Quantifying Diet-Induced Metabolic Changes of the Human Gut Microbiome

Cell Metabolism

Volumn 22, Issue 2, 2015, Pages 320-331

  Shoaie, Saeed ^a   Ghaffari, Pouyan ^a   Kovatcheva Datchary, Petia ^b   Mardinoglu, Adil ^a   Sen, Partho ^a   Pujos Guillot, Estelle ^c   De Wouters, Tomas ^d   Juste, Catherine ^d   Rizkalla, Salwa ^e,f   Chilloux, Julien ^g   Hoyles, Lesley ^g   Nicholson, Jeremy K ^g   Dore, Joel ^d   Dumas, Marc E ^g   Clement, Karine ^e,f,h   Bäckhed, Fredrik ^b,i   Nielsen, Jens ^a  

^a CHALMERS UNIVERSITY OF TECHNOLOGY   (Sweden)

^b UNIVERSITY OF GOTHENBURG   (Sweden)

^c CEMAGREF   (France)

^d University of Paris Saclay   (France)

^e PITIÉ SALPÊTRIÈRE HOSPITAL   (France)

^f INSERM   (France)

^g IMPERIAL COLLEGE LONDON   (United Kingdom)

^h SORBONNE UNIVERSITÉ   (France)

ⁱ Capital Region   (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID;

AMINO ACID BLOOD LEVEL; ARTICLE; DIETARY INTAKE; FECES LEVEL; HUMAN; INTESTINE FLORA; MATHEMATICAL COMPUTING; MATHEMATICAL MODEL; METABOLOMICS; MICROBIAL COMMUNITY; MICROBIAL GENOME; MICROBIAL METABOLISM; NONHUMAN; OBESITY; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; SIMULATION; BACTERIUM; BIOLOGICAL MODEL; FEMALE; INTESTINE; MALE; METABOLISM; MICROBIOLOGY; MICROFLORA; PHYSIOLOGY;

BACTERIA; FEMALE; HUMANS; INTESTINES; MALE; MICROBIOTA; MODELS, BIOLOGICAL;

EID: 84938586730     PISSN: 15504131     EISSN: 19327420     Source Type: Journal    
DOI: 10.1016/j.cmet.2015.07.001     Document Type: Article

References (49)

