, Volume 10, Issue 2, pp 241–249 | Cite as

Global metabolomics characterization of bacteria: pre-analytical treatments and profiling

Original Article


Pre-analytical treatments of bacteria are crucial steps in bacterial metabolomics studies. In order to achieve reliable samples that can best represent the global metabolic profile in vivo both qualitatively and quantitatively, many sample treatment procedures have been developed. The use of different methods makes it difficult to compare the results among different groups. In this work, E. coli samples were tested by using NMR spectroscopy. Both liquid N2 and cold methanol quenching procedures reduce the cell membrane integrity and cause metabolites leakage. However, liquid N2 quenching affected the cell viability and the NMR metabolites’ profile less than cold methanol procedure. Samples obtained by metabolite extraction were significantly superior over cell suspensions and cell lysates, with a higher number of detectable metabolites. Methanol/chloroform extraction proved most efficient at extraction of intracellular metabolites from both qualitative and quantitative points of view. Finally, standard operating procedures of bacterial sample treatments for NMR metabolomics study are presented.


NMR Metabolomics Bacteria Pre-analytical treatments Standard operating procedure 

Supplementary material

11306_2013_571_MOESM1_ESM.doc (1.9 mb)
Supplementary material 1 (DOC 1995 kb)


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Copyright information

© Springer Science+Business Media New York 2013

Authors and Affiliations

  1. 1.Magnetic Resonance Center (CERM)University of FlorenceSesto FiorentinoItaly
  2. 2.Department of ChemistryUniversity of FlorenceSesto FiorentinoItaly
  3. 3.FiorGen FoundationSesto FiorentinoItaly

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