An ecological network of polysaccharide utilization among human intestinal symbionts

Current Biology

Volumn 24, Issue 1, 2014, Pages 40-49

  Rakoff Nahoum, Seth ^a,b   Coyne, Michael J ^a   Comstock, Laurie E ^a  

^a BRIGHAM AND WOMEN S HOSPITAL   (United States)

^b BOSTON CHILDREN S HOSPITAL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA (MICROORGANISMS); BACTEROIDALES;

POLYSACCHARIDE;

ARTICLE; BACTEROIDETES; ECOSYSTEM; HUMAN; INTESTINE; METABOLISM; MICROBIOLOGY; SYMBIOSIS;

BACTEROIDETES; ECOSYSTEM; HUMANS; INTESTINES; POLYSACCHARIDES; SYMBIOSIS;

EID: 84891789294     PISSN: 09609822     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cub.2013.10.077     Document Type: Article

References (34)

1. A.L. Kau, P.P. Ahern, N.W. Griffin, A.L. Goodman, and J.I. Gordon Human nutrition, the gut microbiome and the immune system Nature 474 2011 327 336
2. 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
3. L.V. Hooper, D.R. Littman, and A.J. Macpherson Interactions between the microbiota and the immune system Science 336 2012 1268 1273
4. J.J. Faith, J.L. Guruge, M. Charbonneau, S. Subramanian, H. Seedorf, A.L. Goodman, J.C. Clemente, R. Knight, A.C. Heath, and R.L. Leibel et al. The long-term stability of the human gut microbiota Science 341 2013 1237439
5. 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
6. K. Kurokawa, T. Itoh, T. Kuwahara, K. Oshima, H. Toh, A. Toyoda, H. Takami, H. Morita, V.K. Sharma, and T.P. Srivastava et al. Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes DNA Res. 14 2007 169 181
7. J. Qin, R. Li, J. Raes, M. Arumugam, K.S. Burgdorf, C. Manichanh, T. Nielsen, N. Pons, F. Levenez, T. Yamada MetaHIT Consortium A human gut microbial gene catalogue established by metagenomic sequencing Nature 464 2010 59 65
8. L. Dethlefsen, S. Huse, M.L. Sogin, and D.A. Relman The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing PLoS Biol. 6 2008 e280
9. N.L. Zitomersky, M.J. Coyne, and L.E. Comstock Longitudinal analysis of the prevalence, maintenance, and IgA response to species of the order Bacteroidales in the human gut Infect. Immun. 79 2011 2012 2020
10. S.A. West, A.S. Griffin, A. Gardner, and S.P. Diggle Social evolution theory for microorganisms Nat. Rev. Microbiol. 4 2006 597 607
11. O.X. Cordero, H. Wildschutte, B. Kirkup, S. Proehl, L. Ngo, F. Hussain, F. Le Roux, T. Mincer, and M.F. Polz Ecological populations of bacteria act as socially cohesive units of antibiotic production and resistance Science 337 2012 1228 1231
12. O.X. Cordero, L.-A. Ventouras, E.F. DeLong, and M.F. Polz Public good dynamics drive evolution of iron acquisition strategies in natural bacterioplankton populations Proc. Natl. Acad. Sci. USA 109 2012 20059 20064
13. A.A. Salyers, J.R. Vercellotti, S.E. West, and T.D. Wilkins Fermentation of mucin and plant polysaccharides by strains of Bacteroides from the human colon Appl. Environ. Microbiol. 33 1977 319 322
14. E.C. Martens, E.C. Lowe, H. Chiang, N.A. Pudlo, M. Wu, N.P. McNulty, D.W. Abbott, B. Henrissat, H.J. Gilbert, D.N. Bolam, and J.I. Gordon Recognition and degradation of plant cell wall polysaccharides by two human gut symbionts PLoS Biol. 9 2011 e1001221
15. E.D. Sonnenburg, H. Zheng, P. Joglekar, S.K. Higginbottom, S.J. Firbank, D.N. Bolam, and J.L. Sonnenburg Specificity of polysaccharide use in intestinal bacteroides species determines diet-induced microbiota alterations Cell 141 2010 1241 1252
