Nutritional modulation of the metabonome: Applications of metabolic phenotyping in translational nutritional research

Current Opinion in Gastroenterology

Volumn 30, Issue 2, 2014, Pages 196-207

  Kinross, James ^a   Li, Jia V ^a   Muirhead, Laura J ^a   Nicholson, Jeremy ^a  

^a IMPERIAL COLLEGE LONDON   (United Kingdom)

Author keywords

Metabonomics; Microbiome; Nutrition; Systems medicine

Indexed keywords

BIOLOGICAL MARKERS; CARDIOVASCULAR DISEASES; DIET; HUMANS; MALNUTRITION; METABOLIC DISEASES; METABOLOME; METABOLOMICS; NEOPLASMS; NUTRITIONAL PHYSIOLOGICAL PHENOMENA; OBESITY; PHENOTYPE; TRANSLATIONAL MEDICAL RESEARCH;

EID: 84894061404     PISSN: 02671379     EISSN: 15317056     Source Type: Journal    
DOI: 10.1097/MOG.0000000000000036     Document Type: Review

References (70)

1. Nicholson JK, Connelly J, Lindon JC, Holmes E. Metabonomics: A platform for studying drug toxicity and gene function. Nat Rev Drug Discov 2002; 1:153-161
2. Nicholson JK, Lindon JC, Holmes E. 'Metabonomics': Understanding the metabolic responses of living systems to pathophysiological stimuli via multivariate statistical analysis of biological NMR spectroscopic data. Xenobiotica 1999; 29:1181-1189
3. Beckonert O, Keun HC, Ebbels TM, et al. Metabolic profiling, metabolomic and metabonomic procedures for NMR spectroscopy of urine, plasma, serum and tissue extracts. Nat Protoc 2007; 2:2692-2703
4. Nicholson JK, Holmes E, Kinross JM, et al. Metabolic phenotyping in clinical and surgical environments. Nature 2012; 491:384-392
5. Robinette SL, Lindon JC, Nicholson JK. Statistical spectroscopic tools for biomarker discovery and systems medicine. Anal Chem 2013; 85:5297-5303
6. Matsubara T, Tanaka N, Krausz KW, et al. Metabolomics identifies an inflammatory cascade involved in dioxin- and diet-induced steatohepatitis. Cell Metab 2012; 16:634-644
7. Haiser HJ, Gootenberg DB, Chatman K, et al. Predicting and manipulating cardiac drug inactivation by the human gut bacterium Eggerthella lenta. Science 2013; 341:295-298
8. Clayton TA, Baker D, Lindon JC, et al. Pharmacometabonomic identification of a significant host-microbiome metabolic interaction affecting human drug metabolism. Proc Natl Acad Sci U S A 2009; 106:14728-14733
9. Ryan KK, Seeley RJ. Physiology. Food as a hormone. Science 2013; 339:918-919
10. Stella C, Beckwith-Hall B, Cloarec O, et al. Susceptibility of human metabolic phenotypes to dietary modulation. J Proteome Res 2006; 5:2780-2788
11. Rezzi S, Ramadan Z, Martin FP, et al. Human metabolic phenotypes link directly to specific dietary preferences in healthy individuals. J Proteome Res 2007; 6:4469-4477
12. Pettersson J, Karlsson PC, Choi YH, et al. NMR metabolomic analysis of fecal water from subjects on a vegetarian diet. Biol Pharm Bull 2008; 31:1192-1198
13. Edmands WM, Beckonert OP, Stella C, et al. Identification of human urinary biomarkers of cruciferous vegetable consumption by metabonomic profiling. J Proteome Res 2011; 10:4513-4521
14. Sanchez-Tena S, Reyes-Zurita FJ, Diaz-Moralli S, et al. Maslinic acid-enriched diet decreases intestinal tumorigenesis in Apc(Min/') mice through transcriptomic and metabolomic reprogramming. PLoS One 2013; 8:e59392
15. Bertram HC, Hoppe C, Petersen BO, et al. An NMR-based metabonomic investigation on effects of milk and meat protein diets given to 8-year-old boys. Br J Nutr 2007; 97:758-763
