Meta-analyses of human gut microbes associated with obesity and IBD

FEBS Letters

Volumn 588, Issue 22, 2014, Pages 4223-4233

  Walters, William A ^a   Xu, Zech ^a   Knight, Rob ^a,b  

^a UNIVERSITY OF COLORADO   (United States)

^b HOWARD HUGHES MEDICAL INSTITUTE   (United States)

Author keywords

Gut microbiota; Metaanalysis

Indexed keywords

RNA 16S;

ACTINOBACTERIA; AMPLICON; ARTICLE; BACTERIUM DETECTION; BACTEROIDETES; BODY MASS; CORRELATION ANALYSIS; DISEASE ASSOCIATION; DISEASE CLASSIFICATION; FECES ANALYSIS; FIRMICUTES; GENE AMPLIFICATION; GENE CLUSTER; GENE SEQUENCE; HIGH THROUGHPUT SEQUENCING; HUMAN; INFLAMMATORY BOWEL DISEASE; INTESTINE FLORA; METHANOBREVIBACTER SMITHII; NONHUMAN; OBESITY; PHENOTYPE; POPULATION ABUNDANCE; TAXONOMY; ANIMAL; FECES; GASTROINTESTINAL TRACT; META ANALYSIS; MICROBIOLOGY; SEQUENCE ANALYSIS;

ANIMALS; FECES; GASTROINTESTINAL TRACT; HUMANS; INFLAMMATORY BOWEL DISEASES; OBESITY; SEQUENCE ANALYSIS, RNA;

EID: 84908348194     PISSN: 00145793     EISSN: 18733468     Source Type: Journal    
DOI: 10.1016/j.febslet.2014.09.039     Document Type: Article

References (53)

