Environmental and gut Bacteroidetes: The food connection

Frontiers in Microbiology

Volumn 2, Issue MAY, 2011, Pages

  Thomas, François ^a   Hehemann, Jan Hendrik ^a,b,c   Rebuffet, Etienne ^a,b,c   Czjzek, Mirjam ^a   Michel, Gurvan ^a  

^a STATION BIOLOGIQUE DE ROSCOFF   (France)

^b UNIVERSITY OF VICTORIA   (Canada)

^c UNIVERSITY OF GOTHENBURG   (Sweden)

Author keywords

Adaptation to environmental niches; Bacteroidetes; Microbiota

Indexed keywords

ALGAE; ANIMALIA; BACTERIA (MICROORGANISMS); BACTEROIDETES; LANGAT VIRUS;

EID: 80054093637     PISSN: None     EISSN: 1664302X     Source Type: Journal    
DOI: 10.3389/fmicb.2011.00093     Document Type: Article

References (210)

1. Abrams, G. D. (1983). "Impact of the intestinal microflora on intestinal structure and function," in Human Intestinal Microflora in Health and Disease, ed. D. J. Hentges (New York, NY: Academic Press), 292-310.
2. Alldredge, A. L., Cole, J. J., and Caron, D. A. (1986). Production of hetero-trophic bacteria inhabiting macroscopic organic aggregates (marine snow) from surface waters. Limnol Oceanogr. 31,68-78.
3. Amann, R. I., Ludwig, W., and Schleifer, K. H. (1995). Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59,143-169.
4. Anderson,K.L.,and Salyers,A.A. (1989). Biochemical evidence that starch breakdown by Bacteroides thetaio-taomicron involves outer membrane starch-binding sites and periplasmic starch-degrading enzymes.J. Bacteriol 171,3192-3198.
5. Anderson,K.L.,and Salyers,A.A. (1989). Genetic evidence that outer membrane binding of starch is required for starch utilization by Bacteroides thetaiotaomi-cron.J. Bacteriol. 171, 3199-3204.
6. Andersson, A. E, Lindberg, M., Jakobsson, H., Backhed, R, Nyren, P., and Engstrand, L. (2008). Comparative analysis of human gut microbiota by barcoded pyrosequencing. PLoS ONE 3, e2836. doi: 10.1371/journal. pone.0002836
7. Austin, B., and Austin, D. A. (2007). Bacterial Fish Pathogens: Disease of Farmed and Wild Fish. Edinburgh: Springer Verlag.
8. Azam, E, and Malfatti, E (2007). Microbial structuring of marine ecosystems. Nat. Rev. Microbiol. 5,782-791.
9. Backhed, F., Ley, R. E., Sonnenburg, J. L., Peterson, D. A., and Gordon, J. I. (2005). Host-bacterial mutualism in the human intestine. Science 307, 1915-1920.
10. Balakirev, E. S., Pavlyuchkov, V. A., and Ayala, E J. (2008). DNA variation and symbiotic associations in phenotypically diverse sea urchin Strongylocentrotus intermedius. Proc. Natl. Acad. Sci. U.S.A. 105, 16218-16223.
11. Barbeyron, T., L'haridon, S., Corre, E., Kloareg, B., and Potin, P. (2001). Zobellia galactanovorans gen. nov., sp. nov., a marine species of Flavobacteriaceae isolated from a red alga, and classification of. Int. J. Syst. Fvol. Microbiol. 51,985-997.
12. Barbeyron, T., L'haridon, S., Michel, G., and Czjzek, M. (2008). Mariniflexile fucanivorans sp. nov., a marine member of the Flavobacteriaceae that degrades sulphated fucans from brown algae. Int. J. Syst. Fvol. Microbiol. 58,2107-2113.
13. Bauer, M., Kube, M., Teeling, H., Richter, M., Lombardot, T., Allers, E., Wurdemann, C. A., Quast, C, Kuhl, H., Knaust, E, Woebken, D., Bischof, K., Mussmann, M., Choudhuri, J. V., Meyer, F., Reinhardt, R., Amann, R. I., and Glockner, E O. (2006). Whole genome analysis of the marine Bacteroidetes "Gramella forsetii" reveals adaptations to degradation of polymeric organic matter. Environ. Microbiol. 8,2201-2213.
14. Beja, O., Aravind, L., Koonin, E. V., Suzuki, M. T., Hadd, A., Nguyen, L. P., Jovanovich, S. B., Gates, C. M., Feldman, R. A., Spudich, J. L., Spudich, E. N., and Delong, E. F. (2000). Bacterial rhodopsin: evidence for a new type of phototrophy in the sea. Science2S9,1902-1906.
15. Beleneva,I.A.,and Zhukova,N.V.(2006). Bacterial communities of brown and red algae from Peter the Great Bay, the Sea of Japan. Mikrobiologiia 75, 410-419.
16. Benno, Y., Suzuki, K., Narisawa, K., Bruce, W. R., and Mitsuoka, T. (1986). Comparison of the fecal microflora in rural Japanese and urban Canadians. Microbiol. Immunol. 30, 521-532.
17. Berg, J. O., Lindqvist, L., and Nord, C. E. (1980). Purification of glycoside hydrolases from Bacteroides fragilis. Appl. Environ. Microbiol. 40,40-47.
18. Bergey's. (2011). Sergey's Manual of Systematic Bacteriology New York: Springer.
19. Bernardet, J.-E, and Bowman, J. P. (2006). The genus Flavobacterium. Prokaryotes 7,481-531.
20. Bernardet, J.-F., and Nakagawa, Y. (2006). An introduction to the family of Flavobacteriaceae. Prokaryotes 7,455-480.
21. Bik, E. M., Eckburg, P. B., Gill, S. R., Nelson, K. E., Purdom, E. A., Francois, E, Perez-Perez, G., Blaser, M. J., and Relman.D.A. (2006).Molecular analysis of the bacterial microbiota in the human stomach. Proc. Natl. Acad. Sci. U.S.A. 103, 732-737.
22. Borneman, J., Skroch, P. W., O'sullivan, K. M., Palus, J. A., Rumjanek, N. G., Jansen, J. L., Nienhuis, J., and Triplett, E. W. (1996). Molecular microbial diversity of an agricultural soil in Wisconsin. Appl. Environ. Microbiol. 62,1935-1943.
23. Brook, I. (2010). The role of anaerobic bacteria in bacteremia. Anaerobe 16, 183-189.
24. Buckley, D. H., and Schmidt, T. M. (2003). Diversity and dynamics of microbial communities in soils from agro-ecosystems. Environ. Microbiol. 5,441-452.
25. Cantarel, B. L., Coutinho, P. M., Rancurel, C, Bernard, T., Lombard, V., and Henrissat, B. (2009). The carbohydrate-active enzymes database (CAZy): an expert resource for glycogenomics. Nucleic Acids Res. 37, D233-D238.
26. Carpita.N.C, and Gibeaut.D.M. (1993). Structural models of primary cell walls in flowering plants: consistency of molecular structure with the physical properties of the walls during growth. Plant}. 3,1-30.
