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  • AbeT, BignellDE & HigashiM (eds) (2000) Termites: Evolution, Sociality, Symbioses, Ecology. Kluwer Academic Publishers, Dordrecht, The Netherlands.
  • Abrams GD & Bishop JE (1967) Effect of normal microbial flora on gastrointestinal motility. Proc Soc Exp Biol Med 126: 301304.
  • Bäckhed F, Ding H, Wang T, Hooper LV, Koh GY, Nagy A, Semenkovich CF & Gordon JI (2004) The gut microbiota as an environmental factor that regulates fat storage. Proc Natl Acad Sci USA 101: 1571815723.
  • Bäckhed F, Manchester JK, Semenkovich CF & Gordon JI (2007) Mechanisms underlying the resistance to diet-induced obesity in germ-free mice. Proc Natl Acad Sci USA 104: 979984.
  • Barbieri E, Paster BJ, Hughes D, Zurek L, Moser DP, Teske A & Sogin ML (2001) Phylogenetic characterization of epibiotic bacteria in the accessory nidamental gland and egg capsules of the squid Loligo pealei (Cephalopoda: Loliginidae). Environ Microbiol 3: 151167.
  • Baumann P, Baumann L, Lai CY, Rouhbakhsh D, Moran NA & Clark MA (1995) Genetics, physiology and evolutionary relationships of the genus Buchnera: intracellular symbionts of aphids. Ann Rev Microbiol 49: 5594.
  • Bidartondo MI (2005) The evolutionary ecology of myco-heterotrophy. New Phytol 167: 335352.
  • Braun-Fahrländer C, Riedler J, Herz U et al. (2002) Allergy and endotoxin team. Environmental exposure to endotoxin and its relation to asthma in school-age children. New Eng J Med 347: 869877.
  • Breitbart M, Hewson I, Felts B, Mahaffy JM, Nulton J, Salamon P & Rohwer F (2003) Metagenomic analyses of an uncultured viral community from human feces. J Bacteriol 185: 62206223.
  • Buddemeier RW, Baker AC, Fautin DG & Jacobs JR (2004) The adaptive hypothesis of bleaching. Coral Health and Disease (RosenbergE & LoyaY, eds), pp. 427444. Springer-Verlag, Berlin.
  • Buss LW (1987) The Evolution of Individuality. Princeton University Press, Princeton, NJ.
  • Cankar K, Kraigher H, Ravnikar M & Rupnik M (2005) Bacterial endophytes from seeds of Norway spruce (Picea abies L. Karst). FEMS Microbiol Lett 244: 341345.
  • Cary SC (1994) Vertical transmission of a chemoautotrophic symbiont in the protobranch bivalve, Solemya reidi. Mol Mar Biol Biotechnol 3: 121130.
  • Chelius MK & Triplett EW (2001) The diversity of Archaea and bacteria in association with the roots of Zea mays L. Microb Ecol 41: 252263.
  • Day RL, Laland KN & Odling-Smee J (2003) Rethinking adaptation: the niche-construction perspective. Perspect Biol Med 46: 8095.
  • Dehority BA (2003) Rumen Microbiology. Nottingham University Press, Nottingham, UK.
  • De La Cruz F & Davies J (2005) Industrial revolution and microbial evolution. The Influence of Cooperative Bacteria on Animal Host Biology (McFall-NgaiMJ, HendersonB & RubyEG, eds), pp. 7382. Cambridge University Press, New York.
  • Dethlefsen L, Eckburg PB, Bik EM & Relman DA (2006) Assembly of the human intestinal microbiota. Trends Ecol Evol 21: 517523.
  • Dethlefsen L, McFall-Ngai M & Relman DA (2007) An ecological and evolutionary perspective on human-microbe mutualism and disease. Nature 449: 811818.
  • Dinsdale EA, Edwards RA, Hall D et al. (2008) Functional metagenomics profiling of nine biomes. Nature 452: 629632.
  • Edwards JE, McEwan NR, Travis AJ & Wallace RJ (2004) 16S rDNA library-based analysis of ruminal bacterial diversity. Antonie van Leeuwenhoek 86: 263281.
  • Egamberdieva D, Kamilova F, Validov S, Gafurova L, Kucharova Z & Lugtenberg B (2008) High incidence of plant growth-stimulating bacteria associated with the rhizosphere of wheat growth on salinated soil in Uzbekistan. Environ Microbiol 10: 19.
