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References

  • Abubucker S, Segata N, Goll J et al. (2012) Metabolic reconstruction for metagenomic data and its application to the human microbiome. PLoS Comput Biol 8: e1002358.
  • Ahmed A, Earl J, Retchless A et al. (2012) Comparative genomic analyses of 17 clinical isolates of Gardnerella vaginalis provide evidence of multiple genetically isolated clades consistent with subspeciation into genovars. J Bacteriol 194: 39223937.
  • Allen EE, Tyson GW, Whitaker RJ, Detter JC, Richardson PM & Banfield JF (2007) Genome dynamics in a natural microbial strain population. P Natl Acad Sci USA 104: 18831888.
  • Amann RI, Ludwig W & Schleifer KH (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59: 143169.
  • Andam CP & Gogarten JP (2011) Biased gene transfer in microbial evolution. Nat Rev Microbiol 9: 543555.
  • Andersson AF & Banfield JF (2008) Virus population dynamics and acquired virus resistance in natural microbial communities. Science 320: 10471050.
  • Antonova E & Hammer B (2011) Quorum-sensing autoinducer molecules produced by members of a multispecies biofilm promote horizontal gene transfer to Vibrio cholerae. FEMS Microbiol Lett 322: 6876.
  • Arumugam M, Raes J, Pelletier E et al. (2011) Enterotypes of the human gut microbiome. Nature 473: 174180.
  • Atamna-Ismaeel N, Sabehi G, Sharon I, Witzel KP, Labrenz M, Jürgens K, Barkay T, Stomp M, Huisman J & Beja O (2008) Widespread distribution of proteorhodopsins in freshwater and brackish ecosystems. ISME J 2: 656662.
  • Baas Becking LGM (1934) Geobiologie of inleiding tot de milieukunde. W.P. Van Stockum & Zoon, The Hague, the Netherlands.
  • Badri DV, Zolla G, Barkker MG, Manter DK & Vivanco JM (2013) Potential impact of soil microbiomes on the leaf metabolome and on herbivore feeding behavior. New Phytol 198: 264273.
  • Bailey JK, Deckert R, Schweitzer JA, Rehill BJ, Lindroth RL, Gehring C & Whitham TG (2005) Host plant genetics affect hidden ecological players: links among Populus, condensed tannins, and fungal endophyte infection. Can J Bot 83: 356361.
  • Bailey JK, Wooley SC, Lindroth RL & Whitham TG (2006) Importance of species interactions to community heritability: a genetic basis to trophic-level interactions. Ecol Lett 9: 7885.
  • Baker BJ, Hugenholtz P, Dawson SC & Banfield JF (2003) Extremely acidophilic protists from acid mine drainage host Rickettsiales-lineage endosymbionts that have intervening sequences in their 16S rRNA genes. Appl Environ Microbiol 69: 55125518.
  • Baker BJ, Tyson GW, Webb RI, Flanagan J, Hugenholtz P, Allen EE & Banfield JF (2006) Lineages of acidophilic archaea revealed by community genomic analysis. Science 314: 19331935.
  • Baker BJ, Tyson GW, Goosherst L & Banfield JF (2009) Insights into the diversity of eukaryotes in acid mine drainage biofilm communities. Appl Environ Microbiol 75: 21922199.
  • Bakker MG, Manter DK, Sheflin AM, Weir TL & Vivanco JM (2012) Harnessing the rhizosphere microbiome through plant breeding and agricultural management. Plant Soil 360: 113.
  • Baldo L, Desjardins CA, Russell JA, Stahlhut JK & Werren JH (2010) Accelerated microevolution in an outer membrane protein (OMP) of the intracellular bacteria Wolbachia. BMC Evol Biol 10: 48.
  • Ballal SA, Gallini CA, Segata N, Huttenhower C & Garrett WS (2011) Host and gut microbiota symbiotic factors: lessons from inflammatory bowel disease and successful symbionts. Cell Microbiol 13: 508517.
  • Bapteste E & Boucher Y (2008) Lateral gene transfer challenges principles of microbial systematics. Trends Microbiol 16: 200207.
