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  • Ansede, J.H., Friedman, R., and Yoch, D.C. (2001) Phylogenetic analysis of culturable dimethyl sulfide-producing bacteria from a Spartina-dominated salt marsh and estuarine water. Appl Environ Microbiol 67: 12101217.
  • Antoine, E., Cilia, V., Meunier, J.R., Guezennec, J., Lesongeur, F., and Barbier, G. (1997) Thermosipho melanesiensis sp. nov., a new thermophilic anaerobic bacterium belonging to the order Thermotogales, isolated from deep-sea hydrothermal vents in the southwestern Pacific Ocean. Int J Syst Bacteriol 47: 11181123.
  • Audic, S., Robert, C., Campagna, B., Parinello, H., Claverie, J.-M., Raoult, D., and Drancourt, M. (2007) Genome analysis of Minibacterium massiliensis highlights the convergent evolution of water living bacteria. PLoS Genet (in press). doi:10.1371/journal.pgen.0030138.eor.
  • Brinig, M.M., Lepp, P.W., Ouverney, C.C., Armitage, G.C., and Relman, D.A. (2003) Prevalence of bacteria of division TM7 in human subgingival plaque and their association with disease. Appl Environ Microbiol 69: 16871694.
  • Chen, X.H., Vater, J., Piel, J., Franke, P., Scholz, R., Schneider, K., et al. (2006) Structural and functional characterization of three polyketide synthase gene clusters in Bacillus amyloliquefaciens FZB42. J Bacteriol 188: 40244036.
  • Chen, X.-H., Koumoutsi, A., Reva, O., Scholz, R., Eisenreich, A., Schneider, K., et al. (2007) Comparative analysis of the complete genome sequence of the plant growth promoting Bacillus amyloliquefaciens FZB42. Nat Biotechnol, 25, in press.
  • Cutraro, J. (2007) A complex tail, simply told. ScienceNOW Daily News, 17 April 2007.
  • Doolittle, W.F., and Zhaxybayeva, O. (2007) Evolution: reducible complexity – the case for bacterial flagella. Curr Biol 17: R510R512.
  • Duchaud, E., Boussaha, M., Loux, V., Bernardet, J.F., Michel, C., Kerouault, B., et al. (2007) Complete genome sequence of the fish pathogen Flavobacterium psychrophilum. Nat Biotechnol 25: 763769.
  • Fujita, M., Mihara, H., Goto, S., Esaki, N., and Kanehisa, M. (2007) Mining prokaryotic genomes for unknown amino acids: a stop-codon-based approach. BMC Bioinformatics 8: 225.
  • Guettler, M.V., Rumler, D., and Jain, M.K. (1999) Actinobacillus succinogenes sp. nov., a novel succinic-acid-producing strain from the bovine rumen. Int J Syst Bacteriol 49: 207216.
  • Gundogdu, O., Bentley, S.D., Holden, M.T., Parkhill, J., Dorrell, N., and Wren, B.W. (2007) Re-annotation and re-analysis of the Campylobacter jejuni NCTC11168 genome sequence. BMC Genomics 8: 162.
  • Hobman, J.L., Penn, C.W., and Pallen, M.J. (2007) Laboratory strains of Escherichia coli: model citizens or deceitful delinquents growing old disgracefully? Mol Microbiol 64: 881885.
  • Hugenholtz, P., Tyson, G.W., Webb, R.I., Wagner, A.M., and Blackall, L.L. (2001) Investigation of candidate division TM7, a recently recognized major lineage of the domain Bacteria with no known pure-culture representatives. Appl Environ Microbiol 67: 411419.
  • Idriss, E.E., Makarewicz, O., Farouk, A., Rosner, K., Greiner, R., Bochow, H., et al. (2002) Extracellular phytase activity of Bacillus amyloliquefaciens FZB45 contributes to its plant-growth-promoting effect. Microbiology 148: 20972109.