27. Carroll, E. J., and Hungate, R. E. (1954). The magnitude of the microbial fermentation in the bovine rumen. Appl. Microbiol. 2,205-214.
28. Cerdeno-Tarraga, A. M., Patrick, S., Crossman, L. C, Blakely, G., Abratt, V., Lennard, N., Poxton, I., Duerden, B., Harris, B., Quail, M. A., Barron, A., Clark, L., Corton, C, Doggett, J., Holden, M. T, Larke, N., Line, A., Lord, A.,Norbertczak,H.,Ormond,D.,Price, C, Rabbinowitsch, E., Woodward, J., Barrell, B., and Parkhill, J. (2005). Extensive DNA inversions in the B. fragilis genome control variable gene expression. Science 307,1463-1465.
29. Chin, W. C, Orellana, M.V., and Verdugo, P. (1998). Spontaneous assembly of marine dissolved organic matter into polymer gels. Nature 391, 568-572.
30. Church, M. J. (2008). Resource control of bacterial dynamics in the sea, in Microbial Ecology of the Oceans, 2nd Edn, ed. D. L. Kirchman (Hoboken, NJ: Wiley & Sons), 335-382.
31. Clements, K. D., and Bullivant, S. (1991). An unusual symbiont from the gut of surgeonfishes may be the largest known prokaryote.J. Bacterial 173, 5359-5362.
32. Cottrell, M. T., and Kirchman, D. L. (2000). Community composition of marine bacterioplankton determined by 16S rRNA gene clone libraries and fluorescence in situ hybridization. Appl. Environ. Microbiol. 66, 5116-5122.
33. Crump, B. C, Armbrust, E. V., and Baross, J. A. (1999). Phylogenetic analysis of particle-attached and free-living bacterial communities in the Columbia river, its estuary, and the adjacent coastal ocean. Appl. Environ. Microbiol 65,3192-3204.
34. Crump, B. C, and Koch, E. W. (2008). Attached bacterial populations shared by four species of aquatic angiosperms. Appl Environ. Microbiol 74,5948-5957.
35. Davies, G. J., Gloster, T. M., and Henrissat, B. (2005). Recent structural insights into the expanding world of carbohydrate-active enzymes. Curr. Opin. Struct. Biol 15, 637-645.
36. Davis, H. S. (1922). A new bacterial disease of fresh-water fishes," in Bulletin of the U.S. Bureau of Fisheries, Washington, DC, 261-280.
37. De Filippo, C, Cavalieri, D., Di Paola, M., Ramazzotti, M., Poullet, J. B., Massart, S., Collini, S., Pieraccini, G., and Lionetti, P. (2010). Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proc. Natl. Acad. Sci. U.S.A. 107,14691-14696.
38. D'Elia, J. N., and Salyers, A. A. (1996). Effect of regulatory protein levels on utilization of starch by Bacteroides thetaiotaomicron. J. Bacterial 178, 7180-7186.
39. Del Rio, T. G., Abt, B., Spring, S., Lapidus, A., Nolan, M., Tice, H., Copeland, A., Cheng, J.-E, Chen, E, Hugenholtz, P., Kyrpides, N. C, Klenk, H.-R, and Lucas, S. (2010). Complete genome sequence of Chitinophaga pinensis type strain (UQM 2034T). Stand GenomicSci. 2,87-95.
40. DeLong, E. E, and Beja, O. (2010). The light-driven proton pump proteor-hodopsin enhances bacterial survival during tough times. PLoS Biol 8, el000359. doi: 10.1371/journal. pbio.1000359
41. DeLong, E. E, Franks, D. G., and Alldredge, A. L. (1993). Phylogenetic diversity of aggregate-attached vs. free-living marine bacterial assemblages. Limnol Oceanogr. 38, 924-934.
42. Dubos, R., Schaedler, R.W., Costello, R., and Hoet, P. (1965). Indigenous, normal, and autochthonous flora of the gastrointestinal tract. J. Exp. Med. 122, 67.
43. Duchaud, E., Boussaha, M., Loux, V., Bernardet, J. E, Michel, C, Kerouault, B., Mondot, S., Nicolas, P., Bossy, R., Caron, C, Bessieres, P., Gibrat, J. F., Claverol, S., Dumetz, E, Le Henaff, M., andBenmansour,A. (2007). Complete genome sequence of the fish pathogen Elavobacterium psychrophilum. Nat. Biotechnol 25, 763-769.
44. Duerden, B. I. (1994). Virulence factors in anaerobes. Clin. Infect. Dis. 18, 253-259.
45. Eckburg, P. B., Bik, E. M., Bernstein, C. N., Purdom, E., Dethlefsen, L., Sargent, M., Gill, S. R., Nelson, K. E., andRelman.D.A. (2005).Diversity of the human intestinal microbial flora. Science 308,1635-1638.
46. Edwards, J. L., Smith, D. L., Connolly, J., Mcdonald, J. E., Cox, M. J., Joint, I., Edwards, C, and McCarthy, A. J. (2010). Identification of carbohydrate metabolism genes in the metagenome of a marine biofilm community shown to be dominated by Gammaproteobacteria and Bacteroidetes. Genes 1, 371-384.
47. Fandino, L. B., Riemann, L., Steward, G. E, Long, R. A., and Azam, E (2001). Variations in bacterial community structure during a dinoflagellate bloom analyzed by DGGE and 16S rDNA sequencing. Aquat. Microb. Ecol 23,119-130.
48. Ferraris, R.P. (2001). Dietary and developmental regulation of intestinal sugar transport. Biochem. J. 360,265-276.
49. Figge, R. M., Schubert, M., Brinkmann, H., and Cerff, R. (1999). Glyceraldehyde-3-phosphate dehydrogenase gene diversity in eubacteria and eukaryotes: evidence for intra- and inter-kingdom gene transfer. Mol Biol. Evol 16, 429-440.
50. Fletcher, H. M., Schenkein, H. A., Morgan, R. M., Bailey, K. A., Berry, C. R., and Macrina, E L. (1995). Virulence of a Porphyromonas gmgrra/zsW8 3 mutant defective in the prtH gene. Infect. Immun. 63,1521-1528.
51. Flint, H. J., Bayer, E. A., Rincon, M. T., Lamed, R., and White, B. A. (2008). Polysaccharide utilization by gut bacteria: potential for new insights from genomic analysis. Nat. Rev. Microbiol. 6,121-131.
52. Frias-Lopez, J., Zerkle, A. L., Bonheyo, G. T., and Fouke, B. W. (2002). Partitioning of bacterial communities between seawater and healthy, black band diseased, and dead coral surfaces. Appl. Environ. Microbiol. 68, 2214-2228.
53. Fukuda, S., Saito, H., Nakaji, S., Yamada, M., Ebine, N., Tsushima, E., Oka, E., Kumeta, K., Tsukamoto, T., and Tokunaga, S. (2007). Pattern of dietary fiber intake among the Japanese general population. Eur. J. Clin. Nutr. 61,99-103.
