Nutritional metabolomics: Progress in addressing complexity in diet and health

Annual Review of Nutrition

Volumn 32, Issue , 2012, Pages 183-202

  Jones, Dean P ^a   Park, Youngja ^a   Ziegler, Thomas R ^a  

^a EMORY UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Exposome; Mass spectrometry; Microbiome; Personalized medicine; Prevention; Systems biology

Indexed keywords

ARTIFICIAL INTELLIGENCE; BIOINFORMATICS; DIET; EPIGENETICS; FOOD; GENOMICS; HEALTH ECONOMICS; HUMAN; METABOLOME; METABOLOMICS; MICROBIOME; NONHUMAN; NUTRITION; PHENOTYPE; PRIORITY JOURNAL; REVIEW;

ARTIFICIAL INTELLIGENCE; COMPUTATIONAL BIOLOGY; DIET; HEALTH PROMOTION; HUMANS; INDIVIDUALIZED MEDICINE; METABOLOME; METABOLOMICS; NUTRITIONAL SCIENCES;

EID: 84864223921     PISSN: 01999885     EISSN: 15454312     Source Type: Book Series    
DOI: 10.1146/annurev-nutr-072610-145159     Document Type: Review

References (101)

1. Alcock RE, Halsall CJ, Harris CA, Johnston AE, Lead WA, et al. 1994. Contamination of environmental samples prepared for PCB analysis. Environ. Sci. Technol. 28:1838-42 (Pubitemid 24326085)
2. Argov Z, Chance B. 1991. Phosphorus magnetic resonance spectroscopy in nutritional research. Annu. Rev. Nutr. 11:449-64 (Pubitemid 21903839)
3. Bais P, Moon SM, He K, Leitao R, Dreher K, et al. 2010. PlantMetabolomics.org: a web portal for plant metabolomics experiments. Plant Physiol. 152:1807-16
4. Bang JW, Crockford DJ, Holmes E, Pazos F, Sternberg MJ, et al. 2008. Integrative top-down system metabolic modeling in experimental disease states via data-driven Bayesian methods. J. Proteome Res. 7:497-503 (Pubitemid 351297668)
5. Benjamini Y, Hochberg Y. 1995. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Statist. Soc. B 57:289-300
6. Beste DJ, Bonde B, Hawkins N, Ward JL, Beale MH, et al. 2011. 13C metabolic flux analysis identifies an unusual route for pyruvate dissimilation in mycobacteria which requires isocitrate lyase and carbon dioxide fixation. PLoS Pathog. 7:e1002091
7. Brown SD, Tauler R, Walczak B, eds. 2009. Comprehensive Chemometrics: Chemical and Biochemical Data Analysis. Amsterdam: Elsevier
8. Caspi R, Altman T, Dale JM, Dreher K, Fulcher CA, et al. 2010. The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res. 38:D473-79
9. Ceglarek U, Leichtle A, Brugel M, Kortz L, Brauer R, et al. 2009. Challenges and developments in tandem mass spectrometry based clinical metabolomics. Mol. Cell Endocrinol. 301:266-71
10. Cent. Disease Control Prev. 2011. Fourth National Report on Human Exposure to Environmental Chemicals: Updated Tables. Atlanta, GA: Natl. Cent. Environ. Health, Cent. Disease Control Prev.
11. 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. 20:557-66
12. Clayton TA, BakerD, Lindon JC, Everett JR, Nicholson JK. 2009. Pharmacometabonomic identification of a significant host-microbiome metabolic interaction affecting human drug metabolism. Proc. Natl. Acad. Sci. USA 106:14728-33
13. Corte L, Rellini P, Roscini L, Fatichenti F, Cardinali G. Corte L, Rellini P, Roscini L, Fatichenti F, Cardinali G. 2010. Development of a novel, FTIR (Fourier transform infrared spectroscopy) based, yeast bioassay for toxicity testing and stress response study. Anal. Chim. Acta 659:258-65
14. de Mul M, Alons P, van der Velde P, Konings I, Bakker J, Hazelzet J. 2012. Development of a clinical data warehouse from an intensive care clinical information system. Comput. Methods Programs Biomed. 105:22-30
15. Deo RC, Hunter L, Lewis GD, Pare G, Vasan RS, et al. 2010. Interpreting metabolomic profiles using unbiased pathway models. PLoS Comput. Biol. 6:e1000692
