Development of high-throughput phenotyping of metagenomic clones from the human gut microbiome for modulation of eukaryotic cell growth

Applied and Environmental Microbiology

Volumn 73, Issue 11, 2007, Pages 3734-3737

  Gloux, Karine ^a   Leclerc, Marion ^a   Iliozer, Harout ^a   L'Haridon, René ^b   Manichanh, Chaysavanh ^a   Corthier, Gérard ^a   Nalin, Renaud ^c   Blottière, Hervé M ^a   Doré, Joël ^a  

^a CEMAGREF   (France)

^b INRA Institut National de la Recherche Agronomique   (France)

^c LibraGen   (France)

Author keywords

[No Author keywords available]

Indexed keywords

CELL GROWTH; MICROBIOLOGY; MUTAGENESIS;

HUMAN GUT MICROBIOME; METAGENOMIC LIBRARIES; TRANSPOSON;

CLONING;

BIOME; CLONE; DIGESTIVE SYSTEM; EUKARYOTE; IDENTIFICATION METHOD; PHENOTYPE;

ARTICLE; CELL GROWTH; EUKARYOTIC CELL; GENE LIBRARY; GENE LOCUS; INTESTINE FLORA; MOLECULAR CLONING; MUTAGENESIS; NUCLEOTIDE SEQUENCE; PHENOTYPE; TRANSPOSON;

EUKARYOTA;

EID: 34249865095     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.02204-06     Document Type: Article

References (32)