54. Gibson, F. C, and Attardo Genco, C. (2006). The genus Porphyromonas. Prokaryotes 7,428-454.
55. Gihring, T. M., Humphrys, M., Mills, H. J., Huettel, M., and Kostka, J. E. (2009). Identification of phytodetri-tus-degrading microbial communities in sublittoral Gulf of Mexico sands. Limnol. Oceanogr. 54,1073-1083.
56. Glöckner, E O., Fuchs, B. M., and Amann, R. (1999). Bacterioplankton compositions of lakes and oceans: a first comparison based on fluorescence in situ hybridization. Appl. Environ. Microbiol. 65,3721-3726.
57. Goldberg, M. J., Smith, J. W, and Nichols, R. L. (1977). Comparison of the fecal microflora of seventh-day adventists with individuals consuming a general diet. Implications concerning colonic carcinoma. Ann. Surg 186, 97-100.
58. Gomez-Consarnau, L., Gonzalez, J. M., Coll-Llado, M., Gourdon, P., Pascher, T., Neutze, R., Pedros-Alio, C, and Pinhassi, J. (2007). Light stimulates growth of proteorhodopsin-containing marine Flavobacteria. Nature 445,210-213.
59. Gomez-Pereira, P. R., Fuchs, B. M., Alonso, C, Oliver, M. J., Van Beusekom, J. E., and Amann, R. (2010). Distinct flavo-bacterial communities in contrasting water masses of the north Atlantic Ocean. ISMEJ. 4,472-487.
60. Gonzalez, J. M., Fernandez-Gomez, B., Fernandez-Guerra, A., Gomez-Consarnau, L., Sanchez, O., Coll-Llado, M., Del Campo, J., Escudero, L., Rodriguez-Martinez, R., Alonso-Saez, L., Latasa, M., Paulsen, I., Nedashkovskaya, O., Lekunberri, I., Pinhassi, J., and Pedros-Alio, C. (2008). Genome analysis of the proteorhodopsin-containing marine bacterium Pohribacter sp. MED 152 (Flavobacteria). Proc. Natl. Acad. Sci. U.S.A. 105, 8724-8729.
61. Gooday, A. J. (2002). Biological responses to seasonally varying fluxes of organic matter to the ocean floor: a review. J. Oceanogr. 58, 305-332.
62. Graham, L. E., Cook, M. E., and Busse, J. S. (2000).The origin of plants: body plan changes contributing to a major evolutionary radiation. Proc. Natl. Acad. Sci. U.S.A. 97,4535-4540.
63. Greiner, D., and Mayrand, D. (1987). Selected characteristics of pathogenic and nonpathogenic strains of Bacteroides gingivalis. J. Clin. Microbiol. 25, 738-740.
64. Han, C, Spring, S., Lapidus, A., Del Rio, T. G., Tice, H., Copeland, A., Cheng, J.-E, Lucas, S., Chen, E, Nolan, M., Bruce, D., Hugenholtz, P., Kyrpides, N. C, Klenk, H.-R, and Detter, J. C. (2009). Complete genome sequence of Pedobacterheparinustype strain (HIM 762-3T). Stand. GenomicSci. 1,54-62.
65. Hehemann, J. H., Correc, G., Barbeyron, T, Helbert, W, Czjzek, M., and Michel, G. (2010). Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota. Nature 464,908-912.
66. Henrissat, B. (1991). A classification of glycosyl hydrolases based on amino acid sequence similarities. Biochem. J. 280,309-316.
67. Hildebrandt, M. A., Hoffmann, C, Sherrill-Mix, S. A., Keilbaugh, S. A., Hamady M., Chen, Y. Y, Knight, R., Ahima, R. S., Bushman, F., and Wu, G. D. (2009).High-fat diet determines the composition of the murine gut microbiome independently of obesity. Gastroenterology 137, 1716-1724, el711-1712.
68. Hongoh, Y, Sharma, V K., Prakash, T., Nodal, S., Toh, H., Taylor, T. D., Kudo 1, T, Sakaki, Y, Toyoda, A., Hattori, M., and Ohkumal, M. (2008). Genome of an endosymbiont coupling N2 fixation to cellulolysis within protist cells in termite gut. Science 322,1108-1109.
69. Hooper, L. V, Midtvedt, T., and Gordon, J. I. (2002).How host-microbial interactions shape the nutrient environment of the mammalian intestine. Annu. Rev. Nutr. 22,283-307.
70. Hugo, C. J., Bruun, B., and Jooste, P. J. (2006). The genera Bergeyella and Weeksella. Prokaryotes 7, 532-538.
71. Hugo, C. J., Bruun, B., and Jooste, P. J. (2006). The genera Empedobacter and Myroides. Prokaryotes 7,630-637.
72. Hugo, C. J., Jooste, P. J., Segers, P., Vancanneyt, M., and Kersters, K. (1999). A polyphasic taxonomic study of Chryseobacterium strains isolated from dairy sources. Syst. Appl. Microbiol. 22, 586-595.
73. Jenkinson, H. E, and Lamont, R. J. (2005). Oral microbial communities in sickness and in health. Trends Microbiol. 13,589-595.
74. Jooste, P. J., and Hugo, C. J. (1999). The taxonomy, ecology and cultivation of bacterial genera belonging to the family Flavobacteriaceae. Int. J. Food Microbiol. 53, 81-94.
75. Juries, E. M., Fuchs, B. M., Arnosti, C, and Briichert, V. (2010). Organic carbon degradation in anoxicorganic-rich shelf sediments: biogeo-chemical rates and microbial abundance. Geomicrobiol J. 27, 303-314.
76. Keijser, B. J.,Zaura, E., Huse, S. M., Van Der Vossen, J. M., Schuren, F. H., Montijn, R. C, Ten Cate, J. M., and Crielaard, W. (2008).Pyrosequencing analysis of the oral microflora of healthy adults. J. Dent. Res. 87,1016-1020.
77. Kim, B. Y., Weon, H. Y., Cousin, S., Yoo, S. H., Kwon, S. W., Go, S. J., and Stackebrandt, E. (2006). Flavobacterium daejeonense sp. nov. and Flavobacterium suncheonense sp. nov., isolated from greenhouse soils in Korea. Int. J. Syst. Evol. Microbiol. 56, 1645-1649.
78. Kim, H.-J., Miller, A. J., Mcgowan, J., and Carter, M. L. (2009). Coastal phyto-plankton blooms in the Southern California Bight. Prog. Oceanogr. 82, 137-147.
79. Kim, K. K., Kim, M. K., Lim, J. H., Park, H. Y, and Lee, S. T. (2005). Transfer of Chryseobacterium meningosep-ticum and Chryseobacterium miri-cola to Elizabethkingia gen. nov. as Elizabethkingia meningoseptica comb. nov. and Elizabethkingia miricola comb. nov. Int. J. Syst. Evol. Microbiol. 55,1287-1293.
80. Kim, Y.S., and Milner J.A. (2007).Dietary modulation of colon cancer risk. J. Nutr. 137,2576-2579.
81. King, E. O. (1959). Studies on a group of previously unclassified bacteria associated with meningitis in infants. Am. J. Clin.Pathol. 31,241-247.
82. Kirchman, D. L. (2002). The ecology of Cytophaga-Flavobacteria in aquatic environments. FEMS Microbiol. Ecol. 39,91-100.