16. H.J. Flint, E.A. Bayer, M.T. Rincon, R. Lamed, and B.A. White Polysaccharide utilization by gut bacteria: potential for new insights from genomic analysis Nat. Rev. Microbiol. 6 2008 121 131
17. A.A. Salyers, F. Gherardini, and M. O'Brien Utilization of xylan by two species of human colonic Bacteroides Appl. Environ. Microbiol. 41 1981 1065 1068
18. N.M. Koropatkin, E.A. Cameron, and E.C. Martens How glycan metabolism shapes the human gut microbiota Nat. Rev. Microbiol. 10 2012 323 335
19. E.C. Martens, N.M. Koropatkin, T.J. Smith, and J.I. Gordon Complex glycan catabolism by the human gut microbiota: the Bacteroidetes Sus-like paradigm J. Biol. Chem. 284 2009 24673 24677
20. A.R. Reeves, G.R. Wang, and A.A. Salyers Characterization of four outer membrane proteins that play a role in utilization of starch by Bacteroides thetaiotaomicron J. Bacteriol. 179 1997 643 649
21. J.A. Shipman, K.H. Cho, H.A. Siegel, and A.A. Salyers Physiological characterization of SusG, an outer membrane protein essential for starch utilization by Bacteroides thetaiotaomicron J. Bacteriol. 181 1999 7206 7211
22. L.M. Mashburn, and M. Whiteley Membrane vesicles traffic signals and facilitate group activities in a prokaryote Nature 437 2005 422 425
23. A. Kulp, and M.J. Kuehn Biological functions and biogenesis of secreted bacterial outer membrane vesicles Annu. Rev. Microbiol. 64 2010 163 184
24. C.M. Fletcher, M.J. Coyne, O.F. Villa, M. Chatzidaki-Livanis, and L.E. Comstock A general O-glycosylation system important to the physiology of a major human intestinal symbiont Cell 137 2009 321 331
25. R.E. McCarthy, M. Pajeau, and A.A. Salyers Role of starch as a substrate for Bacteroides vulgatus growing in the human colon Appl. Environ. Microbiol. 54 1988 1911 1916
26. M.A. Fischbach, and J.L. Sonnenburg Eating for two: how metabolism establishes interspecies interactions in the gut Cell Host Microbe 10 2011 336 347
27. A.L. Goodman, N.P. McNulty, Y. Zhao, D. Leip, R.D. Mitra, C.A. Lozupone, R. Knight, and J.I. Gordon Identifying genetic determinants needed to establish a human gut symbiont in its habitat Cell Host Microbe 6 2009 279 289
28. F.E. Rey, M.D. Gonzalez, J. Cheng, M. Wu, P.P. Ahern, and J.I. Gordon Metabolic niche of a prominent sulfate-reducing human gut bacterium Proc. Natl. Acad. Sci. USA 110 2013 13582 13587
29. C. Spence, W.G. Wells, and C.J. Smith Characterization of the primary starch utilization operon in the obligate anaerobe Bacteroides fragilis: Regulation by carbon source and oxygen J. Bacteriol. 188 2006 4663 4672
30. A.W. Walker, S.H. Duncan, H.J.M. Harmsen, G. Holtrop, G.W. Welling, and H.J. Flint The species composition of the human intestinal microbiota differs between particle-associated and liquid phase communities Environ. Microbiol. 10 2008 3275 3283
31. S.M. Lee, G.P. Donaldson, Z. Mikulski, S. Boyajian, K. Ley, and S.K. Mazmanian Bacterial colonization factors control specificity and stability of the gut microbiota Nature 501 2013 426 429
32. J.J. Morris, R.E. Lenski, and E.R. Zinser The black queen hypothesis: evolution of dependencies through adaptive gene loss MBio 3 2012 e00036-12
33. J.L. Sachs, and A.C. Hollowell The origins of cooperative bacterial communities MBio 3 2012 e00099-12
34. K.R. Foster, and T. Wenseleers A general model for the evolution of mutualisms J. Evol. Biol. 19 2006 1283 1293