Abstract
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.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Beckonert O, Keun HC, Ebbels TMD, Bundy J, Holmes E, Lindon JC, Nicholson JK (2007) Metabolic profiling, metabolomic and metabonomic procedures for NMR spectroscopy of urine, plasma, serum and tissue extracts. Nat Protoc 2:2692–2703
Nicholson JK, Holmes E, Kinross J, Burcelin R, Gibson G, Jia W, Pettersson S (2012) Host-gut microbiota metabolic interactions. Science 336:1262–1267
Bjerrum JT, Wang Y, Hao F, Coskun M, Ludwig C, Günther U, Nielsen OH (2015) Metabonomics of human fecal extracts characterize ulcerative colitis, Crohn’s disease and healthy individuals. Metabolomics 11:122–133
Le Gall G, Noor SO, Ridgway K, Scovell L, Janieson C, Johnson IT, Colquhoun IJ, Kemsley EK, Narbad A (2011) Metabolomics of fecal extracts detects altered metabolic activity of gut microbiota in ulcerative colitis and irritable bowel syndrome. J Proteome Res 10:4208–4218
Marchesi JR, Holmes E, Khan F, Kochhar S, Scanlan P, Shanahan F, Wilson ID, Wang Y (2007) Rapid and noninvasive metabonomic characterization of inflammatory bowel disease. J Proteome Res 6:546–551
Kostidis S, Kokova D, Dementeva N, Saltykova KHK, Choi YH, Mayboroda OA (2017) 1H-NMR analysis of feces: new possibilities in the helminthes infections research. BMC Infect Dis 17:275
Saccenti E, Hoefsloot HCJ, Smilde AK, Westerhuis JA, Hendriks MMWB (2014) Reflections on univariate and multivariate analysis of metabolomics data. Metabolomics 10:361–374
McKenzie JS, Donarski JA, Wilson JC, Charlton AJ (2011) Analysis of complex mixtures using high-resolution nuclear magnetic resonance spectroscopy and chemometrics. Prog Nucl Magn Reson Spectrosc 59:336–359
Gratton J, Phetcharaburanin J, Mullish BH, Williams HRT, Mark Thursz M, Nicholson JK, Holmes E, Marchesi JR, Li JV (2016) Optimized sample handling strategy for metabolic profiling of human feces. Anal Chem 88:4661–4668
Lamichhane S, Yde CC, Schmedes MS, Jensen HM, Meier S, Bertram HC (2015) Strategy for nuclear magnetic resonance-based metabolomics of human feces. Anal Chem 87:5930−5937
Deda O, Gika HG, Wilson ID, Theodoridis GA (2015) An overview of fecal sample preparation for global metabolic profiling. J Pharm Biomed Anal 113:137–150
Wu J, An Y, Yao J, Wang Y, Tang H (2010) An optimized sample preparation method for NMR-based faecal metabonomic analysis. Analyst 135:1023–1030
Wu P, Gottfried O (2005) Rapid pulse length determination in high-resolution NMR. J Magn Reson 176:115–119
Izquierdo-García JL, Villa P, Kyriazis A, del Puerto-Nevado L, Pérez-Rial S, Rodriguez I, Hernandez N, Ruiz-Cabello J (2011) Descriptive review of current NMR-based metabolomic data analysis packages. Prog Nucl Magn Reson Spectrosc 59:263–270
Astle W, De Iorio M, Richardson S, Stephens D, Ebbels T (2012) A Bayesian model of NMR spectra for the deconvolution and quantification of metabolites in complex biological mixtures. J Am Stat Assoc 107:1259–1271
Hao J, Liebeke M, Astle W, Maria De Iorio M, Bundy JG, Ebbels T (2014) Bayesian deconvolution and quantification of metabolites in complex 1D NMR spectra using BATMAN. Nat Protoc 9:1416–1427
Zheng C, Zhang S, Ragg S, Raftery D, Vitek O (2011) Identification and quantification of metabolites in 1H NMR spectra by Bayesian model selection. Bioinformatics 27:1637–1644
Findeisen M, Brand T, Berger S (2007) A 1H-NMR thermometer suitable for cryoprobes. Magn Reson Chem 45:175–178
De Meyer T, Sinnaeve D, Van Gasse B, Tsiporkova E, Rietzschel ER, De Buyzere ML, Gillebert TC, Bekaert S, Martins JC, Van Criekinge W (2008) NMR-based characterization of metabolic alterations in hypertension using an adaptive intelligent binning algorithm. Anal Chem 80:3783–3790
Forshed J, Torgrip RJO, Åberg KM, Karlberg B, Lindberg J, Jacobsson SP (2005) A comparison of methods for alignment of NMR peaks in the context of cluster analysis. J Pharma Biomed Anal 38:824–832
Liland KH (2011) Multivariate methods in metabolomics - from pre-processing to dimension reduction and statistical analysis. Trends Analyt Chem 30:827–841
Cevallos-Cevallos JM, Reyes-De-Corcuera JI, Etxeberria E, Danyluk MD, Rodrick GE (2009) Metabolomic analysis in food science: a review. Trends Food Sci Technol 20:557–566
Smolinska A, Blanchet L, Buydens LMC, Wijmenga SS (2012) NMR and pattern recognition methods in metabolomics: from data acquisition to biomarker discovery: a review. Anal Chim Acta 750:82–97
Lutz NW, Sweedler JV, Wevers RA (2013) Ch. 1. Exploring the human metabolome by NMR spectroscopy and mass spectrometry, Wishart DS. In: Methodologies for metabolomics: experimental strategies and techniques. Cambridge University Press, London, pp 3–29
Acknowledgments
The authors thank Dr. E.G. Wilson for her comments and review of the manuscript.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2018 Springer Science+Business Media, LLC
About this protocol
Cite this protocol
Kim, H.K., Kostidis, S., Choi, Y.H. (2018). NMR Analysis of Fecal Samples. In: Giera, M. (eds) Clinical Metabolomics. Methods in Molecular Biology, vol 1730. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7592-1_24
Download citation
DOI: https://doi.org/10.1007/978-1-4939-7592-1_24
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-7591-4
Online ISBN: 978-1-4939-7592-1
eBook Packages: Springer Protocols