83. Kirchman, D. L. (2008). New light on an important microbe in the ocean. Proc. Natl.Acad.Sci. U.S.A. 105,8487-8488.
84. Kitamura, M., Okuyama, M., Tanzawa, E, Mori, H., Kitago, Y., Watanabe, N., Kimura, A., Tanaka, I., and Yao, M. (2008). Structural and functional analysis of a glycoside hydrolase family 97 enzyme from Bacteroides thetaiotaomicron. J. Biol. Chem. 283, 36328-36337.
85. Knapp, B. A., Seeber, J., Rief, A., Meyer, E., and Insam, H. (2010). Bacterial community composition of the gut microbiota of Cylindroiulus fulviceps (diplopoda) as revealed by molecular fingerprinting and cloning. Folia Microbiol. (Praha) 55,489-496.
86. Koropatkin, N. M., Martens, E. C, Gordon, J. I., and Smith, T. J. (2008). Starch catabolism by a prominent human gut symbiont is directed by the recognition of amylose helices. Structure 16,1105-1115.
87. Koropatkin,N.M.,and Smith,T.J.(2010). SusG: a unique cell-membrane-associated alpha-amylase from a prominent human gut symbiont targets complex starch molecules. Structure 18,200-215.
88. Kuwahara, T., Yamashita, A., Hirakawa, H., Nakayama, H., Toh, H., Okada, N., Kuhara, S., Hattori, M., Hayashi, T., and Ohnishi, Y. (2004). Genomic analysis of Bacteroides fragilis reveals extensive DNA inversions regulating cell surface adaptation. Proc. Nail. Acad. Sci. U.S.A. 101,14919-14924.
89. Lail, K., Sikorski, J., Saunders, E., Lapidus, A., Del Rio, T. G., Copeland, A., Tice, H., Cheng, J.-F., Lucas, S., Kyrpides, N. C, Klenk, H.-P., and Chen, E (2010). Complete genome sequence of Spirosomalinguale type strain (IT). Stand. Genomic Sci. 2,176-185.
90. Laine, R. A. (1994). A calculation of all possible oligosaccharide isomers both branched and linear yields 1.05 × 10(12) structures for a reducing hexasaccharide: the isomer barrier to development of single-method sac-charide sequencing or synthesis systems. Glycobiology 4, 759-767.
91. Lang, E., Lapidus, A., Chertkov, O., Brettin, T., Detter, J. C, Han, C, Copeland, A., Del Rio, T. G., Nolan, M., Chen, F., Hugenholtz, P., Goker, M., Rohde, M., Kyrpides, N. C, and Klenk,H.-P. (2009). Complete genome sequence of Dyadobacter fermentans type strain (NSIHT).Stand. Genomic Sci. 1,133-140.
92. Largo, D. B., Fukami, K., and Nishijima, T. (1995). Occasional pathogenic bacteria promoting ice-ice disease in the carrageenan-producing red algae Kappaphycus alvarezii and Eucheuma denticulatum (Solieriaceae, Gigartinales, Rhodophyta). J. Appl. Phycol. 7, 545-554.
93. Lauber, C. L., Hamady, M., Knight, R., andFierer, N. (2009). Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Appl Environ. Microbiol. 75, 5111-5120.
94. Leadbetter, E. R. (2006). The genus Capnocytophaga. Prokaryotes 7, 709-711.
95. Lee, M., Woo, S. G., Park, J., and Yoo, S. A. (2010). Dyadobacter soli sp. nov, a starch-degrading bacterium isolated from farm soil. Int. J. Syst. Evol. Microbiol. 60,2577-2582.
96. Leng, J., Xie, L, Zhu, R., Yang, S., Gou, X., Li, S., and Mao, H. (2010). Dominant bacterial communities in the rumen of Gayals (Bos frontalis), Yaks (Bos grun-niens) and Yunnan Yellow Cattle (Bos taurs) revealed by denaturing gradient gel electrophoresis. Mol. Biol. Rep. PMD: 21140219. [Epub ahead of print]
97. Leser, T. D., Amenuvor, J. Z., Jensen, T. K., Lindecrona, R. H., Boye, M., and Moller, K. (2002). Culture-independent analysis of gut bacteria: the pig gastrointestinal tract microbiota revisited. Appl. Environ. Microbiol. 68, 673-690.
98. Ley, R. E., Peterson, D. A., and Gordon, J. I. (2006). Ecological and evolutionary forces shaping microbial diversity in the human intestine. Cell 124, 837-848.
99. Ley, R. E., Turnbaugh, P. J., Klein, S., and Gordon, J. I. (2006). Microbial ecology: human gut microbes associated with obesity. Nature 444,1022-1023.
100. Liao, C. H., and Wells, J. M. (1986). Properties of Cytophaga johnsonae strains causing spoilage of fresh produce at food markets. Appl. Environ. Microbiol. 52,1261-1265.
101. Llobet-Brossa, E., Rossello-Mora, R., and Amann, R. (1998). Microbial community composition of Wadden Sea sediments as revealed by fluorescence in situ hybridization. Appl. Environ. Microbiol. 64,2691-2696.
102. Loesche, W.J. (1993). Bacterial mediators in periodontal disease. Clin. Infect. Dis. 16,203-210.
103. Lopez-Sanchez, M. J., Neef, A., Pereto, J., Patifio-Navarrete, R., Pignatelli, M., Latorre, A., and Moya, A. (2009). Evolutionary convergence and nitrogen metabolism in Blattabacterium strain Bge, primary endosymbiont of the cockroach Blattella germanica. PLoS Genet. 5,el000721.doi: 10.1371/joumal.pgen.1000721
104. Lozupone, C. A., Hamady, M., Cantarel, B. L., Coutinho, P. M., Henrissat, B., Gordon, J. I., and Knight, R. (2008). The convergence of carbohydrate active gene repertoires in human gut microbes. Proc. Natl. Acad. Sci. U.S.A. 105,15076-15081.
105. Lu, J., Santo Domingo, J. W, Hill, S., and Edge, T. A. (2009). Microbial diversity and host-specific sequences of Canada goose feces. Appl. Environ. Microbiol. 75,5919-5926.
106. Mammeri, H., Bellais, S., and Nordmann, P. (2002). Chromosome-encoded beta-lactamases TUS-1 and MUS-1 from Myroides odoratus and Myroides odo-ratimimus (formerly Flavobacterium odoratum), new members of the lineage of molecular subclass Bl metalloenzymes. Antimicrob. Agents Chemother. 46, 3561-3567.
107. Manrique, J., and Jensen, H. H. (2001). Spanish household demand for seafood. J. Agric Econ. 52,23-37.
108. Marchesi, J. R. (2010). Prokaryotic and eukaryotic diversity of the human gut. Adv. Appl. Microbiol. 72,43-62.
109. Martens, E. C, Chiang, H. C, and Gordon, J. I. (2008). Mucosal glycan foraging enhances fitness and transmission of a saccharolytic human gut bacterial symbiont. Cell Host Microbe 4, 447-457.
