Metabolic modeling of common Escherichia coli strains in human gut microbiome

BioMed Research International

Volumn 2014, Issue , 2014, Pages

  Gao, Yue Dong ^a   Zhao, Yuqi ^a   Huang, Jingfei ^a,b  

^a KUNMING INSTITUTE OF ZOOLOGY   (China)

^b CHINESE UNIVERSITY OF HONG KONG   (Hong Kong)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIAL GENE; BACTERIAL METABOLISM; BACTERIAL STRAIN; BIOMASS PRODUCTION; CARBON SOURCE; COMPUTER MODEL; ESCHERICHIA COLI; GENETIC VARIABILITY; GROWTH RATE; HOST PATHOGEN INTERACTION; HUMAN; INTESTINE FLORA; NONHUMAN; OBESITY; PHENOTYPE; SEQUENCE ANALYSIS; BACTERIAL GENOME; BIOLOGICAL MODEL; GASTROINTESTINAL TRACT; GENETICS; HIGH THROUGHPUT SEQUENCING; METABOLISM; MICROBIOLOGY; MICROFLORA; PATHOGENICITY;

ESCHERICHIA COLI; GASTROINTESTINAL TRACT; GENOME, BACTERIAL; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; METABOLIC NETWORKS AND PATHWAYS; MICROBIOTA; MODELS, BIOLOGICAL;

EID: 84929057178     PISSN: 23146133     EISSN: 23146141     Source Type: Journal    
DOI: 10.1155/2014/694967     Document Type: Article

References (46)