16. Dixon RA, Gang DR, Charlton AJ, Fiehn O, Kuiper HA, et al. 2006. Applications of metabolomics in agriculture. J. Agric. Food Chem. 54:8984-94 (Pubitemid 44953593)
17. Draper J, Enot DP, Parker D, Beckmann M, Snowdon S, et al. 2009. Metabolite signal identification in accurate mass metabolomics data with MZedDB, an interactive m/z annotation tool utilising predicted ionisation behaviour "rules." BMC Bioinformatics 10:227
18. Duarte NC, Herrgard MJ, Palsson BO. 2004. Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model. Genome Res. 14:1298-309 (Pubitemid 39036129)
19. Faith JJ, McNulty NP, Rey FE, Gordon JI. 2011. Predicting a human gut microbiota's response to diet in gnotobiotic mice. Science 333:101-4
20. Feist AM, Palsson BO. 2008. The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli. Nat. Biotechnol. 26:659-67 (Pubitemid 351824691)
21. Felig P, Kim YJ, Lynch V, Hendler R. 1972. Amino acid metabolism during starvation in human pregnancy. J. Clin. Invest. 51:1195-202
22. Ferrara CT, Wang P, Neto EC, Stevens RD, Bain JR, et al. 2008. Genetic networks of liver metabolism revealed by integration of metabolic and transcriptional profiling. PLoS Genet. 4:e1000034
23. Fiehn O, Barupal DK, Kind T. 2011. Extending biochemical databases by metabolomic surveys. J. Biol. Chem. 286:23637-43
24. Finkel T. 2003. Oxidant signals and oxidative stress. Curr. Opin. Cell Biol. 15:247-54 (Pubitemid 36332201)
25. Flamini R. 2003. Mass spectrometry in grape and wine chemistry. Part I: polyphenols. Mass Spectrom. Rev. 22:218-50
26. German JB, Bauman DE, Burrin DG, Failla ML, Freake HC, et al. 2004. Metabolomics in the opening decade of the 21st century: building the roads to individualized health. J. Nutr. 134:2729-32 (Pubitemid 39315280)
27. German JB, RobertsMA, Watkins SM. 2003. Genomics andmetabolomics as markers for the interaction of diet and health: lessons from lipids. J. Nutr. 133:2078-83S
28. German JB, Roberts MA, Watkins SM. 2003. Personal metabolomics as a next generation nutritional assessment. J. Nutr. 133:4260-66 (Pubitemid 37505511)
29. Gibney MJ, WalshM, Brennan L, Roche HM, German B, van Ommen B. 2005. Metabolomics in human nutrition: opportunities and challenges. Am. J. Clin. Nutr. 82:497-503
30. Go EP. 2010. Database resources in metabolomics: an overview. J. Neuroimmune Pharmacol. 5:18-30
31. Goldberger AL. 1990. Fractal electrodynamics of the heartbeat. Ann. N. Y. Acad. Sci. 591:402-9 (Pubitemid 20255857)
32. Goldberger AL, Amaral LA, Hausdorff JM, Ivanov P, Peng CK, Stanley HE. 2002. Fractal dynamics in physiology: alterations with disease and aging. Proc. Natl. Acad. Sci. USA 99(Suppl. 1):2466-72 (Pubitemid 34165052)
33. Goodacre R, Vaidyanathan S, Dunn WB, Harrigan GG, Kell DB. 2004. Metabolomics by numbers: acquiring and understanding global metabolite data. Trends Biotechnol. 22:245-52 (Pubitemid 38515742)
34. Goodman M, Bostick RM, Kucuk O, Jones DP. 2011. Clinical trials of antioxidants as cancer prevention agents: past, present, and future. Free Radic. Biol. Med. 51:1068-84
35. Gremse M, Chang A, Schomburg I, Grote A, Scheer M, et al. 2011. The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of all organisms for enzyme sources. Nucleic Acids Res. 39:D507-13
36. Grimaldi D, Claessens YE, Mira JP, Chiche JD. 2009. Beyond clinical phenotype: the biologic integratome. Crit. Care Med. 37:S38-49
37. Hall RD, Brouwer ID, Fitzgerald MA. 2008. Plantmetabolomics and its potential application for human nutrition. Physiol. Plant 132:162-75
38. Hammarqvist F, Andersson K, Luo JL, Wernerman J. 2005. Free amino acid and glutathione concentrations in muscle during short-term starvation and refeeding. Clin. Nutr. 24:236-4339.
39. Harkewicz R, Dennis EA. 2011. Applications of mass spectrometry to lipids and membranes. Annu. Rev. Biochem. 80:301-25