110. Martens, E. C, Koropatkin, N. M., Smith, T. J., and Gordon, J. I. (2009). Complex glycan catabolism by the human gut microbiota: the Bacteroidetes Sus-like paradigm. J. Biol. Chem. 284, 24673-24677.
111. Martinez, I., Kim, J., Duffy, P. R., Schlegel, V L., and Walter, J. (2010). Resistant starches types 2 and 4 have differential effects on the composition of the fecal microbiota in human subjects. PLoS ONE 5, el5046. doi: 10.1371/joumal. pone.0015046
112. Martinez-Alonso, M., Escolano, J., Montesinos, E., and Gaju, N. (2010). Diversity of the bacterial community in the surface soil of a pear orchard based on 16SrRNA gene analysis. Int. Microbiol. 13,123-134.
113. Matsui, H., Kato, Y., Chikaraishi, T., Moritani, M., Ban-Tokuda, T., and Wakita, M. (2010). Microbial diversity in ostrich ceca as revealed by 16S ribosomal RNA gene clone library and detection of novel Fibrobacter species. Anaerobe 16, 83-93.
114. Mavrommatis, K., Gronow, S., Saunders, E., Land, M., Lapidus, A., Copeland, A., Del Rio, T. G., Nolan, M., Lucas, S., Chen, F., Tice, H., Cheng, J.-F., Bruce, D., Goodwin, L, Pitluck, S., Pati, A., Ivanova, N., Chen, A., Palaniappan, K., Chain, P., Hauser, L., Chang, Y.-J., Jeffries, C. D., Brettin, T., Detter, J. C, Han, C, Bristow, J., Goker, M., Rohde, M., Eisen, J. A., Markowitz, V, Kyrpides, N. C, Klenk, H.-P., and Hugenholtz, P. (2009). Complete genome sequence of Capnocytophaga ochracea type strain (VPI 2845T). Stand. Genomic Sci. 1,101-109.
115. Mazmanian, S. K. (2008). Capsular polysaccharides of symbiotic bacteria modulate immune responses during experimental colitis. J. Pediatr. Gastroenterol. Nutr. 46(Suppl. 1), E11-E12.
116. Mazmanian, S. K., Round, J. L., and Kasper, D. L. (2008). A microbial symbiosis factor prevents intestinal inflammatory disease. Nature 453, 620-625.
117. McBride, M. J., Xie, G., Martens, E. C, Lapidus, A., Henrissat, B., Rhodes, R. G., Goltsman, E., Wang, W, Xu, J., Hunnicutt, D. W., Staroscik, A. M., Hoover, T. R., Cheng, Y. Q., and Stein, J. L. (2009). Novel features of the polysaccharide-digesting gliding bacterium Flavobacterium johnso-niae as revealed by genome sequence analysis. Appl. Environ. Microbiol. 75, 6864-6875.
118. McCutcheon, J. P., and Moran, N. A. (2010). Functional convergence in reduced genomes of bacterial symbi-onts spanning 200 my of evolution. Genome Biol. Evol. 2, 708-718.
119. Michel, G., Tonon, T., Scornet, D., Cock, J. M., and Kloareg, B. (2010). The cell wall polysaccharide metabolism of the brown alga Ectocarpus silicu-losus. Insights into the evolution of extracellular matrix polysaccharides in Eukaryotes. New Phytol. 188,82-97.
120. Michel, G., Tonon, T., Scornet, D., Cock, J. M., and Kloareg, B. (2010). Central and storage carbon metabolism of the brown alga Ectocarpus siliculosus: insights into the origin and evolution of storage carbohydrates in Eukaryotes. New Phytol. 188,67-81.
121. Middelbos, I. S., Vester Boler, B. M., Qu, A., White, B. A., Swanson, K. S., and Fahey, G. C. Jr. (2010). Phylogenetic characterization of fecal microbial communities of dogs fed diets with or without supplemental dietary fiber using 454 pyrosequencing. PLoS ONE 5, e9768. doi: 10.1371/journal.pone.0009768
122. Mongodin, E. E, Nelson, K. E., Daugherty, S., Deboy R. T, Wister, J., Khouri, H., Weidman, J., Walsh, D. A., Papke, R. T., Sanchez Perez, G., Sharma, A. K., Nesbo, C. L., Macleod, D., Bapteste, E., Doolittle, W. E, Charlebois, R. L., Legault, B., and Rodriguez-Valera, E (2005). The genome of Salinibacter ruber: convergence and gene exchange among hyperhalophilic bacteria and archaea. Proc. Natl. Acad. Sci. U.S.A. 102,18147-18152.
123. Moore,WE.,and Holdeman,L.V. (1974). Special problems associated with the isolation and identification of intestinal bacteria in fecal flora studies. Am. J. Clin. Nutr. 27,1450-1455.
124. Nagata, T. (2008). Organic matter-bacteria interactions in seawater, in Microbial Ecology in the Oceans, 2nd Edn, ed. D. L. Kirchman (Hoboken, NJ: Wiley & Sons), 207-242.
125. Naito, M., Hirakawa, H., Yamashita, A., Ohara, N., Shoji, M., Yukitake, H., Nakayama, K., Toh, H., Yoshimura, F., Kuhara, S., Hattori, M., Hayashi, T., and Nakayama, K. (2008). Determination of the genome sequence of Porphyromonas gin-givalis strain ATCC 33277 and genomic comparison with strain W83 revealed extensive genome rearrangements in P. gingivalis. DNA Res. 15,215-225.
126. Nasidze, I., Li, J., Quinque, D., Tang, K., and Stoneking, M. (2009). Global diversity in the human salivary micro-biome. Genome Res. 19, 636-643.
127. Nasidze, I., Quinque, D., Li, J., Li, M., Tang, K., and Stoneking, M. (2009). Comparative analysis of human saliva microbiome diversity by bar-coded pyrosequencing and cloning approaches. Anal. Biochem. 391, 64-68.
128. Neill, K., Heesch, S., and Nelson, W. (2008). Diseases, Pathogens and Parasites of Undaria pinnatifida. Wellington: Ministary of Agriculture and Foresty.
129. Nelson, K. E., Fleischmann, R. D., Deboy R. T., Paulsen, I. T., Fouts, D. E., Eisen, J. A., Daugherty, S. C, Dodson, R. J., Durkin, A. S., Gwinn, M., Haft, D. H., Kolonay J. F., Nelson, W C, Mason, T., Tallon, L., Gray, J., Granger, D., Tettelin, H., Dong, H., Galvin, J. L., Duncan, M. J., Dewhirst, F. E., and Fraser, C. M. (2003). Complete genome sequence of the oral pathogenic Bacterium Porphyromonas gingivalis strain W83. J. Bacterial. 185,5591-5601.
130. Niklas, K. J. (2004). The cell walls that bind the tree of life. Bioscience 54,831-841.
131. Nisizawa, K., Noda, H., Kikuchi, R., and Watanabe, T. (1987). The main seaweed foods in Japan. Hydrobiologia 151/152,5-29.
