Honor thy symbionts

Proceedings of the National Academy of Sciences of the United States of America

Volumn 100, Issue 18, 2003, Pages 10452-10459

  Xu, Jian ^a   Gordon, Jeffrey I ^a  

^a WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Ecogenomics; Environmental sensing; Glycobiome; Gnotobiotic mice; Gut microbial ecology

Indexed keywords

GLYCOGEN; HYDROLASE; BACTERIAL POLYSACCHARIDE;

ARTICLE; BACTERIAL GENOME; BACTEROIDES THETAIOTAOMICRON; BIOME; ECOSYSTEM; GENE SEQUENCE; GERMFREE ANIMAL; HOST PARASITE INTERACTION; HUMAN; INTESTINE FLORA; MOUSE; NONHUMAN; PRIORITY JOURNAL; SYMBIONT; SYMBIOSIS; ANIMAL; BACTEROIDES; BIOSYNTHESIS; EVOLUTION; GENETICS; GENOMICS; INTESTINE; MICROBIOLOGY;

ANIMALIA; BACTERIA (MICROORGANISMS); BACTEROIDES; BACTEROIDES THETAIOTAOMICRON; MICROBIOTA; NEGIBACTERIA;

ANIMALS; BACTEROIDES; ECOSYSTEM; EVOLUTION; GENOME, BACTERIAL; GENOMICS; GERM-FREE LIFE; HUMANS; INTESTINES; POLYSACCHARIDES, BACTERIAL; SYMBIOSIS;

EID: 0142026205     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.1734063100     Document Type: Article

References (97)