40. Hertkorn N, Ruecker C, Meringer M, Gugisch R, Frommberger M, et al. 2007. High-precision frequencymeasurements: indispensable tools at the core of themolecular-level analysis of complex systems. Anal. Bioanal. Chem. 389:1311-27 (Pubitemid 350023659)
41. Hiller K, Metallo CM, Kelleher JK, Stephanopoulos G. 2010. Nontargeted elucidation of metabolic pathways using stable-isotope tracers and mass spectrometry. Anal. Chem. 82:6621-28
42. InouyeM, Kettunen J, Soininen P, Silander K, Ripatti S, et al. 2010. Metabonomic, transcriptomic, and genomic variation of a population cohort. Mol. Syst. Biol. 6:441
43. Ivanov PC, Amaral LA, Goldberger AL, Havlin S, RosenblumMG, et al. 1999. Multifractality in human heartbeat dynamics. Nature 399:461-65 (Pubitemid 29258850)
44. Johnson JM, Strobel FH, Reed M, Pohl J, Jones DP. 2008. A rapid LC-FTMS method for the analysis of cysteine, cystine and cysteine/cystine steady-state redox potential in human plasma. Clin. Chim. Acta 396:43-48
45. Johnson JM, Yu T, Strobel FH, Jones DP. 2010. A practical approach to detect unique metabolic patterns for personalized medicine. Analyst 135:2864-70
46. Jones DP. 2006. Redefining oxidative stress. Antioxid. Redox Signal. 8:1865-79 (Pubitemid 44726359)
47. Jung YY, Park Y, Jones DP, Ziegler TR, Vidakovic B. 2010. Self-similarity in NMR spectra: an application in assessing the level of cysteine. J. Data Sci. 8:1-19
48. Kanehisa M, Goto S. 2000. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 28:27-30 (Pubitemid 30047706)
49. Karp PD, Caspi R. 2011. A survey of metabolic databases emphasizing the MetaCyc family. Arch. Toxicol. 85:1015-33
50. Keith LH, Crummett W, Deegan J, Libby RA, Taylor JK, WentlerG. 1983. Principles of environmental analysis. Anal. Chem. 55:2210-18 (Pubitemid 14175202)
51. Kensler TW, Wakabayashi N, Biswal S. 2007. Cell survival responses to environmental stresses via the Keap1-Nrf2-ARE pathway. Annu. Rev. Pharmacol. Toxicol. 47:89-116
52. Kind T, Scholz M, Fiehn O. 2009. How large is the metabolome? A critical analysis of data exchange practices in chemistry. PLoS One 4:e5440
53. Kraly JR, Holcomb RE, Guan Q, Henry CS. 2009. Review: microfluidic applications in metabolomics and metabolic profiling. Anal. Chim. Acta 653:23-35
54. Kristal BS, Shurubor YI, Kaddurah-Daouk R, Matson WR. 2007. High-performance liquid chromatography separations coupled with coulometric electrode array detectors: a unique approach to metabolomics. Methods Mol. Biol. 358:159-74
55. Kwan D, Bartle WR, Walker SE. 1995. Abnormal serum transaminases following therapeutic doses of acetaminophen in the absence of known risk factors. Dig. Dis. Sci. 40:1951-55
56. Loscalzo J, Kohane I, Barabasi AL. 2007. Human disease classification in the postgenomic era: a complex systems approach to human pathobiology. Mol. Syst. Biol. 3:124
57. Marrero J, Rhee KY, Schnappinger D, PetheK, Ehrt S. 2010. Gluconeogenic carbon flow of tricarboxylic acid cycle intermediates is critical for Mycobacterium tuberculosis to establish and maintain infection. Proc. Natl. Acad. Sci. USA 107:9819-2462
58. Marshall AG, Hendrickson CL. 2008. High-resolution mass spectrometers. Annu. Rev. Anal. Chem. 1:579-99
59. Martin FP, Dumas ME, Wang Y, Legido-Quigley C, Yap IK, et al. 2007. A top-down systems biology view of microbiome-mammalian metabolic interactions in a mouse model. Mol. Syst. Biol. 3:112
60. Moore S, SpackmanDH, SteinWH.1958. Automatic recording apparatus for use in the chromatography of amino acids. Fed. Proc. 17:1107-15
61. Muegge BD, Kuczynski J, Knights D, Clemente JC, Gonzalez A, et al. 2011. Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans. Science 332:970-74