132. Nolan, M., Tindall, B. J., Pomrenke, H., Lapidus, A., Copeland, A., Glavina Del Rio, T., Lucas, S., Chen, E, Tice, H., Cheng, J. F., Saunders, E., Han, C, Bruce, D., Goodwin, L., Chain, P., Pitluck, S., Ovchinikova, G., Pati, A., Ivanova, N., Mavromatis, K., Chen, A., Palaniappan, K., Land, M., Hauser, L., Chang, Y. J., Jeffries, C. D., Brettin, T., Goker, M., Bristow, J., Eisen, J. A., Markowitz, V., Hugenholtz, P., Kyrpides, N. C, Klenk, H. P., and Detter, J. C. (2009). Complete genome sequence of Rhodothermus marinus type strain (R-10). Stand. Genomic Sci. 1,283-290.
133. Oh, H. M., Giovannoni, S. J., Lee, K., Ferriera, S., Johnson, J., and Cho, J. C. (2009). Complete genome sequence of Robiginitalea biformata HTCC2501. J. Bacteriol. 191,7144-7145.
134. Oh, H. M., Kang, I., Ferriera, S., Giovannoni, S. J., and Cho, J. C. (2010). Complete genome sequence of Croceibacter atlanticus H7CC2559(T). J. Bacteriol. 192,4796-4797.
135. Oh, H. M., Kang, I., Yang, S. J., Jang, Y, Vergin, K. L., Giovannoni, S. J., and Cho, J. C. (2011). Complete genome sequence of strain HTCC2170, anovel member of the genus Maribacter in the family Flavobacteriaceae. J. Bacteriol. 193,303-304.
136. Pankratov, T. A., Kulichevskaya, I. S., Liesack, W, and Dedysh, S. N. (2006). Isolation of aerobic, gliding, xylano-lytic and laminarinolytic bacteria from acidic Sphagnum peatlands and emended description of Chitinophaga arvensicoh Kampfer et al. 2006. Int. J. Syst. Evol. Microbiol. 56,2761-2764.
137. Pei, Z., Bini, E. J., Yang, L., Zhou, M., Francois, E, and Blaser, M. J. (2004). Bacterial biota in the human distal esophagus. Proc Natl. Acad. Sci. U.S.A. 101,4250-4255.
138. Pena, A., Teeling, H., Huerta-Cepas, J., Santos, F., Yarza, P., Brito-Echeverria, J., Lucio, M., Schmitt-Kopplin, P., Meseguer, I., Schenowitz, C, Dossat, C, Barbe, V., Dopazo, J., Rossello-Mora, R., Schüler, M., Glöckner, E O., Amann, R., Gabaldón,T, and Anton, J. (2010). Fine-scale evolution: genomic, phenotypic and ecological differentiation in two coexisting Salinibacter ruber strains. ISMEJ. 4, 882-895.
139. Pinhassi, J., Azam, F., Hemphala, J., Long, R. A., Martinez, J., Zweifel, U. L.,andHagstrom,A. (1999). Coupling between bacterioplankton species composition, population dynamics, and organic matter degradation. Aquat. Microb. Ecol. 17,13-26.
140. Ploug, H., Grossart, H. P., Azam, E, and Jorgensen, B. B. (1999). Photosynthesis, respiration, and carbon turnover in sinking marine snowfrom surface waters of Southern California Bight: implications for the carbon cycle in the ocean. Mar. Ecol. Prog.Ser. 179,1-11.
141. Pommier, T., Canback, B., Riemann, L., Bostrom, K. H., Simu, K., Lundberg, P.,Tunlid,A.,and Hagstrom,A. (2007). Global patterns of diversity and community structure in marine bacterioplankton. Mol. Ecol. 16, 867-880.
142. Pope, P. B., Denman, S. E., Jones, M., Tringe, S. G., Barry, K., Malfatti, S. A., Mchardy, A. C, Cheng, J. E, Hugenholtz, P., Mcsweeney, C. S., and Morrison, M. (2010). Adaptation to herbivory by the Tammar wallaby includes bacterial and glycoside hydrolase profiles different from other herbivores. Proc Natl. Acad. Sci. U.S.A. 107,14793-14798.
143. Popper, Z. A., Michel, G., Herve, C, Domozych, S. C, Willats, W. G. T., Tuohy, M. G., Kloareg, B., and Stengel, D.B. (2011).Evolution and diversity of plant cell walls: from algae to flowering plants. Annu. Rev. Plant Biol. 62, 567-590.
144. Purushe, J., Fouts, D. E., Morrison, M., White, B. A., Mackie, R. I., Coutinho, P. M., Henrissat, B., and Nelson, K. E. (2010). Comparative genome analysis of Prevotella ruminicola and Prevotella bryantii: insights into their environmental niche. Microb. Ecol. 60,721-729.
145. Qin, Q. L., Zhang, X. Y, Wang, X. M., Liu, G. M., Chen, X. L., Xie, B. B., Dang, H. Y, Zhou, B. C, Yu, J., and Zhang, Y Z. (2010). The complete genome of Zunongwangia profunda SM-A87 reveals its adaptation to the deep-sea environment and ecological role in sedimentary organic nitrogen degradation. BMC Genomics 11, 247. doi: 10.1186/1471-2164-11-247
146. Raman, R., Sasisekharan, V., and Sasisekharan, R. (2005). Structural insights into biological roles of protein-glycosaminoglycan interactions. Chem. Biol. 12,267-277.
147. Rath, J., Wu, K. Y., Herndl, G. J., and Delong, E. F. (1998). High phylogenetic diversity in a marine-snow-associated bacterial assemblage. Aquat. Microb. Ecol. 14,261-269.
148. Ratner,H. (1984). Flavobacterium menin-gosepticum. Infect. Control5,237-239.
149. Rebuffet, E., Groisillier, A., Thompson, A., Jeudy, A., Barbeyron, T., Czjzek, M., and Michel, G. (2011). Discovery and structural characterization of a novel glycosidase family of marine origin. Environ. Microbiol. 13,1253-1270.
150. Redford, A. J., Bowers, R. M., Knight, R., Linhart, Y, and Fierer, N. (2010). The ecology of the phyllosphere: geographic and phylogenetic variability in the distribution of bacteria on tree leaves. Environ. Microbiol. 12, 2885-2893.
151. Reeves, A. R., Wang, G. R., and Salyers, A. A. (1997). Characterization of four outer membrane proteins that play a role in utilization of starch by Bacteroides thetaiotaomicron. J. Bacteriol. 179, 643-649.
152. Reichenbach, H. (2006). The order cytophagales. Prokaryotes 7, 549-590.
153. Riemann, L., Steward, G. E, and Azam, E (2000). Dynamics of bacterial community composition and activity during a mesocosm diatom bloom. Appl. Environ. Microbiol. 66, 578-587.
154. Riepe, S. P., Goldstein, J., and Alpers, D. H. (1980). Effect of secreted Bacteroides proteases on human intestinal brush border hydrolases. J. Clin. Invest. 66, 314-322.
155. Rohwer, F., Seguritan, V., Azam, F., and Knowlton, N. (2002). Diversity and distribution of coral-associated bacteria. Mar. Ecol. Prog. Ser. 243,1-10.