1. P. B. Eckburg, E. M. Bik, C. N. Bernstein et al. , "Microbiology: diversity of the human intestinal microbial flora, " Science, vol. 308, no. 5728, pp. 1635-1638, 2005.
2. G. Reid, J. Howard, and B. S. Gan, "Can bacterial interference prevent infection?" Trends inMicrobiology, vol. 9, no. 9, pp. 424-428, 2001.
3. D. McCloskey, B. O. Palsson, and A. M. Feist, "Basic andapplied uses of genome-scale metabolic network reconstructions of Escherichia coli, " Molecular Systems Biology, vol. 9, no. 1, article 661, 2013.
4. S. Nakamura, T. Nakaya, and T. Iida, "Metagenomic analysis of bacterial infections by means of high-throughput DNA sequencing, " Experimental Biology and Medicine, vol. 236, no. 8, pp. 968-971, 2011.
5. M. S. Donia and M. A. Fischbach, "Dyeing to learnmore about the gut microbiota, " Cell Host and Microbe, vol. 13, no. 2, pp. 119-120, 2013.
6. L. Rup, "The human microbiome project, " Indian Journal of Microbiology, vol. 52, no. 3, p. 315, 2012.
7. P. J. Turnbaugh, R. E. Ley, M. Hamady, C. M. Fraser-Liggett, R. Knight, and J. I. Gordon, "The human microbiome project, " Nature, vol. 449, no. 7164, pp. 804-810, 2007.
8. S. A. Jones, F. Z. Chowdhury, A. J. Fabich et al. , "Respiration of Escherichia coli in themouse intestine, " Infection and Immunity, vol. 75, no. 10, pp. 4891-4899, 2007.
9. S. E. Winter, M. G. Winter, M. N. Xavier et al. , "Host-derived nitrate boosts growth of E. coli in the inflamed gut, " Science, vol. 339, no. 6120, pp. 708-711, 2013.
10. I. Cho and M. J. Blaser, "The human microbiome: at the interface of health and disease, " Nature Reviews Genetics, vol. 13, no. 4, pp. 260-270, 2012.
11. C. Huttenhower, D. Gevers, R. Knight et al. , "Structure, function and diversity of the healthy human microbiome, " Nature, vol. 486, no. 7402, pp. 207-214, 2012.
12. C. F. Maurice, H. J. Haiser, and P. J. Turnbaugh, "Xenobiotics shape the physiology and gene expression of the active human gut microbiome, " Cell, vol. 152, no. 1-2, pp. 39-50, 2013.
13. A. Heinken, S. Sahoo, R. M. Fleming, and I. Thiele, "Systemslevel characterization of a host-microbe metabolic symbiosis in themammalian gut, " GutMicrobes, vol. 4, no. 1, pp. 28-40, 2013.
14. S. Shoaie, F. Karlsson, A. Mardinoglu, I. Nookaew, S. Bordel, and J. Nielsen, "Understanding the interactions between bacteria in the human gut through metabolicmodeling, " Scientific Reports, vol. 3, article 2532, 2013.
15. C. Lozupone, K. Faust, J. Raes et al. , "Identifying genomic and metabolic features that can underlie early successional and opportunistic lifestyles of human gut symbionts, " Genome Research, vol. 22, no. 10, pp. 1974-1984, 2012.
16. Y. Q. Zhao and J. F. Huang, "Reconstruction and analysis of human heart-specific metabolic network based on transcriptome and proteome data, " Biochemical and Biophysical Research Communications, vol. 415, no. 3, pp. 450-454, 2011.
17. J. Zhao, C. Geng, L. Tao et al. , "Reconstruction and analysis of human liver-specific metabolic network based on CNHLPP data, " Journal of Proteome Research, vol. 9, no. 4, pp. 1648-1658, 2010.
18. K. Yizhak, T. Benyamini, W. Liebermeister, E. Ruppin, and T. Shlomi, "Integrating quantitative proteomics and metabolomics with a genome-scalemetabolic networkmodel, " Bioinformatics, vol. 26, no. 12, pp. i255-i260, 2010.
19. B. A. Methe, K. E. Nelson, M. Pop et al. , "A framework for human microbiome research, " Nature, vol. 486, no. 7402, pp. 215-221, 2012.
20. D. J. Baumler, R. G. Peplinski, J. L. Reed, J. D. Glasner, and N. T. Perna, "The evolution ofmetabolic networks of E. coli, " BMC Systems Biology, vol. 5, article 182, 2011.
21. S. A. Becker and B. O. Palsson, "Context-specific metabolic networks are consistentwith experiments, " PLoS Computational Biology, vol. 4, no. 5, Article ID e1000082, 2008.
22. H. Zur, E. Ruppin, and T. Shlomi, "iMAT: an integrative metabolic analysis tool, " Bioinformatics, vol. 26, no. 24, pp. 3140-3142, 2010.
23. J. D. Orth, I. Thiele, and B. O. Palsson, "What is flux balance analysis?" Nature Biotechnology, vol. 28, no. 3, pp. 245-248, 2010.
24. A. M. Feist, C. S. Henry, J. L. Reed et al. , "A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information, " Molecular Systems Biology, vol. 3, article 121, 2007.
25. S. A. Becker, A. M. Feist, M. L. Mo, G. Hannum, B. O. Palsson, and M. J. Herrgard, "Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox, " Nature Protocols, vol. 2, no. 3, pp. 727-738, 2007.