  • Barberán A, Bates ST, Casamayor EO & Fierer N (2012a) Using network analysis to explore co-occurrence patterns in soil microbial communities. ISME J 6: 343351.
  • Barberán A, Fernández-Guerra A, Bohannan BJ & Casamayor EO (2012b) Exploration of community traits as ecological markers in microbial metagenomes. Mol Ecol 21: 19091917.
  • Beiko RG (2011) Telling the whole story in a 10,000-genome world. Biol Direct 6: 34.
  • Beiko RG, Harlow TJ & Ragan MA (2005) Highways of gene sharing in prokaryotes. P Natl Acad Sci USA 102: 1433214337.
  • Belnap CP, Pan C, VerBerkmoes NC, Power ME, Samatova NF, Carver RL, Hettich RL & Banfield JF (2010) Cultivation and quantitative proteomic analyses of acidophilic microbial communities. ISME J 4: 520530.
  • Bielawski JP, Dunn KA, Sabehi G & Béjà O (2004) Darwinian adaptation of proteorhodopsin to different light intensities in the marine environment. P Natl Acad Sci USA 101: 1482414829.
  • Bittner L, Halary S, Payri C, Cruaud C, de Reviers B, Lopez P & Bapteste E (2010) Some considerations for analyzing biodiversity using integrative metagenomics and gene networks. Biol Direct 5: 47.
  • Boc A, Philippe H & Makarenkov V (2010) Inferring and validating horizontal gene transfer events using bipartition dissimilarity. Syst Biol 59: 195211.
  • Bokulich NA, Bamforth CW & Mills DA (2012) Brewhouse-resident microbiota are responsible for multi-stage fermentation of American coolship ale. PLoS ONE 7: e35507.
  • Booijink CC, El-Aidy S, Rajilic-Stojanovic M, Heilig HG, Troost FJ, Smidt H, Kleerebezem M, De Vos WM & Zoetendal EG (2010) High temporal and inter-individual variation detected in the human ileal microbiota. Environ Microbiol 12: 32133227.
  • Borriello SP (1990) The influence of the normal flora on Clostridium difficile colonisation of the gut. Ann Med 22: 6167.
  • Brousseau R, Hill JE, Prefontaine G, Goh SH, Harel J & Hemmingsen SM (2001) Streptococcus suis serotypes characterized by analysis of cpn60 gene sequences. Appl Environ Microbiol 67: 48284833.
  • Brown MV, Lauro FM, DeMaere MZ et al. (2012) Global biogeography of SAR11 marine bacteria. Mol Syst Biol 8: 595.
  • Bru D, Ramette A, Saby NP, Dequiedt S, Ranjard L, Jolivet C, Arrouays D & Philippot L (2010) Determinants of the distribution of nitrogen-cycling microbial communities at the landscape scale. ISME J 5: 532542.
  • Brune KD & Bayer TS (2012) Engineering microbial consortia to enhance biomining and bioremediation. Front Microbiol 3: 203.
  • Burke C, Steinberg P, Rusch D, Kjelleberg S & Thomas T (2011a) Bacterial community assembly based on functional genes rather than species. P Natl Acad Sci USA 108: 1428814293.
  • Burke C, Thomas T, Lewis M, Steinberg P & Kjelleberg S (2011b) Composition, uniqueness and variability of the epiphytic bacterial community of the green alga Ulva australis. ISME J 5: 590600.
  • Caporaso JG, Lauber CL, Costello EK et al. (2011) Moving pictures of the human microbiome. Genome Biol 12: R50.
  • Carini P, Steindler L, Beszteri S & Giovannoni SJ (2012) Nutrient requirements for growth of the extreme oligotroph ‘Candidatus Pelagibacter ubique’ HTCC1062 on a defined medium. ISME J 7: 592602.
  • Carson JK, Campbell L, Rooney D, Clipson N & Gleeson DB (2009) Minerals in soil select distinct bacterial communities in their microhabitats. FEMS Microbiol Ecol 67: 381388.
  • Case RJ, Boucher Y, Dahllöf I, Holmström C, Doolittle WF & Kjelleberg S (2007) Use of 16S rRNA and rpoB genes as molecular markers for microbial ecology studies. Appl Environ Microbiol 73: 278288.