156. Rook, G. A., and Brunet, L. R. (2005). Microbes, immunoregulation, and the gut. Gut 54, 317-320.
157. Rudek, W., and Haque, R. U. (1976). Extracellular enzymes of the genus Bacteroides. J. Clin. Microbiol. 4, 458-460.
158. Sabree, Z. L., Kambhampati, S., and Moran, N. A. (2009). Nitrogen recycling and nutritional provisioning by Blattabacterium, the cockroach endo-symbiont. Proc. Natl. Acad. Sci. U.S.A. 106,19521-19526.
159. Salaun, S., Kervarec, N., Potin, P., Haras, D., Piotto, M., and La Barre, S. (2010). Whole-cell spectroscopy is a convenient tool to assist molecular identification of cultivatable marine bacteria and to investigate their adaptive metabolism. Talanta 80, 1758-1770.
160. Salyers, A. A., Vercellotti, J. R., West, S. E., and Wilkins, T. D. (1977). Fermentation of mucinandplant polysaccharides by strains of Bacteroides from the human colon. Appl Environ. Microbiol 33,319-322.
161. Savage, D. C, Dubos, R., and Schaedler, R. W. (1968). The gastrointestinal epithelium and its autochthonous bacterial flora.J. Exp. Med. 127, 67-76.
162. Schmitt-Wagner, D., Friedrich, M. W., Wagner, B., and Brune, A. (2003). Phylogenetic diversity, abundance, and axial distribution of bacteriain the intestinal tract of two soil-feeding termites (Cubitermesspp.). Appl Environ. Microbiol. 69, 6007-6017.
163. Schmitz-Esser, S., Tischler, P., Arnold, R., Montanaro, J., Wagner, M., Rattei, T., and Horn, M. (2010). The genome of the amoeba symbiont "Candidatus Amoebophilus asiaticus" reveals common mechanisms for host cell interaction among amoeba-associated bacteria.J. Bacteriol. 192,1045-1057.
164. Scupham, A. J., Patton, T. G., Bent, E., and Bayles, D. O. (2008). Comparison of the cecal microbiota of domestic and wild turkeys. Microb. Ecol. 56,322-331.
165. Segers, P., Mannheim, W., Vancanneyt, M., De Brandt, K., Hinz, K. H., Kersters, K., and Vandamme, P. (1993). Riemerella anatipestifer gene nov. comb, nov., the causative agent of septicemia anserum exsudativa, and its phylogenetic affiliation within the Flavobacterium-Cytophaga rRNA homologygroup. Int. J. Syst. Bacteriol 43, 768-776.
166. Sghir, A., Gramet, G., Suau, A., Rochet, V., Pochart, P., and Dore, J. (2000). Quantification of bacterial groups within human fecal flora by oligonu-cleotide probe hybridization. Appl Environ. Microbiol 66,2263-2266.
167. Shah, H. N., and Collins, D. M. (1990). Prevotella, a new genus to include Bacteroides melaninogenicus and related species formerly classified in the genus Bacteroides. Int. J. Syst. Bacteriol 40,205-208.
168. Shipman, J. A., Berleman, J. E., and Salyers, A. A. (2000). Characterization of four outer membrane proteins involved in binding starch to the cell surface of Bacteroides thetaiotaomicron. J. Bacteriol 182,5365-5372.
169. Shipman, J. A., Cho, K. H., Siegel, H. A., andSalyers.A. A. (1999). Physiological characterization of SusG, an outer membrane protein essential for starch utilization by Bacteroides thetaiotaomicron. J. Bacteriol 181,7206-7211.
170. Shoemaker, N. B., Vlamakis, H., Hayes, K., and Salyers, A. A. (2001). Evidence for extensive resistance gene transfer among Bacteroides spp. and among Bacteroides and other genera in the human colon. Appl. Environ. Microbiol 67, 561-568.
171. Sievert, S. M., Kuever, J., and Muyzer, G. (2000). Identification of 16S ribosomal DNA-defined bacterial populations at a shallow submarine hydrothermal vent near Milos Island (Greece). Appl. Environ. Microbiol. 66, 3102-3109.
172. Silvi, S., Rumney, C. J., Cresci, A., and Rowland, I. R. (1999). Resistant starch modifies gut microflora and microbial metabolism in human flora-associated rats inoculated with faeces from Italian and UK donors. J. Appl Microbiol 86, 521-530.
173. Simek, K., Armengol, J., Comerma, M., Garcia, J. C, Kojecka, P., Nedoma, J., and Hejzlar, J. (2001). Changes in the epilimnetic bacterial community composition, production, and protist-induced mortality along the longitudinal axis of a highly eutrophic reservoir. Microb.Ecol 42, 359-371.
174. Simon, M., Glockner, E O., and Amann, R. (1999). Different community structure and temperature optima of heterotrophic picoplankton in various regions of the Southern Ocean. Aquat. Microb.Ecol 18,275-284.
175. Skerratt, J. H., Bowman, J. P., Hallegraeff G., James, S., and Nichols, P. D. (2002). Algicidal bacteria associated with blooms of a toxic dinoflagellate in a temperate Australian estuary. Mar. Ecol Prog. Ser. 244,1-15.
176. Smith, C. J., and Bryant, M. P. (1979). Introduction to metabolic activities of intestinal bacteria. Am. J. Clin. Nutr. 32,149-157.
177. Smith, C. J., Rocha, E. R., and Paster, B. J. (2006). The medically important Bacteroides spp. in health and disease. Prokaryotes 7, 381-427.
178. Sohn, J. H., Lee, J. H., Yi, H., Chun, J., Bae, K. S., Ahn, T. Y., and Kim, S. J. (2004). Kordia algicida gen. nov, sp. nov., an algicidal bacterium isolated from red tide. Int. J. Syst. Evol Microbiol 54, 675-680.
179. Sonnenburg, E. D., Zheng, H., Joglekar, P., Higginbottom, S. K., Firbank, S. J., Bolam, D. N., and Sonnenburg, J. L. (2010). Specificity of polysaccharide use in intestinal bacteroides species determines diet-induced microbiota alterations. Cell 141,1241-1252.
180. Sonnenburg, J. L. (2010). Microbiology: genetic pot luck. Nat Mre, 464,837-838.
181. Stahl.E. A., and Bishop, J.G. (2000). Plant-pathogen arms races at the molecular level. Curr. Opin. Plant Biol. 3, 299-304.
182. Staufenberger, T, Thiel, V., Wiese, J., and Imhoff, J. F. (2008). Phylogenetic analysis of bacteria associated with Laminaria saccharina. FEMS Microbiol Ecol 64, 65-77.
183. Sugahara, K., and Kitagawa, H. (2002). Heparin and heparan sulfate biosynthesis. IUBMB Life 54,163-175.
184. Sunairi, M., Tsuchiya, H., Tsuchiya, T., Omura, Y., Koyanagi, Y., Ozawa, M., Iwabuchi, N., Murooka, H., and Nakajima, M. (1995). Isolation of a bacterium that causes anaaki disease of the red algae Porphyra yezoensis. J. Appl. Microbiol. 79,225-229.
185. Suomalainen, L.-R., Tiirola, M., and Valtonen, E. T. (2006). Chondroitin AC lyase activity is related to virulence of fish pathogenic Flavobacterium columnare. J. Fish Dis. 29, 701-770.