26. R. Mahadevan and C. H. Schilling, "The effects of alternate optimal solutions in constraint-based genome-scale metabolic models, "Metabolic Engineering, vol. 5, no. 4, pp. 264-276, 2003.
27. S. L. Chen, M. Wu, J. P. Henderson et al. , "Genomic diversity and fitness of E. coli strains recovered from the intestinal and urinary tracts of women with recurrent urinary tract infection, " Science Translational Medicine, vol. 5, no. 184, 2013.
28. J. S. Ayres, N. J. Trinidad, and R. E. Vance, "Lethal inflammasome activation by a multidrug-resistant pathobiont upon antibiotic disruption of the microbiota, " Nature Medicine, vol. 18, no. 5, pp. 799-806, 2012.
29. P. Jain, N. M. Krishnan, and B. Panda, "Augmenting transcriptome assembly by combining de novo and genome-guided tools, " PeerJ, vol. 1, article e133, 2013.
30. I. Thiele, N. Swainston, R. M. T. Fleming et al. , "A communitydriven global reconstruction of human metabolism, " Nature Biotechnology, vol. 31, no. 5, pp. 419-425, 2013.
31. D. J. Becker and J. B. Lowe, "Fucose: biosynthesis and biological function in mammals, " Glycobiology, vol. 13, no. 7, pp. 41R-53R, 2003.
32. Y. Wenger and B. Galliot, "RNAseq versus genome-predicted transcriptomes: a large population of novel transcripts identified in an Illumina-454 Hydra transcriptome, " BMC Genomics, vol. 14, no. 1, article 204, 2013.
33. Z. Qi and M. R. OBrian, "Interaction between the bacterial iron response regulator and ferrochelatase mediates genetic control of heme biosynthesis, " Molecular Cell, vol. 9, no. 1, pp. 155-162, 2002.
34. S. Greenblum, P. J. Turnbaugh, and E. Borenstein, "Metagenomic systems biology of the human gut microbiome reveals topological shifts associated with obesity and inflammatory bowel disease, " Proceedings of the National Academy of Sciences of the United States of America, vol. 109, no. 2, pp. 594-599, 2012.
35. J. J. Qin, Y. R. Li, Z. M. Cai et al. , "A metagenome-wide association study of gut microbiota in type 2 diabetes, " Nature, vol. 490, no. 7418, pp. 55-60, 2012.
36. M. Martinez-Medina, X. Aldeguer, M. Lopez-Siles et al. , "Molecular diversity of Escherichia coli in the human gut: new ecological evidence supporting the role of adherent-invasive E. coli (AIEC) in Crohns disease, " Inflammatory Bowel Diseases, vol. 15, no. 6, pp. 872-882, 2009.
37. J. R. Karr, J. C. Sanghvi, D. N. MacKlin et al. , "A whole-cell computational model predicts phenotype from genotype, " Cell, vol. 150, no. 2, pp. 389-401, 2012.
38. M. Donnenberg, Escherichia coli: Pathotypes and Principles of Pathogenesis, Academic Press, New York, NY, USA, 2013.
39. H. Tlaskalova-Hogenova, R. Tpankova, H. Koźakova et al. , "The role of gut microbiota (commensal bacteria) and the mucosal barrier in the pathogenesis of inflammatory and autoimmune diseases and cancer: Contribution of germ-free and gnotobiotic animal models of human diseases, " Cellular and Molecular Immunology, vol. 8, no. 2, pp. 110-120, 2011.
40. N. Larsen, F. K. Vogensen, F. W. J. van den Berg et al. , "Gut microbiota in human adults with type 2 diabetes differs from non-diabetic adults, " PLoS ONE, vol. 5, no. 2, Article ID e9085, 2010.
41. R. M. Robins-Browne, "Traditional enteropathogenic Escherichia coli of infantile diarrhea, " Reviews of Infectious Diseases, vol. 9, no. 1, pp. 28-53, 1987.
42. K. Guan and Y. Xiong, "Regulation of intermediarymetabolism by protein acetylation, " Trends in Biochemical Sciences, vol. 36, no. 2, pp. 108-116, 2011.
43. J. R. Johnson, M. A. Kuskowski, K. Smith, T. T. OBryan, and S. Tatini, "Antimicrobial-resistant and extraintestinal pathogenic Escherichia coli in retail foods, " Journal of Infectious Diseases, vol. 191, no. 7, pp. 1040-1049, 2005.
44. J. C. Clemente, L. K. Ursell, L. W. Parfrey, and R. Knight, "The impact of the gut microbiota on human health: an integrative view, " Cell, vol. 148, no. 6, pp. 1258-1270, 2012.
45. P. D. Gluckman, K. A. Lillycrop, M. H. Vickers et al. , "Metabolic plasticity during mammalian development is directionally dependent on early nutritional status, " Proceedings of the National Academy of Sciences of the United States of America, vol. 104, no. 31, pp. 12796-12800, 2007.
46. J. Chow, S. M. Lee, Y. Shen, A. Khosravi, and S. K. Mazmanian, "Host-bacterial symbiosis in health and disease, " Advances in Immunology, vol. 107, pp. 243-274, 2010.