16. Kleemann R, Verschuren L, van Erk MJ, et al. Atherosclerosis and liver inflammation induced by increased dietary cholesterol intake: A combined transcriptomics and metabolomics analysis. Genome Biol 2007; 8:R200
17. Wang Y, Tang H, Nicholson JK, et al. A metabonomic strategy for the detection of the metabolic effects of chamomile (Matricaria recutita L.) ingestion. J Agric Food Chem 2005; 53:191-196
18. Boulange CL, Claus SP, Chou CJ, et al. Early metabolic adaptation in C57BL/ 6 mice resistant to high fat diet induced weight gain involves an activation of mitochondrial oxidative pathways. J Proteome Res 2013; 4:1956-1968
19. Sampey BP, Freemerman AJ, Zhang J, et al. Metabolomic profiling reveals mitochondrial-derived lipid biomarkers that drive obesity-associated inflammation. PLoS One 2012; 7:e38812
20. Etxeberria U, dela Garza AL, Martinez JA, Milagro FI. Diet-induced hyperinsulinemia differentially affects glucose and protein metabolism: A high-Throughput metabolomic approach in rats. J Physiol Biochem 2013; 69:613-623
21. Hanhineva K, Barri T, Kolehmainen M, et al. Comparative nontargeted profiling of metabolic changes in tissues and biofluids in high-fat diet-fed Ossabaw pig. J Proteome Res 2013; 12:3980-3992
22. Floegel A, von Ruesten A, Drogan D, et al. Variation of serum metabolites related to habitual diet: A targeted metabolomic approach in EPIC-Potsdam. Eur J Clin Nutr 2013; 67:1100-1108
23. Holmes E, Loo RL, Stamler J, et al. Human metabolic phenotype diversity and its association with diet and blood pressure. Nature 2008; 453:396-400
24. Menni C, Zhai G, Macgregor A, et al. Targeted metabolomics profiles are strongly correlated with nutritional patterns in women. Metabolomics 2013; 9:506-514
25. De Guzman JM, Ku G, Fahey R, et al. Chronic caloric restriction partially protects against age-related alteration in serum metabolome. Age (Dordr) 2013; 35:1091-1104
26. Johansson-Persson A, Barri T, Ulmius M, et al. LC-QTOF/MS metabolomic profiles in human plasma after a 5-week high dietary fiber intake. Anal Bioanal Chem 2013; 405:4799-4809
27. Rasmussen LG, Winning H, Savorani F, et al. Assessment of the effect of high or low protein diet on the human urine metabolome as measured by NMR. Nutrients 2012; 4:112-131
28. Heinzmann SS, Merrifield CA, Rezzi S, et al. Stability and robustness of human metabolic phenotypes in response to sequential food challenges. J Proteome Res 2012; 11:643-655
29. Xu J, Yang S, Cai S, et al. Identification of biochemical changes in lactovegetarian urine using 1H NMR spectroscopy and pattern recognition. Anal Bioanal Chem 2010; 396:1451-1463
30. O'Sullivan A, Gibney MJ, Connor AO, et al. Biochemical and metabolomic phenotyping in the identification of a vitamin D responsive metabotype for markers of the metabolic syndrome. Mol Nutr Food Res 2011; 55:679-690
31. Wu Z, Li M, Zhao C, et al. Urinary metabonomics study in a rat model in response to protein-energy malnutrition by using gas chromatography-mass spectrometry and liquid chromatography-mass spectrometry. Mol Biosyst 2010; 6:2157-2163
32. Kim JY, Park JY, Kim OY, et al. Metabolic profiling of plasma in overweight/ obese and lean men using ultra performance liquid chromatography and Q-TOF mass spectrometry (UPLC-Q-TOF MS). J Proteome Res 2010; 9:4368-4375