1. Stahl, D. A. & Tiedje, J. (2002) in Microbial Ecology and Genomics: A Crossroads of Opportunity, Critical Issues Colloquia (Am. Soc. Microbiol., Washington, DC).
2. McFall-Ngai, M. J. (2002) Dev. Biol. 242, 1-14.
3. Schultze, M. & Kondorosi, A. (1998) Annu. Rev. Genet. 32, 33-57.
4. Favier, C. F., Vaughan, E. E., De Vos, W. M. & Akkermans, A. D. (2002) Appl. Environ. Microbiol. 68, 219-226.
5. Savage, D. C. (1977) Annu. Rev. Microbiol. 31, 107-133.
6. Berg, R. D. (1996) Trends Microbiol. 4, 430-435.
7. Zengler, K., Toledo, G., Rappe, M., Elkins, J., Mathur, E. J., Short, J. M. & Keller, M. (2002) Proc. Natl. Acad. Sci. USA 99, 15681-15686.
8. Eckburg, P. B., Lepp, P. W. & Relman, D. A. (2003) Infect. Immun. 71, 591-596.
9. Croft, D. N. (1970) Proc. R. Soc. Med. 63, 1221-1224.
10. Croft, D. N. & Cotton, P. B. (1973) Digestion 8, 144-160.
11. Edwards, C. A. & Parrett, A. M. (2002) Br. J. Nutr. 88, Suppl. 1, S11-S18.
12. Hopkins, M. J., Sharp, R. & Macfarlane, G. T. (2001) Gut 48, 198-205.
13. Zoetendal, E. G., Akkermans, A. D. L., Akkermans-van Vliet, W. M., de Visser, J. A. G. M. & De Vos, W. M. (2001) Microb. Ecol. Health Dis. 13, 129-134.
14. Sullivan, A., Edlund, C. & Nord, C. E. (2001) Lancet Infect. Dis. 1, 101-114.
15. Moore, W. E. & Holdeman, L. V. (1974) Appl. Microbiol. 27, 961-979.
16. Gibson, G. R. & Roberfroid, M. B. (1999) in Colonic Microbiota, Nutrition and Health (Chapman & Hall, London), pp. 37-53.
17. Hooper, L. V., Midtvedt, T. & Gordon, J. I. (2002) Annu. Rev. Nutr. 22, 283-307.
18. Hylemon, P. B. & Harder, J. (1998) FEMS Microbiol. Rev. 22, 475-488.
19. Duncan, S. H., Richardson, A. J., Kaul, P., Holmes, R. P., Allison, M. J. & Stewart, C. S. (2002) Appl. Environ. Microbiol. 68, 3841-3847.
20. Hill, M. J. (1997) Eur. J. Cancer Prev. 6, Suppl. 1, S43-S45.
21. Braun-Fahrlander, C., Riedler, J., Herz, U., Eder, W., Waser, M., Grize, L., Maisch, S., Carr, D., Gerlach, F., Bufe, A., et al. (2002) N. Engl. J. Med. 347, 869-877.
22. Fagarasan, S., Muramatsu, M., Suzuki, K., Nagaoka, H., Hiai, H. & Honjo, T. (2002) Science 298, 1424-1427.
23. McFall-Ngai, M. J. & Gordon, J. I. (2003) in Evolution of Microbial Virulence, eds. Seifert, H. & DiRita, V. (Am. Soc. Microbiol., Washington, DC), in press.
24. Xu, J., Bjursell, M. K., Himrod, J., Deng, S., Carmichael, L. K., Chiang, H. C., Hooper, L. V. & Gordon, J. I. (2003) Science 299, 2074-2076.
25. Reyniers, J. A. (1956) in Proceedings Third International Congress of Biochemistry, ed. Lierbecq, C. (Academic, New York).
26. Pleasants, J. R. (1965) Proc. Indiana Acad. Sci. 75, 220-226.
27. Hooper, L. V., Mills, J. C., Roth, K. A., Stappenbeck, T. S., Wong, M. H. & Gordon, J. I. (2002) Methods Microbiol. 31, 559-589.
28. Stappenbeck, T. S., Hooper, L. V., Manchester, J. K., Wong, M. H. & Gordon, J. I. (2002) Methods Enzymol. 356, 168-196.
29. Salyers, A. A., Valentine, P. & Hwa, V. (1993) in Genetics and Molecular Biology of Anaerobic Bacteria, ed. Sebald, M. (Springer, New York), pp. 505-516.
30. Salyers, A. A., Bonheyo, G. & Shoemaker, N. B. (2000) Methods 20, 35-46.
31. Mackie, R. I., Sghir, A. & Gaskins, H. R. (1999) Am. J. Clin. Nutr. 69, 1035S-1045S.
32. Bry, L., Falk, P. G., Midtvedt, T. & Gordon, J. I. (1996) Science 273, 1380-1383.
33. Hooper, L. V., Xu, J., Falk, P. G., Midtvedt, T. & Gordon, J. I. (1999) Proc. Natl. Acad. Sci. USA 96, 9833-9838.
34. Stappenbeck, T. S., Hooper, L. V. & Gordon, J. I. (2002) Proc. Natl. Acad. Sci. USA 99, 15451-15455.
35. Hooper, L. V., Wong, M. H., Thelin, A., Hansson, L., Falk, P. G. & Gordon, J. I. (2001) Science 291, 881-884.