1. R. Agren, L. Liu, S. Shoaie, W. Vongsangnak, I. Nookaew, and J. Nielsen The RAVEN toolbox and its use for generating a genome-scale metabolic model for Penicillium chrysogenum PLoS Comput. Biol. 9 2013 e1002980
2. D. Amaratunga, and J. Cabrera Analysis of data from viral DNA microchips J. Am. Stat. Assoc. 96 2001 1161 1170
3. F. Bäckhed, R.E. Ley, J.L. Sonnenburg, D.A. Peterson, and J.I. Gordon Host-bacterial mutualism in the human intestine Science 307 2005 1915 1920
4. A. Cotillard, S.P. Kennedy, L.C. Kong, E. Prifti, N. Pons, E. Le Chatelier, M. Almeida, B. Quinquis, F. Levenez, N. Galleron, et al. ANR MicroObes Consortium Dietary intervention impact on gut microbial gene richness Nature 500 2013 585 588
5. J.H. Cummings, and G.T. Macfarlane Colonic microflora: nutrition and health Nutrition 13 1997 476 478
6. L.A. David, C.F. Maurice, R.N. Carmody, D.B. Gootenberg, J.E. Button, B.E. Wolfe, A.V. Ling, A.S. Devlin, Y. Varma, M.A. Fischbach, and et al. Diet rapidly and reproducibly alters the human gut microbiome Nature 505 2014 559 563
7. D.R. Donohoe, N. Garge, X. Zhang, W. Sun, T.M. O'Connell, M.K. Bunger, and S.J. Bultman The microbiome and butyrate regulate energy metabolism and autophagy in the mammalian colon Cell Metab. 13 2011 517 526
8. I.E. El-Semman, F.H. Karlsson, S. Shoaie, I. Nookaew, T.H. Soliman, and J. Nielsen Genome-scale metabolic reconstructions of Bifidobacterium adolescentis L2-32 and Faecalibacterium prausnitzii A2-165 and their interaction BMC Syst. Biol. 8 2014 41
9. J. Fernandes, W. Su, S. Rahat-Rozenbloom, T.M. Wolever, and E.M. Comelli Adiposity, gut microbiota and faecal short chain fatty acids are linked in adult humans Nutr. Diabetes 4 2014 e121
10. P. Ghaffari, A. Mardinoglu, A. Asplund, S. Shoaie, C. Kampf, M. Uhlen, and J. Nielsen Identifying anti-growth factors for human cancer cell lines through genome-scale metabolic modeling Sci. Rep. 5 2015 8183
11. S. Greenblum, H.C. Chiu, R. Levy, R. Carr, and E. Borenstein Towards a predictive systems-level model of the human microbiome: progress, challenges, and opportunities Curr. Opin. Biotechnol. 24 2013 810 820
12. V. Grimm, E. Revilla, U. Berger, F. Jeltsch, W.M. Mooij, S.F. Railsback, H.H. Thulke, J. Weiner, T. Wiegand, and D.L. DeAngelis Pattern-oriented modeling of agent-based complex systems: lessons from ecology Science 310 2005 987 991
13. W.R. Harcombe, W.J. Riehl, I. Dukovski, B.R. Granger, A. Betts, A.H. Lang, G. Bonilla, A. Kar, N. Leiby, P. Mehta, and et al. Metabolic resource allocation in individual microbes determines ecosystem interactions and spatial dynamics Cell Rep. 7 2014 1104 1115
14. C.S. Henry, M. DeJongh, A.A. Best, P.M. Frybarger, B. Linsay, and R.L. Stevens High-throughput generation, optimization and analysis of genome-scale metabolic models Nat. Biotechnol. 28 2010 977 982
15. C. Huttenhower, D. Gevers, R. Knight, S. Abubucker, J.H. Badger, A.T. Chinwalla, H.H. Creasy, A.M. Earl, M.G. FitzGerald, R.S. Fulton, et al. Human Microbiome Project Consortium Structure, function and diversity of the healthy human microbiome Nature 486 2012 207 214
16. F.H. Karlsson, V. Tremaroli, I. Nookaew, G. Bergström, C.J. Behre, B. Fagerberg, J. Nielsen, and F. Bäckhed Gut metagenome in European women with normal, impaired and diabetic glucose control Nature 498 2013 99 103
17. E. Le Chatelier, T. Nielsen, J. Qin, E. Prifti, F. Hildebrand, G. Falony, M. Almeida, M. Arumugam, J.M. Batto, S. Kennedy, et al. MetaHIT Consortium Richness of human gut microbiome correlates with metabolic markers Nature 500 2013 541 546
18. P. Louis, P. Young, G. Holtrop, and H.J. Flint Diversity of human colonic butyrate-producing bacteria revealed by analysis of the butyryl-CoA:acetate CoA-transferase gene Environ. Microbiol. 12 2010 304 314
19. G.T. Macfarlane, C. Allison, S.A. Gibson, and J.H. Cummings Contribution of the microflora to proteolysis in the human large intestine J. Appl. Bacteriol. 64 1988 37 46
20. O. Manor, R. Levy, and E. Borenstein Mapping the inner workings of the microbiome: genomic- and metagenomic-based study of metabolism and metabolic interactions in the human microbiome Cell Metab. 20 2014 742 752
21. A. Mardinoglu, and J. Nielsen New paradigms for metabolic modeling of human cells Curr. Opin. Biotechnol. 34C 2015 91 97
22. A. Mardinoglu, R. Agren, C. Kampf, A. Asplund, M. Uhlen, and J. Nielsen Genome-scale metabolic modelling of hepatocytes reveals serine deficiency in patients with non-alcoholic fatty liver disease Nat. Commun. 5 2014 3083
23. J.M. Monk, P. Charusanti, R.K. Aziz, J.A. Lerman, N. Premyodhin, J.D. Orth, A.M. Feist, and B.O. Palsson Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments Proc. Natl. Acad. Sci. USA 110 2013 20338 20343
24. J. Monk, J. Nogales, and B.O. Palsson Optimizing genome-scale network reconstructions Nat. Biotechnol. 32 2014 447 452
25. D.O. Mook-Kanamori, W. Römisch-Margl, G. Kastenmüller, C. Prehn, A.K. Petersen, T. Illig, C. Gieger, R. Wang-Sattler, C. Meisinger, A. Peters, and et al. Increased amino acids levels and the risk of developing of hypertriglyceridemia in a 7-year follow-up J. Endocrinol. Invest. 37 2014 369 374