33. Loftus N, Miseki K, Iida J, et al. Profiling and biomarker identification in plasma from different Zucker rat strains via high mass accuracy multistage mass spectrometric analysis using liquid chromatography/mass spectrometry with a quadrupole ion trap-Time of flight mass spectrometer. Rapid Commun Mass Spectrom 2008; 22:2547
34. Xie G, Li X, Li H, Jia W. Toward personalized nutrition: Comprehensive phytoprofiling and metabotyping. J Proteome Res 2013; 12:1547-1559
35. Bundy JG, Lenz EM, Osborn D, et al. Metabolism of 4-fluoroaniline and 4-fluorobiphenyl in the earthworm Eisenia veneta characterized by highresolution NMR spectroscopy with directly coupled HPLC-NMR and HPLC-MS. Xenobiotica 2002; 32:479-490
36. McCann SE, Freudenheim JL, Marshall JR, Graham S. Risk of human ovarian cancer is related to dietary intake of selected nutrients, phytochemicals and food groups. J Nutr 2003; 133:1937-1942
37. Griffin JL, Bollard M, Nicholson JK, Bhakoo K. Spectral profiles of cultured neuronal and glial cells derived from HRMAS (1)H NMR spectroscopy. NMR Biomed 2002; 15:375-384
38. Bailey NJ, Sampson J, Hylands PJ, et al. Multicomponent metabolic classification of commercial feverfew preparations via high-field 1H-NMR spectroscopy and chemometrics. Planta Med 2002; 68:734-738
39. Bundy JG, Lenz EM, Bailey NJ, et al. Metabonomic assessment of toxicity of 4-fluoroaniline, 3,5-difluoroaniline and 2-fluoro-4-methylaniline to the earthworm Eisenia veneta (Rosa): Identification of new endogenous biomarkers. Environ Toxicol Chem 2002; 21:1966-1972
40. van Duynhoven J, Vaughan EE, Jacobs DM, et al. Metabolic fate of polyphenols in the human superorganism. Proc Natl Acad Sci U S A 2011; 108 (Suppl 1):4531-4538
41. Blackledge CA, Nicholson JK, Evans JA, et al. Application of (1)H- and (19)FNMR spectroscopy in the investigation of the urinary and biliary excretion of 3,5-, 2,4-ditrifluoromethylbenzoic and pentafluorobenzoic acids in rat. Xenobiotica 2002; 32:605-613
42. Bolca S, Van de Wiele T, Possemiers S. Gut metabotypes govern health effects of dietary polyphenols. Curr Opin Biotechnol 2013; 24:220-225
43. Beckwith-Hall BM, Brindle JT, Barton RH, et al. Application of orthogonal signal correction to minimise the effects of physical and biological variation in high resolution 1H NMR spectra of biofluids. Analyst 2002; 127:1283-1288
44. Griffin JL, Muller D, Woograsingh R, et al. Vitamin E deficiency and metabolic deficits in neuronal ceroid lipofuscinosis described by bioinformatics. Physiol Genomics 2002; 11:195-203
45. Ridaura VK, Faith JJ, Rey FE, et al. Gut microbiota from twins discordant for obesity modulate metabolism in mice. Science 2013; 341:1241214
46. Ageing well: A global priority. Lancet 2012; 379:1274
47. Claesson MJ, Jeffery IB, Conde S, et al. Gut microbiota composition correlates with diet and health in the elderly. Nature 2012; 488:178-184
48. Wijeyesekera A, Selman C, Barton RH, et al. Metabotyping of long-lived mice using 1H NMR spectroscopy. J Proteome Res 2012; 11:2224-2235
49. Smith MI, Yatsunenko T, Manary MJ, et al. Gut microbiomes of Malawian twin pairs discordant for kwashiorkor. Science 2013; 339:548-554
50. Wang Z, Klipfell E, Bennett BJ, et al. Gut flora metabolism of phosphatidylcholine promotes cardiovascular disease. Nature 2011; 472:57-63
51. Koeth RA, Wang Z, Levison BS, et al. Intestinal microbiota metabolism of L-carnitine, a nutrient in red meat, promotes atherosclerosis. Nat Med 2013; 19:576-585