36. Yoshida, K., Shimizugawa, T., Ono, M. & Furukawa, H. (2002) J. Lipid Res. 43, 1770-1772.
37. Weinstock, P. H., Levak-Frank, S., Hudgins, L. C., Radner, H., Friedman, J. M., Zechner, R. & Breslow, J. L. (1997) Proc. Natl. Acad. Sci. USA 94, 10261-10266.
38. Hooper, L. V., Stappenbeck, T. S., Hong, C. V. & Gordon, J. I. (2003) Nat. Immunol. 4, 269-273.
39. Gilbert, S. F. (2001) Dev. Biol. 233, 1-12.
40. Moore, W. E., Cato, E. P. & Holdeman, L. V. (1978) Am. J. Clin. Nutr. 31, S33-S42.
41. Deppenmeier, U., Johann, A., Hartsch, T., Merkl, R., Schmitz, R. A., Martinez-Arias, R., Henne, A., Wiezer, A., Baumer, S., Jacobi, C., et al. (2002) J. Mol. Microbiol. Biotechnol. 4, 453-461.
42. Galagan, J. E., Nusbaum, C., Roy, A., Endrizzi, M. G., Macdonald, P., FitzHugh, W., Calvo, S., Engels, R., Smirnov, S., Atnoor, D., et al. (2002) Genome Res. 12, 532-542.
43. da Silva, A. C., Ferro, J. A., Reinach, F. C., Farah, C. S., Furlan, L. R., Quaggio, R. B., Monteiro-Vitorello, C. B., Van Sluys, M. A., Almeida, N. F., Alves, L. M., et al. (2002) Nature 417, 459-463.
44. Cole, S. T., Eiglmeier, K., Parkhill, J., James, K. D., Thomson, N. R., Wheeler, P. R., Honore, N., Garnier, T., Churcher, C., Harris, D., et al. (2001) Nature 409, 1007-1011.
45. Maier, R. M. (2000) in Environmental Microbiology, eds. Maier, R. M., Pepper, I. L. & Gerba, C. P. (Academic, San Diego), pp. 321-331.
46. Cho, K. H. & Salyers, A. A. (2001) J. Bacteriol. 183, 7224-7230.
47. Buchanan, S. K., Smith, B. S., Venkatramani, L., Xia, D., Esser, L., Palnitkar, M., Chakraborty, R., van der Helm, D. & Deisenhofer, J. (1999) Nat. Struct. Biol. 6, 56-63.
48. Wexler, H. M., Read, E. K. & Tomzynski, T. J. (2002) Gene 283, 95-105.
49. Nakai, K. & Kanehisa, M. (1991) Proteins 11, 95-110.
50. Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., Davis, A. P., Dolinski, K., Dwight, S. S., Eppig, J. T., et al. (2000) Nat. Genet. 25, 25-29.
51. Schell, M. A., Karmirantzou, M., Snel, B., Vilanova, D., Berger, B., Pessi, G., Zwahlen, M. C., Desiere, F., Bork, P., Delley, M., et al. (2002) Proc. Natl. Acad. Sci. USA 99, 14422-14427.
52. Shimizu, T., Ohtani, K., Hirakawa, H., Ohshima, K., Yamashita, A., Shiba, T., Ogasawara, N., Hattori, M., Kuhara, S. & Hayashi, H. (2002) Proc. Natl. Acad. Sci. USA 99, 996-1001.
53. Blattner, F. R., Plunkett, G., Bloch, C. A., Perna, N. T., Burland, V., Riley, M., Collado-Vides, J., Glasner, J. D., Rode, C. K., Mayhew, G. F., et al. (1997) Science 277, 1453-1474.
54. Paulsen, I. T., Banerjei, L., Myers, G. S., Nelson, K. E., Seshadri, R., Read, T. D., Fouts, D. E., Eisen, J. A., Gill, S. R., Heidelberg, J. F., et al. (2003) Science 299, 2071-2074.
55. Biavati, B. & Mattarelli, P. (2001) in The Prokaryotes, eds. Dworkin, M., Falkow, S., Rosenberg, E., Schleifer, K. H. & Stackebrandt, E. (Springer, New York), pp. 1-70.
56. Hatheway, C. L. (1990) Clin. Microbiol. Rev. 3, 66-98.
57. Klare, I., Werner, G. & Witte, W. (2001) Contrib. Microbiol. 8, 108-122.
58. Hwa, V. & Salyers, A. A. (1992) Appl. Environ. Microbiol. 58, 869-876.
59. Lynd, L. R., Weimer, P. J., van Zyl, W. H. & Pretorius, I. S. (2002) Microbiol. Mol. Biol. Rev. 66, 506-577.
60. Shoham, Y., Lamed, R. & Bayer, E. A. (1999) Trends Microbiol. 7, 275-281.
61. Boos, W. & Shuman, H. (1998) Microbiol. Mol. Biol. Rev. 62, 204-229.
62. Moat, A. G., Foster, J. W. & Spector, M. P. (2002) in Microbial Physiology (Wiley-Liss, New York) pp. 390-392.
63. Kondoh, M. (2003) Science 299, 1388-1391.
64. D'Elia, J. N. & Salyers, A. A. (1996) J. Bacteriol. 178, 7180-7186.