26. E.P.J.G. Neis, C.H.C. Dejong, and S.S. Rensen The role of microbial amino acid metabolism in host metabolism Nutrients 7 2015 2930 2946
27. C.B. Newgard, J. An, J.R. Bain, M.J. Muehlbauer, R.D. Stevens, L.F. Lien, A.M. Haqq, S.H. Shah, M. Arlotto, C.A. Slentz, and et al. A branched-chain amino acid-related metabolic signature that differentiates obese and lean humans and contributes to insulin resistance Cell Metab. 9 2009 311 326
28. J.K. Nicholson, E. Holmes, J. Kinross, R. Burcelin, G. Gibson, W. Jia, and S. Pettersson Host-gut microbiota metabolic interactions Science 336 2012 1262 1267
29. P. Pavlidis Using ANOVA for gene selection from microarray studies of the nervous system Methods 31 2003 282 289
30. N. Qin, F. Yang, A. Li, E. Prifti, Y. Chen, L. Shao, J. Guo, E. Le Chatelier, J. Yao, L. Wu, and et al. Alterations of the human gut microbiome in liver cirrhosis Nature 513 2014 59 64
31. B.S. Samuel, A. Shaito, T. Motoike, F.E. Rey, F. Backhed, J.K. Manchester, R.E. Hammer, S.C. Williams, J. Crowley, M. Yanagisawa, and J.I. Gordon Effects of the gut microbiota on host adiposity are modulated by the short-chain fatty-acid binding G protein-coupled receptor, Gpr41 Proc. Natl. Acad. Sci. USA 105 2008 16767 16772
32. S. Shoaie, and J. Nielsen Elucidating the interactions between the human gut microbiota and its host through metabolic modeling Front. Genet. 5 2014 86
33. S. Shoaie, F. Karlsson, A. Mardinoglu, I. Nookaew, S. Bordel, and J. Nielsen Understanding the interactions between bacteria in the human gut through metabolic modeling Sci. Rep. 3 2013 2532
34. E.A. Smith, and G.T. Macfarlane Enumeration of amino acid fermenting bacteria in the human large intestine: effects of pH and starch on peptide metabolism and dissimilation of amino acids FEMS Microbiol. Ecol. 25 1998 355 368
35. C.A. Smith, E.J. Want, G. O'Maille, R. Abagyan, and G. Siuzdak XCMS: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification Anal. Chem. 78 2006 779 787
36. M.I. Smith, T. Yatsunenko, M.J. Manary, I. Trehan, R. Mkakosya, J. Cheng, A.L. Kau, S.S. Rich, P. Concannon, J.C. Mychaleckyj, and et al. Gut microbiomes of Malawian twin pairs discordant for kwashiorkor Science 339 2013 548 554
37. P.M. Smith, M.R. Howitt, N. Panikov, M. Michaud, C.A. Gallini, M. Bohlooly-Y, J.N. Glickman, and W.S. Garrett The microbial metabolites, short-chain fatty acids, regulate colonic Treg cell homeostasis Science 341 2013 569 573
38. R. Tautenhahn, K. Cho, W. Uritboonthai, Z. Zhu, G.J. Patti, and G. Siuzdak An accelerated workflow for untargeted metabolomics using the METLIN database Nat. Biotechnol. 30 2012 826 828
39. G. Tolhurst, H. Heffron, Y.S. Lam, H.E. Parker, A.M. Habib, E. Diakogiannaki, J. Cameron, J. Grosse, F. Reimann, and F.M. Gribble Short-chain fatty acids stimulate glucagon-like peptide-1 secretion via the G-protein-coupled receptor FFAR2 Diabetes 61 2012 364 371
40. V. Tremaroli, and F. Bäckhed Functional interactions between the gut microbiota and host metabolism Nature 489 2012 242 249
41. A.W. Walker, J. Ince, S.H. Duncan, L.M. Webster, G. Holtrop, X. Ze, D. Brown, M.D. Stares, P. Scott, A. Bergerat, and et al. Dominant and diet-responsive groups of bacteria within the human colonic microbiota ISME J. 5 2011 220 230
42. T.J. Wang, M.G. Larson, R.S. Vasan, S. Cheng, E.P. Rhee, E. McCabe, G.D. Lewis, C.S. Fox, P.F. Jacques, C. Fernandez, and et al. Metabolite profiles and the risk of developing diabetes Nat. Med. 17 2011 448 453
43. D.S. Wishart, T. Jewison, A.C. Guo, M. Wilson, C. Knox, Y. Liu, Y. Djoumbou, R. Mandal, F. Aziat, E. Dong, and et al. HMDB 3.0 - The Human Metabolome Database in 2013 Nucleic Acids Res. 41 2013 D801 D807
44. G. Wu Amino acids: metabolism, functions, and nutrition Amino Acids 37 2009 1 17
45. G.D. Wu, J. Chen, C. Hoffmann, K. Bittinger, Y.Y. Chen, S.A. Keilbaugh, M. Bewtra, D. Knights, W.A. Walters, R. Knight, and et al. Linking long-term dietary patterns with gut microbial enterotypes Science 334 2011 105 108
46. G.D. Wu, C. Compher, E.Z. Chen, S.A. Smith, R.D. Shah, K. Bittinger, C. Chehoud, L.G. Albenberg, L. Nessel, E. Gilroy, and et al. Comparative metabolomics in vegans and omnivores reveal constraints on diet-dependent gut microbiota metabolite production Gut 2014 10.1136/gutjnl-2014-308209 Published online November 26, 2014
47. X. Ze, S.H. Duncan, P. Louis, and H.J. Flint Ruminococcus bromii is a keystone species for the degradation of resistant starch in the human colon ISME J. 6 2012 1535 1543
48. G. Zeller, J. Tap, A.Y. Voigt, S. Sunagawa, J.R. Kultima, P.I. Costea, A. Amiot, J. Böhm, F. Brunetti, N. Habermann, and et al. Potential of fecal microbiota for early-stage detection of colorectal cancer Mol. Syst. Biol. 10 2014 766
49. A.R. Zomorrodi, and C.D. Maranas OptCom: a multi-level optimization framework for the metabolic modeling and analysis of microbial communities PLoS Comput. Biol. 8 2012 e1002363