62. Nakanishi Y, Fukuda S, Chikayama E, Kimura Y, Ohno H, Kikuchi J. 2011. Dynamic omics approach identifies nutrition-mediated microbial interactions. J. Proteome Res. 10:824-36
63. Neveu V, Perez-Jimenez J, Vos F, Crespy V, du Chaffaut L, et al. 2010. Phenol-Explorer: an online comprehensive database on polyphenol contents in foods. Database (Oxford) 2010:bap024
64. Nicholson JK, Foxall PJ, Spraul M, Farrant RD, Lindon JC. 1995. 750 MHz 1H and 1H-13C NMR spectroscopy of human blood plasma. Anal. Chem. 67:793-811
65. Otten JJ, Hellwig JP, Meyers LD. 2006. DRI, Dietary Reference Intakes: The Essential Guide to Nutrient Requirements.Washington, DC: Natl. Acad. Press
66. Park Y, Jones DP, Ziegler TR, Lee K, Kotha K, et al. 2011. Metabolic effects of albumin therapy in acute lung injury measured by proton nuclear magnetic resonance spectroscopy of plasma: a pilot study. Crit. Care Med. 39:2308-13
67. Park Y, Kim SB, Wang B, Blanco RA, LeNA, et al. 2009. Individual variation inmacronutrient regulation measured by proton magnetic resonance spectroscopy of human plasma. Am. J. Physiol. Regul. Integr. Comp. Physiol. 297:R202-9
68. Park Y, Le NA, Yu T, Strobel F, Gletsu-Miller N, et al. 2011. A sulfur amino acid-free meal increases plasma lipids in humans. J. Nutr. 141:1424-31
69. Park Y, Lee K, SoltowQA, Strobel FH, Brigham KL, et al. 2012. High-performance metabolic profiling of plasma from seven mammalian species for simultaneous environmental chemical surveillance and bioeffect monitoring. Toxicology. In press
70. Park Y, Zhao T, Miller NG, Kim SB, Accardi CJ, et al. 2012. Sulfur amino acid-free diet results in increased glutamate in humanmidbrain: a pilotmagnetic resonance spectroscopic study. Nutrition 28:235-41 75. Rappaport SM. 2010. Implications of the exposome for exposure science. J. Expo. Sci. Environ. Epidemiol. 21:5-9
71. Rezzi S, Ramadan Z, Fay LB, Kochhar S. 2007. Nutritionalmetabonomics: applications and perspectives. J. Proteome Res. 6:513-25
72. Sandhu AK, Gu L. 2010. Antioxidant capacity, phenolic content, and profiling of phenolic compounds in the seeds, skin, and pulp of Vitis rotundifolia (muscadine grapes) as determined by HPLC-DAD-ESIMS( n). J. Agric. Food Chem. 58:4681-92
73. Sansone SA, Fan T, Goodacre R, Griffin JL, Hardy NW, et al. 2007. The metabolomics standards initiative. Nat. Biotechnol. 25:846-48
74. Scalbert A, Brennan L, Fiehn O, Hankemeier T, Kristal BS, et al. 2009. Mass-spectrometry-based metabolomics: limitations and recommendations for future progress with particular focus on nutrition research. Metabolomics 5:435-58
75. Scheer M, GroteA, Chang A, Schomburg I, Munaretto C, et al. 2011.BRENDA, the enzyme information system in 2011. Nucleic Acids Res. 39:D670-76
76. Schreiber F, Colmsee C, Czauderna T, Grafahrend-Belau E, Hartmann A, et al. 2012. MetaCrop 2.0: managing and exploring information about crop plant metabolism. Nucleic Acids Res. 40:D1173-77
77. Smith CA, O'Maille G, Want EJ, Qin C, Trauger SA, et al. 2005. METLIN: a metabolite mass spectral database. Ther. Drug Monit. 27:747-51 (Pubitemid 44391729)
78. Soga T, Igarashi K, Ito C, Mizobuchi K, Zimmermann HP, Tomita M. 2009. Metabolomic profiling of anionic metabolites by capillary electrophoresis mass spectrometry. Anal. Chem. 81:6165-74
79. Soltow QA, Strobel FH, Mansfield KG, Wachtman L, Park Y, Jones DP. 2011. High-performance metabolic profiling with dual chromatography-Fourier-transform mass spectrometry (DC-FTMS) for study of the exposome. Metabolomics. doi: 10.1007/s11306-011-0332-185.