  • Etterson JR & Shaw RG (2001) Constraint to adaptive evolution in response to global warming. Science 294: 151154.
  • Finan TM (2002) Evolving insights: symbiosis islands and horizontal gene transfer. J Bacteriol 184: 28552856.
  • Foster JS & Kolenbrander PE (2004) Development of a multispecies oral bacterial community in a saliva-conditioned flow cell. Appl Environ Microbiol 70: 43404348.
  • Foster KR & Wenseleers T (2006) A general model for the evolution of mutualism. J Evol Biol 19: 12831293.
  • Frank DN & Pace NR (2008) Gastrointestinal microbiology enters the metagenomics era. Curr Opin Gastroenterol 24: 410.
  • Fraune S & Bosch TCG (2007) Long-term maintenance of species-specific bacterial microbiota in the basal metazoan Hydra. Proc Natl Acad Sci USA 104: 1314613151.
  • Frias-Lopez J, Zerkle AL, Bonheyo GT & Fouke BW (2002) Partitioning of bacterial communities between seawater and healthy, black band diseased, and dead coral surfaces. Appl Environ Microbiol 68: 22142228.
  • Goodacre R (2007) Metabolomics of a superorganism. J Nutr 137: 259S266S.
  • Gros O, Darrasse A, Durand P, Frenkiel L & Mouëza M (1996) Environmental transmission of a sulfur-oxidizing bacterial gill endosymbiont in the tropical lucinid bivalve Codakia orbicularis. Appl Environ Microbiol 62: 23242330.
  • Hacker J & Kaper JB (2000) Pathogenicity islands and the evolution of microbes. Ann Rev Microbiol 54: 641679.
  • Hacker J, Dobrindt U, Steinert M, Merkert H & Hentschel U (2005) Co-evolution of bacteria and their hosts: a marriage made in heaven or hell? The Influence of Cooperative Bacteria on Animal Host Biology (McFall-NgaiMJ, HendersonB & RubyE-G, eds), pp. 5772. Cambridge University Press, New York.
  • Harvell DC, Mitchell CE, Ward JR, Altizer S, Dobson AP, Ostfeld RS & Samuel MD (2002) Climate warming and disease risks for terrestrial and marine biota. Science 296: 21582162.
  • Henderson B (2005) Moonlighting in protein hyperspace: shared moonlighting proteins and bacteria–host cross talk. The Influence of Cooperative Bacteria on Animal Host Biology (McFall-NgaiMJ, HendersonB & RubyEG, eds), pp. 347374. Cambridge University Press, New York.
  • Hentschel U, Steinert M & Hacker J (2000) Common molecular mechanisms of symbiosis and pathogenesis. Trends Microbiol 8: 226231.
  • Herwig RP, Staley JT, Nerini MK & Braham HW (1984) Baleen whales: preliminary evidence for forestomach microbial fermentation. Appl Environ Microbiol 47: 421423.
  • Hickman CS (2005) How have bacteria contributed to the evolution of multicellular animals? The Influence of Cooperative Bacteria on Animal Host Biology (McFall-NgaiMJ, HendersonB & RubyEG, eds), pp. 333. Cambridge University Press, New York.
  • Hongoh Y, Deevong P, Inoue T, Moriya S, Trakulnaleamsai S, Ohkuma M, VongKaluny C, Noparatnaraporn N & Kudo T (2005) Intra- and interspecific comparisons of bacterial diversity and community structure support coevolution of gut microbiota and termite host. Appl Environ Microbiol 71: 65906599.
  • Hooper LV & Gordon JI (2001) Commensal host–bacterial relationships in the gut. Science 292: 11151118.
  • Hooper LV, Midtvedt T & Gordon JI (2002) How host–microbial interactions shape the nutrient environment of the mammalian intestine. Ann Rev Nutr 22: 283307.
  • Hugenholtz P, Goebel BM & Pace NR (1998) Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J Bacteriol 180: 47654774.
  • Hurek T & Reinhold-Hurek B (2003) Azoarcus sp. strain BH72 as a model for nitrogen-fixing grass endophytes. J Biotechnol 106: 169178.
  • Hylemon PB & Harder J (1998) Biotransformation of monoterpenes, bile acids, and other isoprenoids in anaerobic ecosystems. FEMS Microbiol Rev 22: 475488.
  • Iwanaga S & Lee BL (2005) Recent advances in the innate immunity of invertebrate animals. J Biochem Mol Biol 38: 128150.
