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Summary

Accurate microbial metabolomics requires rapid sampling, quenching, and extraction. A differential method is crucial for prokaryotes to distinguish intracellular metabolites from extracellular ones, ensuring reliable endo-metabolome quantification.

Keywords:
EndometabolomeExometabolomeFast samplingIsotope dilution mass spectrometryMicrobial metabolomicsQuenching

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Area of Science:

  • Microbiology
  • Metabolomics
  • Biochemistry

Background:

  • Metabolomics aims to capture cellular metabolite profiles.
  • Accurate microbial metabolomics requires rapid sampling, quenching, and extraction to prevent metabolite changes.
  • Extracellular metabolites can interfere with intracellular metabolite quantification.

Purpose of the Study:

  • To review and present methods for microbial metabolomics.
  • To provide protocols for sampling, quenching, and extraction.
  • To address challenges in quantifying microbial endo-metabolomes, especially for prokaryotes.

Main Methods:

  • Overview of literature-described sampling, quenching, and extraction techniques.
  • Detailed protocols for rapid sampling, quenching, and extraction.
  • Measurement of metabolites in total broth, washed cells, and supernatant for differential analysis.

Main Results:

  • Established methods for rapid microbial sample processing.
  • Protocols applicable to both eukaryotic and prokaryotic microorganisms.
  • A differential method is proposed for accurate prokaryotic endo-metabolome quantification.

Conclusions:

  • Effective microbial metabolomics relies on optimized sampling, quenching, and extraction.
  • The differential method is essential for accurate prokaryotic metabolomics.
  • The presented protocols facilitate quantitative metabolomics in diverse microorganisms.