  • Cavender-Bares J, Kozak KH, Fine PV & Kembel SW (2009) The merging of community ecology and phylogenetic biology. Ecol Lett 12: 693715.
  • Chaffron S, Rehrauer H, Pernthaler J & von Mering C (2010) A global network of coexisting microbes from environmental and whole-genome sequence data. Genome Res 20: 947959.
  • Chan CX, Beiko RG, Darling AE & Ragan MA (2009) Lateral transfer of genes and gene fragments in prokaryotes. Genome Biol Evol 1: 429438.
  • Chan CX, Beiko RG & Ragan MA (2011) Lateral transfer of genes and gene fragments in Staphylococcus extends beyond mobile elements. J Bacteriol 193: 39643977.
  • Chan JZ, Halachev MR, Loman NJ, Constantinidou C & Pallen MJ (2012) Defining bacterial species in the genomic era: insights from the genus Acinetobacter. BMC Microbiol 12: 302.
  • Chen Y & Murrell JC (2010) When metagenomics meets stable-isotope probing: progress and perspectives. Trends Microbiol 18: 157163.
  • Chen I-MA, Markowitz VM, Chu K et al. (2013) Improving microbial genome annotations in an integrated database context. PLoS ONE 8: e54859.
  • Cho JC & Tiedje JM (2000) Biogeography and degree of endemicity of fluorescent Pseudomonas strains in soil. Appl Environ Microbiol 66: 54485456.
  • Claesson MJ, Jeffery IB, Conde S et al. (2012) Gut microbiota composition correlates with diet and health in the elderly. Nature 488: 178184.
  • Clarke M, Lohan AJ, Liu B et al. (2013) Genome of Acanthamoeba castellanii highlights extensive lateral gene transfer and early evolution of tyrosine kinase signaling. Genome Biol 14: R11.
  • Clements FE (1916) Plant Succession; An Analysis of the Development of Vegetation. Carnegie Institution of Washington, Washington DC.
  • Cohan FM (2002) What are bacterial species? Annu Rev Microbiol 56: 457487.
  • Cohan FM (2006) Towards a conceptual and operational union of bacterial systematics, ecology, and evolution. Philos Trans R Soc Lond B Biol Sci 361: 19851996.
  • Cohan FM & Perry EB (2007) A systematics for discovering the fundamental units of bacterial diversity. Curr Biol 17: R373R386.
  • Cohen O, Gophna U & Pupko T (2011) The complexity hypothesis revisited: connectivity rather than function constitutes a barrier to horizontal gene transfer. Mol Biol Evol 28: 14811489.
  • Cole ST, Eiglmeier K, Parkhill J et al. (2001) Massive gene decay in the leprosy bacillus. Nature 409: 10071011.
  • Collins JP & Crump ML (2009) Extinction in Our Times. Global Amphibian Decline. Oxford University Press, Oxford, UK.
  • Comeau AM, Li WK, Tremblay JÉ, Carmack EC & Lovejoy C (2011) Arctic Ocean microbial community structure before and after the 2007 record sea ice minimum. PLoS ONE 6: e27492.
  • Cordero OX & Hogeweg P (2009) The impact of long-distance horizontal gene transfer on prokaryotic genome size. P Natl Acad Sci USA 106: 2174821753.
  • Cornell HV & Lawton JH (1992) Species interactions, local and regional processes, and limits to the richness of ecological communities: a theoretical perspective. J Anim Ecol 61: 112.
  • Costello EK, Stagaman K, Dethlefsen L, Bohannan BJ & Relman DA (2012) The application of ecological theory toward an understanding of the human microbiome. Science 336: 12551262.
  • Cotter PD, Ross RP & Hill C (2013) Bacteriocins – a viable alternative to antibiotics? Nat Rev Microbiol 11: 95105.
  • Cowan ST (1955) Symposium. The principles of microbial classification. Introduction. The philosophy of classification. J Gen Microbiol 12: 314321.
  • Dagan T (2011) Phylogenomic networks. Trends Microbiol 19: 483491.