  • Iyer, L.M., Aravind, L., Bork, P., Hofmann, K., Mushegian, A.R., Zhulin, I.B., and Koonin, E.V. (2001) Quod erat demonstrandum? The mystery of experimental validation of apparently erroneous computational analyses of protein sequences. Genome Biol 2: RESEARCH0051.
  • Kazor, C.E., Mitchell, P.M., Lee, A.M., Stokes, L.N., Loesche, W.J., Dewhirst, F.E., and Paster, B.J. (2003) Diversity of bacterial populations on the tongue dorsa of patients with halitosis and healthy patients. J Clin Microbiol 41: 558563.
  • Van Landschoot, A., and De Ley, J. (1983) Intra- and intergeneric similarities of the rRNA cistrons of Alteromonas, Marinomonas (gen. nov.) and some other gram-negative bacteria. J Gen Microbiol 129: 30573074.
  • Lapidus, A., Goltsman, E., Auger, S., Galleron, N., Segurens, B., Dossat, C., et al. (2007) Extending the Bacillus cereus group genomics to putative food-borne pathogens of different toxicity. Chem Biol Interact 169: (in press). doi: 2010.1016/j.cbi.2007.2003.2003.
  • Lartigue, C., Glass, J.I., Alperovich, N., Pieper, R., Parmar, P.P., Hutchison, C.A., 3rd, et al. (2007) Genome transplantation in bacteria: changing one species to another. Science 317: 632638.
  • Lefebvre, O., Vasudevan, N., Thanasekaran, K., Moletta, R., and Godon, J.J. (2006) Microbial diversity in hypersaline wastewater: the example of tanneries. Extremophiles 10: 505513.
  • Liu, R., and Ochman, H. (2007a) Stepwise formation of the bacterial flagellar system. Proc Natl Acad Sci USA 104: 71167121.
  • Liu, R., and Ochman, H. (2007b) Correction to Stepwise formation of the bacterial flagellar system. Proc Natl Acad Sci USA 104: 11507.
  • Lopez-Garcia, P., Duperron, S., Philippot, P., Foriel, J., Susini, J., and Moreira, D. (2003) Bacterial diversity in hydrothermal sediment and epsilonproteobacterial dominance in experimental microcolonizers at the Mid-Atlantic Ridge. Environ Microbiol 5: 961976.
  • Marcy, Y., Ouverney, C., Bik, E.M., Losekann, T., Ivanova, N., Martin, H.G., et al. (2007) Dissecting biological ‘dark matter’ with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth. Proc Natl Acad Sci USA 104: 1188911894.
  • Matsuzaki, M., Misumi, O., Shin, I.T., Maruyama, S., Takahara, M., Miyagishima, S.Y., et al. (2004) Genome sequence of the ultrasmall unicellular red alga Cyanidioschyzon merolae 10D. Nature 428: 653657.
  • Mulkidjanian, A.Y., Makarova, K.S., Galperin, M.Y., and Koonin, E.V. (2007) Inventing the dynamo machine: on the origin of the F-type and V-type membrane ATPases from membrane RNA/protein translocases. Nat Rev Microbiol (in press).
  • Nakagawa, S., Takai, K., Inagaki, F., Hirayama, H., Nunoura, T., Horikoshi, K., and Sako, Y. (2005) Distribution, phylogenetic diversity and physiological characteristics of epsilon-Proteobacteria in a deep-sea hydrothermal field. Environ Microbiol 7: 16191632.
  • Nakagawa, S., Takaki, Y., Shimamura, S., Reysenbach, A.L., Takai, K., and Horikoshi, K. (2007) Deep-sea vent ε-proteobacterial genomes provide insights into emergence of pathogens. Proc Natl Acad Sci USA 104: 1214612150.
  • Nelson, K.E., Clayton, R.A., Gill, S.R., Gwinn, M.L., Dodson, R.J., Haft, D.H., et al. (1999) Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima. Nature 399: 323329.