80. Stone EA, Ayroles JF. 2009. Modulated modularity clustering as an exploratory tool for functional genomic inference. PLoS Genet. 5:e1000479 86. Storey JD. 20003. The positive false discovery rate: a Bayesian interpretation and the q-value. Ann. Statist. 31:2013-35
81. Stringer KA, Serkova NJ, Karnovsky A, Guire K, Paine R 3rd, Standiford TJ. 2011. Metabolic consequences of sepsis-induced acute lung injury revealed by plasma 1H-nuclear magnetic resonance quantitative metabolomics and computational analysis. Am. J. Physiol. Lung. Cell Mol. Physiol. 300:L4-11
82. U.S. Dep. Agric. 2010. Dietary Guidelines for Americans. Washington, DC: US Gov. Print. Off.
83. Voit E, Neves AR, Santos H. 2006. The intricate side of systems biology. Proc. Natl. Acad. Sci. USA 103:9452-57
84. Voit EO, Brigham KL. 2008. The role of systems biology in predictive health and personalizedmedicine. Open Pathol. J. 2:68-70
85. Voit EO, Qi Z, Miller GW. 2008. Steps of modeling complex biological systems. Pharmacopsychiatry 41(Suppl. 1):S78-84
86. Voit EO, Radivoyevitch T. 2000. Biochemical systems analysis of genome-wide expression data. Bioinformatics 16:1023-37 (Pubitemid 32051016)
87. Walsh MC, Brennan L, Malthouse JP, Roche HM, Gibney MJ. 2006. Effect of acute dietary standardization on the urinary, plasma, and salivary metabolomic profiles of healthy humans. Am. J. Clin. Nutr. 84:531-39 (Pubitemid 44713402)
88. Wang TJ, Larson MG, Vasan RS, Cheng S, Rhee EP, et al. 2011. Metabolite profiles and the risk of developing diabetes. Nat. Med. 17:448-53
89. Wang Z, Klipfell E, Bennett BJ, Koeth R, Levison BS, et al. 2011. Gut florametabolism of phosphatidylcholine promotes cardiovascular disease. Nature 472:57-63
90. Want EJ, Wilson ID, Gika H, Theodoridis G, Plumb RS, et al. 2010. Global metabolic profiling procedures for urine using UPLC-MS. Nat. Protoc. 5:1005-18
91. Weng C, Bigger JT, Busacca L, Wilcox A, Getaneh A. 2010. Comparing the effectiveness of a clinical registry and a clinical data warehouse for supporting clinical trial recruitment: a case study. AMIA Annu. Symp. Proc. 2010:867-71
92. Whitfield PD, German AJ, Noble PJ. 2004. Metabolomics: an emerging post-genomic tool for nutrition. Br. J. Nutr. 92:549-55 (Pubitemid 39406637)
93. Wikoff WR, Anfora AT, Liu J, Schultz PG, Lesley SA, et al. 2009. Metabolomics analysis reveals large effects of gut microflora on mammalian blood metabolites. Proc. Natl. Acad. Sci. USA 106:3698-703
94. Wild CP. 2005. Complementing the genome with an "exposome": the outstanding challenge of environmental exposuremeasurement in molecular epidemiology. Cancer Epidemiol. Biomarkers Prev. 14:1847-50 (Pubitemid 41161186)
95. Wishart DS. 2008. Metabolomics: applications to food science and nutrition research. Trends Food Sci. Technol. 19:482-93 (Pubitemid 352004154)
96. Wishart DS, Knox C, Guo AC, Eisner R, YoungN, et al. 2009. HMDB: a knowledgebase for the human metabolome. Nucleic Acids Res. 37:D603-10
97. Wopereis S, Rubingh CM, van Erk MJ, Verheij ER, van Vliet T, et al. 2009. Metabolic profiling of the response to an oral glucose tolerance test detects subtle metabolic changes. PLoS One 4:e4525
98. Yu T, Park Y, Johnson JM, Jones DP. 2009. apLCMS-adaptive processing of high-resolution LC/MS data. Bioinformatics 25:1930-36
99. Zapletal E, Rodon N, Grabar N, Degoulet P. 2010. Methodology of integration of a clinical data warehouse with a clinical information system: the HEGP case. Stud. Health Technol. Inform. 160:193-97
100. Zeisel SH, Freake HC, Bauman DE, Bier DM, Burrin DG, et al. 2005. The nutritional phenotype in the age of metabolomics. J. Nutr. 135:1613-16 (Pubitemid 40980706)
101. Zhao Q, Wang D, Jayawardhana DA, Guan X. 2008. Stochastic sensing of biomolecules in a nanopore sensor array. Nanotechnology 19:505504