  • Dagan T, Artzy-Randrup Y & Martin W (2008) Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution. P Natl Acad Sci USA 105: 1003910044.
  • Dawkins R (1976) The Selfish Gene. Oxford University Press, New York City.
  • de Wit R & Bouvier T (2006) ‘Everything is everywhere, but, the environment selects’; what did Baas Becking and Beijerinck really say? Environ Microbiol 8: 755758.
  • Declerck SA, Winter C, Shurin JB, Suttle CA & Matthews B (2013) Effects of patch connectivity and heterogeneity on metacommunity structure of planktonic bacteria and viruses. ISME J 7: 533542.
  • DeLong EF, Preston CM, Mincer T et al. (2006) Community genomics among stratified microbial assemblages in the ocean's interior. Science 311: 496503.
  • Denamur E, Lecointre G, Darlu P et al. (2000) Evolutionary implications of the frequent horizontal transfer of mismatch repair genes. Cell 103: 711721.
  • Dennis PG, Hirsch PR, Smith SJ, Taylor RG, Valsami-Jones E & Miller AJ (2009) Linking rhizoplane pH and bacterial density at the microhabitat scale. J Microbiol Methods 76: 101104.
  • DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P & Andersen GL (2006) Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 72: 50695072.
  • Diggle SP, Griffin AS, Campbell GS & West SA (2007) Cooperation and conflict in quorum-sensing bacterial populations. Nature 450: 411414.
  • Dobrindt U & Hacker J (2001) Whole genome plasticity in pathogenic bacteria. Curr Opin Microbiol 4: 550557.
  • Dodsworth JA, Li L, Wei S, Hedlund BP, Leigh JA & de Figueiredo P (2010) Interdomain conjugal transfer of DNA from bacteria to archaea. Appl Environ Microbiol 76: 56445647.
  • Doolittle WF & Zhaxybayeva O (2009) On the origin of prokaryotic species. Genome Res 19: 744756.
  • Dowd SE, Wolcott RD, Sun Y, McKeehan T, Smith E & Rhoads D (2008) Polymicrobial nature of chronic diabetic foot ulcer biofilm infections determined using bacterial tag encoded FLX amplicon pyrosequencing (bTEFAP). PLoS ONE 3: e3326.
  • Duan K, McCullough WM, Surette MG, Ware T & Song J (2012) Comprehensive analysis of gene-environmental interactions with temporal gene expression profiles in Pseudomonas aeruginosa. PLoS ONE 7: e35993.
  • Duhamel M, Wehr SD, Yu L, Rizvi H, Seepersad D, Dworatzek S, Cox EE & Edwards EA (2002) Comparison of anaerobic dechlorinating enrichment cultures maintained on tetrachloroethene, trichloroethene, cis-dichloroethene and vinyl chloride. Water Res 36: 41934202.
  • Duhamel M, Mo K & Edwards EA (2004) Characterization of a highly enriched Dehalococcoides-containing culture that grows on vinyl chloride and trichloroethene. Appl Environ Microbiol 70: 55385545.
  • Dumont MG, Radajewski SM, Miguez CB, McDonald IR & Murrell JC (2006) Identification of a complete methane monooxygenase operon from soil by combining stable isotope probing and metagenomic analysis. Environ Microbiol 8: 12401250.
  • Dunn KA, Bielawski JP, Ward TJ, Urquhart C & Gu H (2009) Reconciling ecological and genomic divergence among lineages of Listeria under an “extended mosaic genome concept”. Mol Biol Evol 26: 26052615.
  • Dykhuizen DE & Green L (1991) Recombination in Escherichia coli and the definition of biological species. J Bacteriol 173: 72577268.
  • Ehrlich GD (2001) The biofilm and distributed genome paradigms provide a new theoretical structure for understanding chronic bacterial infections. 41st Interscience Conference on Antimicrobial Agents and Chemotherapy: December 16–19, 2001; Chicago, Illinois.
  • Ehrlich PR & Holm RW (1962) Patterns and populations: basic problems of population biology transcend artificial disciplinary boundaries. Science 137: 652657.