52. Tang WH, Wang Z, Levison BS, et al. Intestinal microbial metabolism of phosphatidylcholine and cardiovascular risk. N Engl J Med 2013; 368:1575-1584
53. Pekkinen J, Olli K, Huotari A, et al. Betaine supplementation causes increase in carnitine metabolites in the muscle and liver of mice fed a high-fat diet as studied by nontargeted LC-MS metabolomics approach. Mol Nutr Food Res 2013; 57:1959-1968
54. Wang-Sattler R, Yu Z, Herder C, et al. Novel biomarkers for prediabetes identified by metabolomics. Mol Syst Biol 2012; 8:615
55. Nicholson JK, Holmes E, Kinross J, et al. Host-gut microbiota metabolic interactions. Science 2012; 336:1262-1267
56. Swann JR, Want EJ, Geier FM, et al. Systemic gut microbial modulation of bile acid metabolism in host tissue compartments. Proc Natl Acad Sci U S A 2011; 108 (Suppl 1):4523-4530
57. Duarte IF, Legido-Quigley C, Parker DA, et al. Identification of metabolites in human hepatic bile using 800MHz 1H NMR spectroscopy, HPLC-NMR/MS and UPLC-MS. Mol Biosyst 2009; 5:180-190
58. Yoshimoto S, Loo TM, Atarashi K, et al. Obesity-induced gut microbial metabolite promotes liver cancer through senescence secretome. Nature 2013; 499:97-101
59. Gavaghan CL, Wilson ID, Nicholson JK. Physiological variation in metabolic phenotyping and functional genomic studies: Use of orthogonal signal correction and PLS-DA. FEBS Lett 2002; 530:191-196
60. Smith PM, Howitt MR, Panikov N, et al. The microbial metabolites, short-chain fatty acids, regulate colonic Treg cell homeostasis. Science 2013; 341:569-573
61. Zheng X, Qiu Y, Zhong W, et al. A targeted metabolomic protocol for shortchain fatty acids and branched-chain amino acids. Metabolomics 2013; 9:818-827
62. Bergeron M, Nicholson JK, Phaneuf S, et al. Selection of lymphocyte gating protocol has an impact on the level of reliability of T-cell subsets in aging specimens. Cytometry 2002; 50:53-61
63. Scarfe GB, Wilson ID, Warne MA, et al. Structure-metabolism relationships of substituted anilines: Prediction of N-acetylation and N-oxanilic acid formation using computational chemistry. Xenobiotica 2002; 32:267-277
64. Duckett CJ, Bailey NJ, Walker H, et al. Quantitation in gradient high performance liquid chromatography/inductively coupled mass spectrometry investigated using diclofenac and chlorpromazine. Rapid Commun Mass Spectrom 2002; 16:245-247
65. Holmes E, Loo RL, Stamler J. Human metabolic phenotype diversity and its association with diet and blood pressure. Nature 2008; 453:396-400
66. Walsh MC, McLoughlin GA, Roche HM, et al. Impact of geographical region on urinary metabolomic and plasma fatty acid profiles in subjects with the metabolic syndrome across Europe: The LIPGENE study. Br J Nutr 2013; 1-8
67. Newgard CB. Interplay between lipids and branched-chain amino acids in development of insulin resistance. Cell Metab 2012; 15:606-614
68. Wang TJ, Larson MG, Vasan RS, et al. Metabolite profiles and the risk of developing diabetes. Nat Med 2011; 17:448-453
69. Floegel A, Stefan N, Yu Z, et al. Identification of serum metabolites associated with risk of type 2 diabetes using a targeted metabolomic approach. Diabetes 2013; 62:639-648
70. Koletzko B, Brands B, Poston L, et al. Early nutrition programming of long-Term health. Proc Nutr Soc 2012; 71:371-378