NMR Analysis of Fecal Samples

  • Hye Kyong Kim
  • Sarantos Kostidis
  • Young Hae ChoiEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1730)


Fecal analysis can generate data that is relevant for the exploration of gut microbiota and their relationship with the host. Nuclear magnetic resonance (NMR) spectroscopy is an excellent tool for the profiling of fecal extracts as it enables the simultaneous detection of various metabolites from a broad range of chemical classes including, among others, short-chain fatty acids, organic acids, amino acids, bile acids, carbohydrates, amines, and alcohols. Compounds present at low μM concentrations can be detected and quantified with a single measurement. Moreover, NMR-based profiling requires a relatively simple sample preparation. Here we describe the three main steps of the general workflow for the NMR-based profiling of feces: sample preparation, NMR data acquisition, and data analysis.

Key words

NMR spectroscopy Feces Sample preparation Data analysis Identification Gut microbiota 



The authors thank Dr. E.G. Wilson for her comments and review of the manuscript.


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Copyright information

© Springer Science+Business Media, LLC 2018

Authors and Affiliations

  • Hye Kyong Kim
    • 1
  • Sarantos Kostidis
    • 2
  • Young Hae Choi
    • 1
    Email author
  1. 1.Natural Product Laboratory, Institute of BiologyLeiden UniversityLeidenThe Netherlands
  2. 2.Center for Proteomics and MetabolomicsLeiden University Medical CenterLeidenThe Netherlands

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