1. C.A. Lozupone, J. Stombaugh, A. Gonzalez, G. Ackermann, D. Wendel, Y. Vazquez-Baeza, J.K. Jansson, J.I. Gordon, and R. Knight Meta-analyses of studies of the human microbiota Genome Res. 23 2013 1704 1714
2. Z. Liu, T.Z. DeSantis, G.L. Andersen, and R. Knight Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers Nucleic Acids Res. 36 2008 e120
3. T.Z. DeSantis, P. Hugenholtz, N. Larsen, M. Rojas, E.L. Brodie, K. Keller, T. Huber, D. Dalevi, P. Hu, and G.L. Andersen Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB Appl. Environ. Microbiol. 72 2006 5069 5072
4. R.C. Edgar Search and clustering orders of magnitude faster than BLAST Bioinformatics 26 2010 2460 2461
5. C. Lozupone, and R. Knight UniFrac: a new phylogenetic method for comparing microbial communities Appl. Environ. Microbiol. 71 2005 8228 8235
6. T. Kelly, W. Yang, C.S. Chen, K. Reynolds, and J. He Global burden of obesity in 2005 and projections to 2030 Int. J. Obes. 32 2008 1431 1437
7. R.E. Ley, P.J. Turnbaugh, S. Klein, and J.I. Gordon Microbial ecology: human gut microbes associated with obesity Nature 444 2006 1022 1023
8. P.J. Turnbaugh, M. Hamady, T. Yatsunenko, B.L. Cantarel, A. Duncan, R.E. Ley, M.L. Sogin, W.J. Jones, B.A. Roe, J.P. Affourtit, M. Egholm, B. Henrissat, A.C. Heath, R. Knight, and J.I. Gordon A core gut microbiome in obese and lean twins Nature 457 2009 480 484
9. D. Knights, L.W. Parfrey, J. Zaneveld, C. Lozupone, and R. Knight Human-associated microbial signatures: examining their predictive value Cell Host Microbe 10 2011 292 296
10. E. Le Chatelier, T. Nielsen, J. Qin, E. Prifti, F. Hildebrand, G. Falony, M. Almeida, M. Arumugam, J.M. Batto, S. Kennedy, P. Leonard, J. Li, K. Burgdorf, N. Grarup, T. Jorgensen, I. Brandslund, H.B. Nielsen, A.S. Juncker, M. Bertalan, F. Levenez, N. Pons, S. Rasmussen, S. Sunagawa, J. Tap, S. Tims, E.G. Zoetendal, S. Brunak, K. Clement, J. Dore, M. Kleerebezem, K. Kristiansen, P. Renault, T. Sicheritz-Ponten, W.M. de Vos, J.D. Zucker, J. Raes, T. Hansen, H.I.T.C. Meta, P. Bork, J. Wang, S.D. Ehrlich, and O. Pedersen Richness of human gut microbiome correlates with metabolic markers Nature 500 2013 541 546
11. P.J. Turnbaugh, R.E. Ley, M.A. Mahowald, V. Magrini, E.R. Mardis, and J.I. Gordon An obesity-associated gut microbiome with increased capacity for energy harvest Nature 444 2006 1027 1031
12. M. Vijay-Kumar, J.D. Aitken, F.A. Carvalho, T.C. Cullender, S. Mwangi, S. Srinivasan, S.V. Sitaraman, R. Knight, R.E. Ley, and A.T. Gewirtz Metabolic syndrome and altered gut microbiota in mice lacking Toll-like receptor 5 Science 328 2010 228 231
13. L. Bervoets, K. Van Hoorenbeeck, I. Kortleven, C. Van Noten, N. Hens, C. Vael, H. Goossens, K.N. Desager, and V. Vankerckhoven Differences in gut microbiota composition between obese and lean children: a cross-sectional study Gut Pathog. 5 2013 10
14. P. Colson, L. Fancello, G. Gimenez, F. Armougom, C. Desnues, G. Fournous, N. Yoosuf, M. Million, B. La Scola, and D. Raoult Evidence of the megavirome in humans J. Clin. Virol. 57 2013 191 200
15. M. Ferrer, A. Ruiz, F. Lanza, S.B. Haange, A. Oberbach, H. Till, R. Bargiela, C. Campoy, M.T. Segura, M. Richter, M. von Bergen, J. Seifert, and A. Suarez Microbiota from the distal guts of lean and obese adolescents exhibit partial functional redundancy besides clear differences in community structure Environ. Microbiol. 15 2013 211 226
16. J.P. Furet, L.C. Kong, J. Tap, C. Poitou, A. Basdevant, J.L. Bouillot, D. Mariat, G. Corthier, J. Dore, C. Henegar, S. Rizkalla, and K. Clement Differential adaptation of human gut microbiota to bariatric surgery-induced weight loss: links with metabolic and low-grade inflammation markers Diabetes 59 2010 3049 3057
17. R.E. Ley, D.A. Peterson, and J.I. Gordon Ecological and evolutionary forces shaping microbial diversity in the human intestine Cell 124 2006 837 848