65. Wosten, M. M. (1998) FEMS Microbiol. Rev. 22, 127-150.
66. Helmann, J. D. (2002) Adv. Microb. Physiol. 46, 47-110.
67. Erickson, J. W. & Gross, C. A. (1989) Genes Dev. 3, 1462-1471.
68. Hershberger, C. D., Ye, R. W., Parsek, M. R., Xie, Z. D. & Chakrabarty, A. M. (1995) Proc. Natl. Acad. Sci. USA 92, 7941-7945.
69. Enz, S., Braun, V. & Crosa, J. H. (1995) Gene 163, 13-18.
70. Tibazarwa, C., Wuertz, S., Mergeay, M., Wyns, L. & van Der Lelie, D. (2000) J. Bacteriol. 182, 1399-1409.
71. Chi, E. & Bartlett, D. H. (1995) Mol. Microbiol. 17, 713-726.
72. Paget, M. S. B., Hong, H.-J., Bibb, M. J. & Buttner, M. J. (2002) in Control of Bacterial Gene Expression, eds. Hodgson, D. A. & Thomas, C. M. (Cambridge Univ. Press, Cambridge, U.K.), pp. 105-125.
73. Wolanin, P. M., Thoomason, P. A. & Stock, J. B. (2002) Genome Biol. 3, REVIEWS3013.1-3013.8.
74. Tatusov, R. L., Galperin, M. Y., Natale, D. A. & Koonin, E. V. (2000) Nucleic Acids Res. 28, 33-36.
75. Stover, C. K., Pham, X. Q., Erwin, A. L., Mizoguchi, S. D., Warrener, P., Hickey, M. J., Brinkman, F. S., Hufnagle, W. O., Kowalik, D. J., Lagrou, M., et al. (2000) Nature 406, 959-964.
76. Gallegos, M. T., Michan, C. & Ramos, J. L. (1993) Nucleic Acids Res. 21, 807-810.
77. McCarthy, R. E., Pajeau, M. & Salyers, A. A. (1988) Appl. Environ. Microbiol. 54, 1911-1916.
78. Salyers, A. A., Vercellotti, J. R., West, S. E. & Wilkins, T. D. (1977) Appl. Environ. Microbiol. 33, 319-322.
79. Salyers, A. A., West, S. E., Vercellotti, J. R. & Wilkins, T. D. (1977) Appl. Environ. Microbiol. 34, 529-533.
80. Coyne, M. J., Tzianabos, A. O., Mallory, B. C., Carey, V. J., Kasper, D. L. & Comstock, L. E. (2001) Infect. Immun. 69, 4342-4350.
81. Babb, J. L. & Cummins, C. S. (1978) Infect. Immun. 19, 1088-1091.
82. Paster, B. J., Dewhirst, F. E., Olsen, I. & Fraser, G. J. (1994) J. Bacteriol. 176, 725-732.
83. Sakamoto, M., Suzuki, M., Umeda, M., Ishikawa, L. & Behno, Y. (2002) Int. J. Syst. Evol. Microbiol. 52, 841-849.
84. Beja, O., Suzuki, M. T., Heidelberg, J. F., Nelson, W. C., Preston, C. M., Hamada, T., Eisen, J. A., Fraser, C. M. & DeLong, E. F. (2002) Nature 415, 630-633.
85. Kanehisa, M., Goto, S., Kawashima, S. & Nakaya, A. (2002) Nucleic Acids Res. 30, 42-46.
86. Overbeek, R., Larsen, N., Pusch, G. D., D'Souza, M. Selkov, E., Jr., Kyrpides, N., Fonstein, M., Maltlsev, N. & Selkov, E. (2000) Nucleic Acids Res. 28, 123-125.
87. Karp, P. D., Riley, M., Saier, M., Paulsen, I. T., Collado-Vides, J., Paley, S. M., Pellegrini-Toole, A., Bonavides, C. & Gama-Castro, S. (2002) Nucleic Acids Res. 30, 56-58.
88. Karp, P. D., Riley, M., Paley, S. M. & Pellegrini-Toole, A. (2002) Nucleic Acids Res. 30, 59-61.
89. Karp, P. D., Paley, S. & Romero, P. (2002) Bioinformatics 18, Suppl. 1, S225-S232.
90. Conway, T. & Schoolnik, G. K. (2003) Mol. Microbiol. 47, 879-889.
91. Walter, J., Heng, N. C., Hammes, W. P., Loach, D. M., Tannock, G. W. & Hertel, C. (2003) Appl. Environ. Microbiol. 69, 2044-2051.
92. Aiello, C. C. & Wheeler, P. (1995) Curr. Anthropol. 36, 199-221.
93. Cano, R. J., Tiefenbrunner, F., Ubaldi, M., del Cueto, C., Luciani, S., Cox, T., Orkand, P., Kunzel, K. H. & Rollo, F. (2000) Am. J. Phys. Anthropol. 112, 297-309.
94. Harmsen, H. J., Raangs, G. C., He, T., Degener, J. E. & Welling, G. W. (2002) Appl. Environ. Microbiol. 68, 2982-2990.
95. Wang, R. F., Beggs, M. L., Robertson, L. H. & Cerniglia, C. E. (2002) FEMS Microbiol. Lett. 213, 175-182.
96. Hauert, C., De Monte, S., Hofbauer, J. & Sigmund, K. (2002) Science 296, 1129-1132.
97. Stephens, D. W., McLinn, C. M. & Stevens, J. R. (2002) Science 298, 2216-2218.