  • Newton, R.J., Kent, A.D., Triplett, E.W., and McMahon, K.D. (2006) Microbial community dynamics in a humic lake: differential persistence of common freshwater phylotypes. Environ Microbiol 8: 956970.
  • Nozaki, H., Takano, H., Misumi, O., Terasawa, K., Matuzaki, M., Maruyama, S., et al. (2007) A 100%-complete sequence reveals unusually simple genomic features in the hot-spring red alga Cyanidioschyzon merolae. BMC Biol 5: 28.
  • Pallen, M.J., and Matzke, N.J. (2006) From the origin of species to the origin of bacterial flagella. Nat Rev Microbiol 4: 784790.
  • Paster, B.J., Russell, M.K., Alpagot, T., Lee, A.M., Boches, S.K., Galvin, J.L., and Dewhirst, F.E. (2002) Bacterial diversity in necrotizing ulcerative periodontitis in HIV-positive subjects. Ann Periodontol 7: 816.
  • Pei, Z., Bini, E.J., Yang, L., Zhou, M., Francois, F., and Blaser, M.J. (2004) Bacterial biota in the human distal esophagus. Proc Natl Acad Sci USA 101: 42504255.
  • Phillips, R.W., Wiegel, J., Berry, C.J., Fliermans, C., Peacock, A.D., White, D.C., and Shimkets, L.J. (2002) Kineococcus radiotolerans sp. nov., a radiation-resistant, gram-positive bacterium. Int J Syst Evol Microbiol 52: 933938.
  • Riley, M., Abe, T., Arnaud, M.B., Berlyn, M.K., Blattner, F.R., Chaudhuri, R.R., et al. (2006) Escherichia coli K-12: a cooperatively developed annotation snapshot – 2005. Nucleic Acids Res 34: 19.
  • Samuel, B.S., Hansen, E.E., Manchester, J.K., Coutinho, P.M., Henrissat, B., Fulton, R., et al. (2007) Genomic and metabolic adaptations of Methanobrevibacter smithii to the human gut. Proc Natl Acad Sci USA 104: 1064310648.
  • Scott, E.C., and Matzke, N.J. (2007) Biological design in science classrooms. Proc Natl Acad Sci USA 104: 86698676.
  • Simó, R. (2001) Production of atmospheric sulfur by oceanic plankton: biogeochemical, ecological and evolutionary links. Trends Ecol Evol 16: 287294.
  • Tatusova, T.A., and Madden, T.L. (1999) blast 2 sequences, a new tool for comparing protein and nucleotide sequences. FEMS Microbiol Lett 174: 247250.
  • Thiel, V., Leininger, S., Schmaljohann, R., Brummer, F., and Imhoff, J.F. (2007) Sponge-specific bacterial associations of the Mediterranean sponge Chondrilla nucula (Demospongiae, Tetractinomorpha). Microb Ecol 54: 101111.
  • Todd, J.D., Rogers, R., Li, Y.G., Wexler, M., Bond, P.L., Sun, L., et al. (2007) Structural and regulatory genes required to make the gas dimethyl sulfide in bacteria. Science 315: 666669.
  • Xu, J., Mahowald, M.A., Ley, R.E., Lozupone, C.A., Hamady, M., Martens, E.C., et al. (2007) Evolution of symbiotic bacteria in the distal human intestine. PLoS Biol 5: e156.
  • Ye, Q., Roh, Y., Carroll, S.L., Blair, B., Zhou, J., Zhang, C.L., and Fields, M.W. (2004) Alkaline anaerobic respiration: isolation and characterization of a novel alkaliphilic and metal-reducing bacterium. Appl Environ Microbiol 70: 55955602.
  • Zeikus, J.G., Jain, M.K., and Elankovan, P. (1999) Biotechnology of succinic acid production and markets for derived industrial products. Appl Environ Microbiol 51: 545552.