18. F.J. Verdam, S. Fuentes, C. de Jonge, E.G. Zoetendal, R. Erbil, J.W. Greve, W.A. Buurman, W.M. de Vos, and S.S. Rensen Human intestinal microbiota composition is associated with local and systemic inflammation in obesity Obesity 21 2013 E607 E615
19. P. Xu, M. Li, J. Zhang, and T. Zhang Correlation of intestinal microbiota with overweight and obesity in Kazakh school children BMC Microbiol. 12 2012 283
20. S.H. Duncan, G.E. Lobley, G. Holtrop, J. Ince, A.M. Johnstone, P. Louis, and H.J. Flint Human colonic microbiota associated with diet, obesity and weight loss Int. J. Obes. 32 2008 1720 1724
21. R. Jumpertz, D.S. Le, P.J. Turnbaugh, C. Trinidad, C. Bogardus, J.I. Gordon, and J. Krakoff Energy-balance studies reveal associations between gut microbes, caloric load, and nutrient absorption in humans Am. J. Clin. Nutr. 94 2011 58 65
22. D.P. Patil, D.P. Dhotre, S.G. Chavan, A. Sultan, D.S. Jain, V.B. Lanjekar, J. Gangawani, P.S. Shah, J.S. Todkar, S. Shah, D.R. Ranade, M.S. Patole, and Y.S. Shouche Molecular analysis of gut microbiota in obesity among Indian individuals J. Biosci. 37 2012 647 657
23. A. Schwiertz, D. Taras, K. Schafer, S. Beijer, N.A. Bos, C. Donus, and P.D. Hardt Microbiota and SCFA in lean and overweight healthy subjects Obesity 18 2010 190 195
24. S. Tims, C. Derom, D.M. Jonkers, R. Vlietinck, W.H. Saris, M. Kleerebezem, W.M. de Vos, and E.G. Zoetendal Microbiota conservation and BMI signatures in adult monozygotic twins ISME J. 7 2013 707 717
25. M.L. Zupancic, B.L. Cantarel, Z. Liu, E.F. Drabek, K.A. Ryan, S. Cirimotich, C. Jones, R. Knight, W.A. Walters, D. Knights, E.F. Mongodin, R.B. Horenstein, B.D. Mitchell, N. Steinle, S. Snitker, A.R. Shuldiner, and C.M. Fraser Analysis of the gut microbiota in the old order Amish and its relation to the metabolic syndrome PLoS One 7 2012 e43052
26. Team, R. D. C. (2008) R: A language and environment for statistical computing. in: Vienna, Austria.
27. R.A. Fisher Statistical Methods for Research Workers 1925 Oliver and Boyd Edinburgh
28. G.D. Wu, J. Chen, C. Hoffmann, K. Bittinger, Y.Y. Chen, S.A. Keilbaugh, M. Bewtra, D. Knights, W.A. Walters, R. Knight, R. Sinha, E. Gilroy, K. Gupta, R. Baldassano, L. Nessel, H. Li, F.D. Bushman, and J.D. Lewis Linking long-term dietary patterns with gut microbial enterotypes Science 334 2011 105 108
29. C.E. Shannon A mathematical theory of communication Bell Syst. Tech. J. 27 1948 379 473
30. J.G. Holt Bergey's Manual of Determinative Bacteriology 1994 Lippincott Williams & Wilkins London
31. L. Breimann Random forests Machine Learn. 45 2001 5 32
32. V.K. Ridaura, J.J. Faith, F.E. Rey, J. Cheng, A.E. Duncan, A.L. Kau, N.W. Griffin, V. Lombard, B. Henrissat, J.R. Bain, M.J. Muehlbauer, O. Ilkayeva, C.F. Semenkovich, K. Funai, D.K. Hayashi, B.J. Lyle, M.C. Martini, L.K. Ursell, J.C. Clemente, W. Van Treuren, W.A. Walters, R. Knight, C.B. Newgard, A.C. Heath, and J.I. Gordon Gut microbiota from twins discordant for obesity modulate metabolism in mice Science 341 2013 1241214
33. D.C. Baumgart, and S.R. Carding Inflammatory bowel disease: cause and immunobiology Lancet 369 2007 1627 1640
34. S.K. Mazmanian, and R.B. Sartor Intestinal microbes in inflammatory bowel diseases Am. J. Gastroenterol. Suppl. 1 2012 15 21
35. P.B. Eckburg, E.M. Bik, C.N. Bernstein, E. Purdom, L. Dethlefsen, M. Sargent, S.R. Gill, K.E. Nelson, and D.A. Relman Diversity of the human intestinal microbial flora Science 308 2005 1635 1638
36. D.N. Frank, A.L. St Amand, R.A. Feldman, E.C. Boedeker, N. Harpaz, and N.R. Pace Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases Proc. Natl. Acad. Sci. U.S.A. 104 2007 13780 13785
37. E. Papa, M. Docktor, C. Smillie, S. Weber, S.P. Preheim, D. Gevers, G. Giannoukos, D. Ciulla, D. Tabbaa, J. Ingram, D.B. Schauer, D.V. Ward, J.R. Korzenik, R.J. Xavier, A. Bousvaros, and E.J. Alm Non-invasive mapping of the gastrointestinal microbiota identifies children with inflammatory bowel disease PLoS One 7 2012 e39242