  • Jones KM, Kobayashi H, Davies BW, Taga ME & Walker GC (2007) How rhizobial symbionts invade plants: the Sinorhizobium medicago model. Nat Rev Microbiol 5: 619633.
  • Kaufman MR, Ikeda Y, Patton C, Van Dykhuizen G & Epel D (1998) Bacterial symbionts colonize the accessory nidamental gland of the squid Loligo opalescens via horizontal transmission. Bio Bull 194: 3643.
  • Kikuchi Y, Hosokawa T & Fukatsu T (2007) Insect–microbe mutualism without vertical transmission: a stinkbug acquires a beneficial gut symbiont from the environment every generation. Appl Environ Microbiol 73: 43084316.
  • Koren O & Rosenberg E (2006) Bacteria associated with mucus and tissues of the coral Oculina patagonica in summer and winter. Appl Environ Microbiol 72: 52545259.
  • Krueger DM, Gustafson RG & Cavanaugh CM (1996) Vertical transmission of chemoautotrophic symbionts in the bivalve Solyema velum (Bivalvia: Protobranchia). Biol Bull 190: 195202.
  • Kushmaro A, Loya Y, Fine M & Rosenberg E (1996) Bacterial infection and coral bleaching. Nature 380: 396.
  • Lambais MR, Crowley DE, Cury JC, Büll RC & Rodrigues RR (2006) Bacterial diversity in tree canopies of the Atlantic Forest. Science 312: 1917.
  • Leibold MA & Norberg J (2004) Biodiversity in metacommunities: plankton as complex adaptive systems. Limnol Oceanogr 49: 12781289.
  • Leser TD, Amenuvor JZ, Jensen TK, Lindecrona RH, Boye M & Møller K (2002) Culture-independent analysis of gut bacteria: the pig gastrointestinal tract microbiota revisited. Appl Environ Microbiol 68: 673690.
  • Ley RE, Bäckhed F, Turnbaugh P, Lozupone CA, Knigh RD & Gordon JI (2005) Obesity alters gut microbial ecology. Proc Natl Acad Sci USA 102: 1107011075.
  • Ley RE, Peterson DA & Gordon JI (2006a) Ecological and evolutionary forces shaping microbial diversity in the human intestine. Cell 124: 837848.
  • Ley RE, Turnbaugh PJ, Klein S & Gordon JI (2006b) Human gut microbes associated with obesity. Nature 444: 10221023.
  • Lloyd EA (1994) The Structure and Confirmation of Evolutionary Theory. Princeton University Press, Princeton, NJ.
  • Margulis L (1993) Symbiosis in Cell Evolution: Microbial Communities in the Archean and Proterozoic Eons. 2nd edn. W.H. Freeman and Co., New York.
  • Martínez-García M, Díaz-Valdéz M, Wanner G, Ramos-Esplá A & Antón J (2007) Microbial community associated with the colonial ascidian Cyctodytes dellechiajei. Environ Microbiol 9: 521534.
  • Mateos M, Castrezana SJ, Nankivell BJ, Estes AM, Markow TA & Moran NA (2006) Heritable endosymbionts of Drosophila. Genetics 174: 363376.
  • Maynard Smith J & Szathmary E (1995) The Major Transitions in Evolution. W.H. Freeman, Oxford.
  • McFall-Ngai MJ (1999) Consequences of evolving with bacterial symbionts: insights from the squid–Vibrio association. Ann Rev Ecol Syst 30: 235256.
  • McFall-Ngai MJ (2002) Unseen forces: the influence of bacteria on animal development. Develop Biol 242: 114.
  • Minkley N, Fujita A, Brune A & Kirchner WH (2006) Nest specificity of the bacterial community in termite guts (Hodotermes mossambicus). Insect Soc 53: 339344.
  • Mueller S, Saunier K, Hanisch C et al. (2006) Differences in fecal microbiota in different European study populations in relation to age, gender and country: a cross-sectional study. Appl Environ Microbiol 72: 10271033.
  • Nandasena KG, O'Hara GW, Tiwari RP, Sezmis E & Howieson JG (2007) In situ lateral transfer of symbiosis islands results in rapid evolution of diverse competitive strains of mesorhizobia suboptimal in symbiotic nitrogen fixation on the pasture legume Biserrula pelecinus L. Environ Microbiol 9: 24962511.