186. Tajima, K., Aminov, R. I., Nagamine, T., Ogata, K., Nakamura, M., Matsui, H., and Benno.Y. (1999).Rumen bacterial diversity as determined by sequence analysis of 16S rDNA libraries. FEMS Microbiol Ecol 29,159-169.
187. Tanner, A. C. R., Listgarten, M. A., Ebersole, J. L., and Strzempko, M. N. (1986). Bacteroidesforsythus sp. nov, a slow-growing, Fusiform Bacteroides sp. from the human oral cavity. Int. J. Syst. Bacteriol 36,213-221.
188. Thomas, C. M., and Nielsen, K. M. (2005). Mechanisms of, and barriers to, horizontal gene transfer between bacteria. Nat. Rev. Microbiol 3, 711-721.
189. Tierny, Y, Bechet, M., Joncquiert, J. C, Dubourguier, H. C, and Guillaume, J. B. (1994). Molecular cloning and expression in Escherichia coli of genes encoding pectate lyase and pectin methylesterase activities from Bacteroides thetaiotaomicron. J. Appl Bacteriol 76, 592-602.
190. Turnbaugh, P. J., Henrissat, B., and Gordon, J. I. (2010). Viewing the human microbiome through three-dimensional glasses: integrating structural and functional studies to better define the properties of myriad carbohydrate-active enzymes. Acta Crystallogr. Sect. F Struct. Biol Cryst. Commun. 66,1261-1264.
191. Turnbaugh, P. J., Ley, R. E., Hamady M., Fraser-Liggett, C. M., Knight, R., and Gordon, J. I. (2007). The human microbiome project. Nature 449, 804-810.
192. Turnbaugh, P. J., Ridaura, V. K., Faith, J. J., Rey F. E., Knight, R., and Gordon, J. I. (2009). The effect of diet on the human gut microbiome: a metagen-omic analysis in humanized gnotobiotic mice. Sci. Transl Med. 1, 6ral4.
193. Uyenco, F. R. (1977). Microbiological studies of diseased Eucheuma sp. and other seaweeds," in National Seaweeds Symposium, Manilla, Philippines.
194. van Hannen, E. J., Zwart, G., Van Agterveld, M. P., Gons, H. J., Ebert, J., and Laanbroek, H. J. (1999). Changes in bacterial and eukaryotic community structure after mass lysis of filamentous cyanobacteria associated with viruses. Appl Environ. Microbiol 65,795-801.
195. Vandamme, P., Segers, P., Vancanneyt, M., Van Hove, K., Mutters, R., Hommez, J., Dewhirst, E, Paster, B., Kersters, K., Falsen, E., Devriese, L. A., Bisgaard, M., Hinz, K.H.,andMannheim,W (1994). Ornithobacterium rhinotracheale gen. nov, sp. nov. isolated from the avian respiratory tract. Int. J. Syst. Bacteriol 44,24-37.
196. Vandamme, P., Vancanneyt, M., Segers, P., Ryll, M., Kohler, B., Ludwig, W, and Hinz, K.H. (1999). Coenonia anatina gen. nov., sp. nov, a novel bacterium associated with respiratory disease in ducks and geese. Int. J. Syst. Bacteriol 49, 867-874.
197. Wen, L, Ley, R. E., Volchkov, P. Y, Stranges, P. B., Avanesyan, L., Stonebraker, A. C, Hu, C, Wong, F. S., Szot, G. L., Bluestone, J. A., Gordon, J. I., and Chervonsky, A. V. (2008). Innate immunity and intestinal microbiota in the development of type 1 diabetes. Nature 455,1109-1113.
198. Wexler, H. M. (2007). Bacteroides: the good, the bad, and the nitty-gritty. Clin. Microbiol Rev. 20, 593-621.
199. Whitman, W B., Coleman, D. C, and Wiebe, W J. (1998). Prokaryotes: the unseen majority. Proc. Nail. Acad. Sci. U.S.A. 95, 6578-6583.
200. Woese, C. R. (1987). Bacterial evolution. Microbiol Rev. 51,221-271.
201. Woese, C. R., Yang, D., Mandelco, L., and Stetter, K. O. (1990). The flexibacter-flavobacter connection. Syst. Appl. Microbiol 13,161-165.
202. Wostmann, B. S., Larkin, C, Moriarty A., and Bruckner-Kardoss, E. (1983). Dietary intake, energy metabolism, and excretory losses of adult male germfree Wistar rats. Lab. Anim. Sci. 33,46-50.
203. Woyke, T., Xie, G., Copeland, A., Gonzalez, J. M., Han, C, Kiss, H., Saw, J. H., Senin, P., Yang, C, Chatterji, S., Cheng, J. E, Eisen, J. A., Sieracki, M. E., and Stepanauskas, R. (2009). Assembling the marine metagenome, one cell at a time. PLoS ONE 4,e5299.doi: 10.1371/journal.pone.0005299
204. Xie, G., Bruce, D. C, Challacombe, J. E, Chertkov, O., Detter, J. C, Gilna, P., Han, C. S., Lucas, S., Misra, M., Myers, G. L., Richardson, P., Tapia, R., Thayer, N., Thompson, L. S., Brettin, T. S., Henrissat, B., Wilson, D.B., and McBride, M. J. (2007). Genome sequence of the cellulolytic gliding bacterium Cytophaga hutch-insonii. Appl. Environ. Microbiol. 73, 3536-3546.
205. Xu, J., Bjursell, M. K., Himrod, J., Deng, S., Carmichael, L. K., Chiang, H. C, Hooper, L. V, and Gordon, J.I. (2003). A genomic view of the human-Bac-teroides thetaiotaomicron symbiosis. Science 299,2074-2076.
206. Xu, J., Mahowald, M. A., Ley, R. E., Lozupone, C. A., Hamady, M., Martens, E. C, Henrissat, B., Coutinho, P. M., Minx, P., Latreille, P., Cordum, H., Van Brunt, A., Kim, K., Fulton, R. S., Fulton, L. A, Clifton, S. W., Wilson, R. K., Knight, R. D., and Gordon, J. I. (2007). Evolution of symbiotic bacteria in the distal human intestine. PLoS Biol. 5, el56. doi: 10.1371/journal. pone.0005299
207. Zhou, J. P., Huang, Y., and Mo, M. (2009). Phylogenetic analysis on the soil bacteria distributed in karst forest. Braz.]. Microbiol. 40, 827-837.
208. Zhu, X. Y., Zhong, T., Pandya, Y, and Joerger,R.D. (2002). 16SrRNA-based analysis of microbiota from the cecum of broiler chickens. Appl. Environ. Microbiol. 68,124-137.
209. +- dependent family of alpha-mannosidases in a human gut symbiont.Nat Chem. Biol. 6,125-132.
210. Zwart, G., Crump, B. C, Kamst-Van Agterveld, M. P., Hagen, F., and Han, S. K. (2002). Typical freshwater bacteria: an analysis of available 16S rRNA gene sequences from plankton of lakes and rivers. Aquat. Microb. Ecol. 28,141-155.