38. Y. Momozawa, V. Deffontaine, E. Louis, and J.F. Medrano Characterization of bacteria in biopsies of colon and stools by high throughput sequencing of the V2 region of bacterial 16S rRNA gene in human PLoS One 6 2011 e16952
39. X.C. Morgan, T.L. Tickle, H. Sokol, D. Gevers, K.L. Devaney, D.V. Ward, J.A. Reyes, S.A. Shah, N. LeLeiko, S.B. Snapper, A. Bousvaros, J. Korzenik, B.E. Sands, R.J. Xavier, and C. Huttenhower Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment Genome Biol. 13 2012 R79
40. B.P. Willing, J. Dicksved, J. Halfvarson, A.F. Andersson, M. Lucio, Z. Zheng, G. Jarnerot, C. Tysk, J.K. Jansson, and L. Engstrand A pyrosequencing study in twins shows that gastrointestinal microbial profiles vary with inflammatory bowel disease phenotypes Gastroenterology 139 1844-1854 2010 e1
41. D. Gevers, S. Kugathasan, L.A. Denson, Y. Vazquez-Baeza, W. Van Treuren, B. Ren, E. Schwager, D. Knights, S.J. Song, M. Yassour, X.C. Morgan, A.D. Kostic, C. Luo, A. Gonzalez, D. McDonald, Y. Haberman, T. Walters, S. Baker, J. Rosh, M. Stephens, M. Heyman, J. Markowitz, R. Baldassano, A. Griffiths, F. Sylvester, D. Mack, S. Kim, W. Crandall, J. Hyams, C. Huttenhower, R. Knight, and R.J. Xavier The treatment-naive microbiome in new-onset Crohn's disease Cell Host Microbe 15 2014 382 392
42. B. Sheil, F. Shanahan, and L. O'Mahony Probiotic effects on inflammatory bowel disease J. Nutr. 137 2007 819S 824S
43. E.S. Pierce Ulcerative colitis and Crohn's disease: is Mycobacterium avium subspecies paratuberculosis the common villain? Gut Pathog. 2 2010 21
44. Human Microbiome Project, C Structure, function and diversity of the healthy human microbiome Nature 486 2012 207 214
45. T. Yatsunenko, F.E. Rey, M.J. Manary, I. Trehan, M.G. Dominguez-Bello, M. Contreras, M. Magris, G. Hidalgo, R.N. Baldassano, A.P. Anokhin, A.C. Heath, B. Warner, J. Reeder, J. Kuczynski, J.G. Caporaso, C.A. Lozupone, C. Lauber, J.C. Clemente, D. Knights, R. Knight, and J.I. Gordon Human gut microbiome viewed across age and geography Nature 486 2012 222 227
46. L.J. Brandt, and O.C. Aroniadis An overview of fecal microbiota transplantation: techniques, indications, and outcomes Gastrointest. Endosc. 78 2013 240 249
47. M.C. Collado, M. Derrien, E. Isolauri, W.M. de Vos, and S. Salminen Intestinal integrity and Akkermansia muciniphila, a mucin-degrading member of the intestinal microbiota present in infants, adults, and the elderly Appl. Environ. Microbiol. 73 2007 7767 7770
48. S. Miquel, R. Martín, O. Rossi, L.G. Bermúdez-Humarán, J.M. Chatel, H. Sokol, M. Thomas, J.M. Wells, and P. Langella Faecalibacterium prausnitzii and human intestinal health Curr. Opin. Microbiol. 16 2013 255 261
49. P. Gauffin Cano, A. Santacruz, Á. Moya, and Y. Sanz Bacteroides uniformis CECT 7771 ameliorates metabolic and immunological dysfunction in mice with high-fat-diet induced obesity PLoS One 7 2012 e41079
50. J. Strauss, G.G. Kaplan, P.L. Beck, K. Rioux, R. Panaccione, R. Devinney, T. Lynch, and E. Allen-Vercoe Invasive potential of gut mucosa-derived Fusobacterium nucleatum positively correlates with IBD status of the host Inflamm. Bowel Dis. 17 2011 1971 1978
51. M. Vijay-Kumar, and A.T. Gewirtz Flagellin: key target of mucosal innate immunity Mucosal Immunol. 2 2009 197 205
52. S. Shimamura, F. Abe, N. Ishibashi, H. Miyakawa, T. Yaeshima, T. Araya, and M. Tomita Relationship between oxygen sensitivity and oxygen metabolism of Bifidobacterium species J. Dairy Sci. 75 1992 3296 3306
53. C. Juste, D.P. Kreil, C. Beauvallet, A. Guillot, S. Vaca, C. Carapito, S. Mondot, P. Sykacek, H. Sokol, F. Blon, P. Lepercq, F. Levenez, B. Valot, W. Carré, V. Loux, N. Pons, O. David, B. Schaeffer, P. Lepage, P. Martin, V. Monnet, P. Seksik, L. Beaugerie, S.D. Ehrlich, J.-F. Gibrat, A. Van Dorsselaer, and J. Doré Bacterial protein signals are associated with Crohn's disease Gut 2014