting, Marianna Lucio, Dimitrios Tziotis & Philippe Schmitt-Kopplin

Authors
  1. Michael Witting
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  2. Marianna Lucio
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  3. Dimitrios Tziotis
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  4. Philippe Schmitt-Kopplin
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Corresponding author

Correspondence to Philippe Schmitt-Kopplin .

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Editors and Affiliations

  1. Qatar Foundation-Education City, Weill Cornell Medical College in Qatar, Education City – Qatar Foundation, Doha, 24144, Qatar

    Karsten Suhre

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Witting, M., Lucio, M., Tziotis, D., Schmitt-Kopplin, P. (2012). Ultrahigh Resolution Mass Spectrometry Based Non-targeted Microbial Metabolomics. In: Suhre, K. (eds) Genetics Meets Metabolomics. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-1689-0_5

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