  • O'Hara AM & Shanahan F (2006) The gut flora as a forgotten organ. EMBO Rep 7: 688693.
  • Olsen MA, Aagnes TH & Mathiesen SD (1994) Digestion of herring by indigenous bacteria in the minke whale forestomach. Appl Environ Microbiol 60: 44454455.
  • Olsen MA, Blix AS, Utsi THA, Sørmo W & Mathiesen SD (2000) Chitinolytic bacteria in the minke whale forestomach. Can J Microbiol 46: 8594.
  • Paster BJ, Boches SK, Galvin JL, Ericson RE, Lau CN, Levanos VA, Sahasrabudhe A & Dewhirst FE (2001) Bacterial diversity in human subgingival plaque. J Bacteriol 183: 37703783.
  • Perez-Brocal V, Gil R, Ramos S, Lamelas A, Postigo M, Michelena JM, Silva FJ, Moya A & Latorre A (2006) A small microbial genom: the end of a long symbiotic relationship? Science 314: 312313.
  • Rajilić-Stojanović M, Smidt H & De Vos WM (2007) Diversity of the human gastrointestinal tract microbiota revisited. Environ Microbiol 9: 21252136.
  • Reeve HK & Hölldobler B (2007) The emergence of a superorganism through intergroup competition. Proc Natl Acad Sci 104: 97369740.
  • Relman DA & Falkow S (2001) The meaning and impact of the human genome sequence for microbiology. Trends Microbiol 9: 206208.
  • Reshef L, Koren O, Loya Y, Zilber-Rosenberg I & Rosenberg E (2006) The coral probiotic hypothesis. Environ Microbiol 8: 20682073.
  • Ritchie KB (2006) Regulation of microbial populations by coral surface mucus and mucus-associated bacteria. Mar Ecol Prog Ser 322: 114.
  • Rohwer F, Seguritan V, Azam F & Knowlton N (2002) Diversity and distribution of coral-associated bacteria. Mar Ecol Prog Ser 243: 110.
  • Rosenberg E & Falkovitz L (2004) The Vibrio shiloi/Oculina pagagonica model system of coral bleaching. Ann Rev Microbiol 58: 143159.
  • Rosenberg E, Koren O, Reshef L, Efrony R & Zilber-Rosenberg I (2007) The role of microorganisms in coral health, disease and evolution. Nat Rev Microbiol 5: 355362.
  • Russell JB & Rychlik JL (2001) Factors that alter rumen ecology. Science 292: 11191122.
  • Russell JA, Latorre A, Sabater-Muñoz B, Moya A & Moran NA (2003) Side-stepping secondary symbionts: widespread horizontal transfer across and beyond the Aphidoidea. Mol Ecol 12: 10611075.
  • Sachs JL, Mueller UG, Wilcox TP & Bull JJ (2004) The evolution of cooperation. Q Rev Biol 79: 135160.
  • Sandström JP, Russel JA, White JP & Moran NA (2001) Independent origins and horizontal transfer of bacterial symbionts of aphids. Mol Ecol 10: 217228.
  • Sapp J (1994) Evolution by Association. Oxford University Press, New York.
  • Savage DC, Siegel JD, Snellen JE & Whitt DD (1981) Transit time of epithelial cells in the small intestines of germfree mice and ex-germfree mice associated with indigenous microorganisms. Appl Environ Microbiol 42: 9961001.
  • Sharp KH, Eam B, Faulkner DJ & Haygood MG (2007) Vertical transmission of diverse microbes in the tropical sponge Corticium sp. Appl Environ Microbiol 73: 622629.
  • She X, Jiang Z, Clark RA, Liu G, Cheng Z, Tuzun D, Church DM, Sutton G, Halpern AL & Eichler EE (2004) Shotgun sequence assembly and recent segmental duplications within the human genome. Nature 431: 927930.
  • Silva AM, Barbosa FHF, Duarte R, Vieira LQ, Arantes RME & Nicoli JR (2004) Effect of Bifidobacterium longum ingestion on experimental salmonellosis in mice. J Appl Microbiol 97: 2937.
  • Singh BK, Millard P, Whiteley AS & Murrell JC (2004) Unravelling rhizosphere–microbial interactions: opportunities and limitations. Trends Microbiol 12: 386393.
  • Smith KP, Handelsman J & Goodman RM (1999) Genetic basis in plants for interactions with disease-suppressive bacteria. Proc Natl Acad Sci USA 96: 47864790.