1. Alam, M., T. Midtvedt, and A. Uribe. 1994. Differential cell kinetics in the ileum and colon of germfree rats. Scand. J. Gastroenterol. 29:445-451.
2. Andersson, J. O., and A. J. Roger. 2002. Evolutionary analyses of the small subunit of glutamate synthase: gene order conservation, gene fusions, and prokaryote to eukaryote lateral gene transfers. Eukaryot. Cell 1:304-310.
3. Backhed, F., H. Ding, T. Wang, L. V. Hooper, G. Y. Koh, A. Nagy, C. F. Semenkovich, and J. I. Gordon. 2004. The gut microbiota as an environmental factor that regulates fat storage. Proc. Natl. Acad. Sci. USA 101:15718-15723.
4. Backhed, F., R. E. Ley, J. L. Sonnenburg, D. A. Peterson, and J. I. Gordon. 2005. Host-bacterial mutualism in the human intestine. Science 307:1915-1920.
5. Blottiere, H. M., B. Buecher, J. P. Galmiche, and C. Cherbut. 2003. Molecular analysis of the effect of short-chain fatty acids on intestinal cell proliferation. Proc. Nutr. Soc. 62:101-106.
6. Campieri, M., and P. Gionchetti. 2001. Bacteria as the cause of ulcerative colitis. Gut 48:132-135.
7. Diaz-Torres, M. L., R. McNab, D. A. Spratt, A. Villedieu, N. Hunt, M. Wilson, and P. Mullany. 2003. Novel tetracycline resistance determinant from the oral metagenome. Antimicrob. Agents Chemother. 47:1430-1432.
8. Duchmann, R., M. Neurath, E. Marker-Hermann, and K. H. Meyer Zum Buschenfelde. 1997. Immune responses towards intestinal bacteria - current concepts and future perspectives. Z. Gastroenterol. 35:337-346.
9. Gabor, E. M., W. B. Alkema, and D. B. Janssen. 2004. Quantifying the accessibility of the metagenome by random expression cloning techniques. Environ. Microbiol. 6:879-886.
10. Gill, S. R., M. Pop, R. T. Deboy, P. B. Eckburg, P. J. Turnbaugh, B. S. Samuel, J. I. Gordon, D. A. Relman, C. M. Fraser-Liggett, and K. E. Nelson. 2006. Metagenomic analysis of the human distal gut microbiome. Science 312:1355-1359.
11. Goryshin, I. Y., and W. S. Reznikoff. 1998. Tn5 in vitro transposition. J. Biol. Chem. 273:7367-7374.
12. Handelsman, J. 2004. Metagenomics: application of genomics to uncultured microorganisms. Microbiol. Mol. Biol. Rev. 68:669-685.
13. Hartand, D. N., H. S. Garmory, K. A. Brown, and R. W. Titball. 2005. An association between ATP binding cassette systems, genome sizes and life-styles of bacteria. Res. Microbiol. 156:434-442.
14. Henne, A., R. A. Schmitz, M. Bomeke, G. Gattschalk, and R. Daniel. 2000. Screening of environmental DNA libraries for the presence of genes conferring lipolytic activity on Escherichia coli. Appl. Environ. Microbiol. 66: 3113-3116.
15. Hooper, L. V., and J. I. Gordon. 2001. Commensal host-bacterial relationships in the gut. Science 292:1115-1118.
16. Jones, B. V., and J. R. Marchesi. 2007. Transposon-aided capture (TRACA) of plasmids resident in the human gut mobile metagenome. Nat. Methods 4:55-61.
17. Leschelle, X., S. Delpal, M. Goubern, H. M. Blottiere, and F. Blachier. 2000. Butyrate metabolism upstream and downstream acetyl-CoA synthesis and growth control of human colon carcinoma cells. Eur. J. Biochem. 267:6435-6442.
18. L'Haridon, R. December 2006. INRA patent FR0611090.
19. Manichanh, C., L. Rigottier-Gois, E. Bonnaud, K. Gloux, E. Pelletier, L. Frangeul, R. Nalin, C. Jarrin, P. Chardon, P. Marteau, J. Roca, and J. Dore. 2006. Reduced diversity of faecal microbiota in Crohn's disease revealed by a metagenomic approach. Gut 55:205-211.
20. Marteau, P., P. Seksik, and F. Shanahan. 2003. Manipulation of the bacterial flora in inflammatory bowel disease. Best Pract. Res. Clin. Gastroenterol. 17:47-61.
21. Meslin, J. C., and E. Sacquet. 1984. Effects of microflora on the dimensions of enterocyte microvilli in the rat. Reprod. Nutr. Dev. 24:307-314.
22. Muller, V., and G. Gruber. 2003. ATP syntheses: structure, function and evolution of unique energy converters. Cell. Mol. Life Sci. 60:474-494.
23. Okada, M., C. Bothin, K. Kanazawa, and T. Midtvedt. 1999. Experimental study of the influence of intestinal flora on the healing of intestinal anastomoses. Br. J. Surg. 86:961-965.
24. Riesenfeld, C. S., R. M. Goodman, and J. Handelsman. 2004. Uncultured soil bacteria are a reservoir of new antibiotic resistance genes. Environ. Microbiol. 6:981-989.
25. Rondon, M. R., P. R. August, A. D. Bettermann, S. F. Brady, T. H. Grossman, M. R. Liles, K. A. Loiacono, B. A. Lynch, I. A. MacNeil, C. Minor, C. L. Tiong, M. Gilman, M. S. Osburne, J. Clardy, J. Handelsman, and R. M. Goodman. 2000. Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms. Appl. Environ. Microbiol. 66:2541-2547.
26. Saurin, W., M. Hofnung, and E. Dassa. 1999. Getting in or out: early segregation between importers and exporters in the evolution of ATP-binding cassette (ABC) transporters. J. Mol. Evol. 48:22-41.
27. Siavoshian, S., H. M. Blottiere, E. Le Foll, B. Kaeffer, C. Cherbut, and J. P. Galmiche. 1997. Comparison of the effect of different short chain fatty acids on the growth and differentiation of human colonic carcinoma cell lines in vitro. Cell Biol. Int. 21:281-287.
28. Stappenbeck, T. S., L. V. Hooper, and J. I. Gordon. 2002. Developmental regulation of intestinal angiogenesis by indigenous microbes via Paneth cells. Proc. Natl. Acad. Sci. USA 99:15451-15455.
29. Tomii, K., and M. Kanehisa. 1998. A comparative analysis of ABC transporters in complete microbial genomes. Genome Res. 8:1048-1059.
30. Walker, J. E., M. Saraste, M. J. Runswick, and N. J. Gay. 1982. Distantly related sequences in the alpha- and beta-subunits of ATP synthase, myosin, kinases and other ATP-requiring enzymes and a common nucleotide binding fold. EMBO J. 1:945-951.
31. Woese, C. R., O. Kandler, and M. L. Wheelis. 1990. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria and Eucarya. Proc. Natl. Acad. Sci. USA 87:4576-1579.
32. Xu, J., and J. I. Gordon. 2003. Inaugural article: honor thy symbionts. Proc. Natl. Acad. Sci. USA 100:10452-10459.