  • Somers E, Vanderleyden J & Srinivasan M (2004) Rhizosphere bacterial signalling: a love parade beneath our feet. Crit Rev Microbiol 30: 205240.
  • Stappenbeck TS, Hooper LV & Gordon JI (2002) Developmental regulation of intestinal angiogenesis by indigenous microbes via Paneth cells. Proc Natl Acad Sci USA 99: 1545115455.
  • Stougaard J (2000) Regulators and regulation of legume root nodule development. Plant Physiol 124: 531540.
  • Sundset MA, Praesteng KE, Cann IK, Mathiesen SD & Mackie RI (2007) Novel rumen bacterial diversity in two geographically separated sub-specie of reindeer. Microb Ecol 54: 424438.
  • Tannock G (1995) Normal Microflora. Chapman & Hall, London.
  • Taylor MW, Radax R, Steger D & Wagner M (2007) Sponge-associated microorganisms: evolution, ecology and biotechnological potentials. Microbiol Mol Biol Rev 71: 295347.
  • Thingstad TF & Lignell R (1997) Theoretical models for the control of bacterial growth rate, abundance, diversity and carbon demand. Aquat Microb Ecol 13: 1927.
  • Turnbaugh PJ, Ley RE, Mahowald MA, Magrini V, Mardis ER & Gordon JI (2006) An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444: 10271031.
  • Veneti ZL, Reuter M, Montenegro H, Hornett EA, Charlat S & Hurst GD (2005) Interactions between inherited bacteria and their hosts: the Wolbachia paradigm. The influence of Cooperative Bacteria on Animal Host Biology (McFall-NgaiM-J, HendersonB & RubyE-G, eds), pp. 119141. Cambridge University Press, New York.
  • Visick KL, Foster J, Doino J, McFall-Ngai MJ & Ruby EG (2000) Vibrio fischeri lux genes play an important role in colonization and development of the host light organ. J Bact 182: 45784586.
  • Wallace RJ (2004) Antimicrobial properties of plant secondary metabolites. Proc Nutr Soc 63: 621629.
  • Wang B & Qui YL (2006) Phylogenetic distribution and evolution of mycorrhizas in land plants. Mycorrhiza 16: 299363.
  • Webster NS, Wilson KJ, Blackall LL & Hill RT (2001) Phylogenetic diversity of bacteria associated with the marine sponge Rhopaloeides odorabile. Appl Environ Microbiol 67: 434444.
  • Weimer PJ, Waghorn GC, Odt CL & Mertens DR (1999) Effect of diet on populations of three species of ruminal cellulolytic bacteria in lactating dairy cows. J Dairy Sci 82: 122134.
  • Weitz JS, Hartman H & Levin SA (2005) Coevolutionary arms races between bacteria and bacteriophage. Proc Natl Acad Sci USA 102: 95359540.
  • Wernegreen JJ (2002) Genome evolution in bacterial endosymbionts of insects. Nat Rev Genet 3: 850861.
  • West SA, Griffin AS, Gardner A & Diggle SP (2006) Social evolution theory for microorganisms. Nat Rev Microbiol 4: 597607.
  • Wilkinson DM (2001) Mycorrhizal evolution. Trends Ecol Evol 16: 6465.
  • Wilson DS & Sober E (1989) Reviving the superorganism. J Theor Biol 136: 337356.
  • Wostmann BS (1981) The germ-free animal in nutritional studies. Ann Rev Nutr 1: 257297.
  • Wostmann BS, Larkin C, Moriarty A & Bruckner-Kardoss E (1983) Dietary intake, energy metabolism and excretory losses of adult male germfree Wistar rats. Lab Anim Sci 33: 4650.
  • Xu J & Gordon JI (2003) Honor thy symbionts. Proc Natl Acad Sci USA 100: 1045210459.
  • Xu J, Mahowald MA, Ley RE et al. (2007) Evolution of symbiotic bacteria in the distal human intestine. PLOS Biol 5: 15741586.
  • Yachi S & Loreau M (1999) Biodiversity and ecosystem productivity in a fluctuating environment: the insurance hypothesis. Proc Natl Acad Sci USA 96: 14631468.
  • Zoetendal EG, Akkermans ADL, Akkermans van Vliet WM, De Visser JAGM & De Vos WM (2001) A host genotype affects the bacterial community in the human gastrointestinal tract. Microb Ecol Health Dis 13: 129134.