  • Ehrlich GD, Ahmed A, Earl J, Hiller NL, Costerton JW, Stoodley P, Post JC, DeMeo P & Hu FZ (2010) The distributed genome hypothesis as a rubric for understanding evolution in situ during chronic bacterial biofilm infectious processes. FEMS Immunol Med Microbiol 59: 269279.
  • Ellrott K, Jaroszewski L, Li W, Wooley JC & Godzik A (2010) Expansion of the protein repertoire in newly explored environments: human gut microbiome specific protein families. PLoS Comput Biol 6: e1000798.
  • Elton CS (1927) Animal Ecology. Sidgwick and Jackson, London.
  • Engelhardt BE, Jordan MI, Srouji JR & Brenner SE (2011) Genome-scale phylogenetic function annotation of large and diverse protein families. Genome Res 21: 19691980.
  • Eppley JM, Tyson GW, Getz WM & Banfield JF (2007) Genetic exchange across a species boundary in the archaeal genus Ferroplasma. Genetics 177: 407416.
  • Ereshefsky M & Pedroso M (2013) Biological individuality: the case of biofilms. Biol Philos 28: 331349.
  • Falony G, Vlachou A, Verbrugghe K & De Vuyst L (2006) Cross-feeding between Bifidobacterium longum BB536 and acetate-converting, butyrate-producing colon bacteria during growth on oligofructose. Appl Environ Microbiol 72: 78357841.
  • Fan L, Reynolds D, Liu M, Stark M, Kjelleberg S, Webster NS & Thomas T (2012) Functional equivalence and evolutionary convergence in complex communities of microbial sponge symbionts. P Natl Acad Sci USA 109: E1878E1887.
  • Faust K, Sathirapongsasuti JF, Izard J, Segata N, Gevers D, Raes J & Huttenhower C (2012) Microbial co-occurrence relationships in the human microbiome. PLoS Comput Biol 8: e1002606.
  • Fauth JE, Bernardo J, Camara M, Resetarits WJ Jr, Van Buskirk J & McCollum SA (1996) Simplifying the jargon of community ecology: a conceptual approach. Am Nat 147: 282286.
  • Fierer N & Jackson RB (2006) The diversity and biogeography of soil bacterial communities. P Natl Acad Sci USA 103: 626631.
  • Floodgate GD (1962) Some remarks on the theoretical aspects of bacterial taxonomy. Bacteriol Rev 26: 277291.
  • Friedman J & Alm EJ (2012) Inferring correlation networks from genomic survey data. PLoS Comput Biol 8: e1002687.
  • Fuhrman JA (2012) Metagenomics and its connection to microbial community organization. F1000 Biol Rep 4: 15.
  • Gabor E, Niehaus F, Aehle W & Eck J (2012) Zooming in on metagenomics: molecular microdiversity of Subtilisin Carlsberg in soil. J Mol Biol 418: 1620.
  • Galperin MY & Koonin EV (2004) ‘Conserved hypothetical’ proteins: prioritization of targets for experimental study. Nucleic Acids Res 32: 54525463.
  • Ge F, Wang LS & Kim J (2005) The cobweb of life revealed by genome-scale estimates of horizontal gene transfer. PLoS Biol 3: e316.
  • Geisinger E, George EA, Chen J, Muir TW & Novick RP (2008) Identification of ligand specificity determinants in AgrC, the Staphylococcus aureus quorum-sensing receptor. J Biol Chem 283: 89308938.
  • Gevers D, Cohan FM, Lawrence JG et al. (2005) Opinion: re-evaluating prokaryotic species. Nat Rev Microbiol 3: 733739.
  • Gibbons SM, Caporaso JG, Pirrung M, Field D, Knight R & Gilbert JA (2013) Evidence for a persistent microbial seed bank throughout the global ocean. P Natl Acad Sci USA 110: 46514655.
  • Gilbert JA, Mühling M & Joint I (2008) A rare SAR11 fosmid clone confirming genetic variability in the ‘Candidatus Pelagibacter ubique’ genome. ISME J 2: 790793.
  • Gilbert JA, Meyer F, Jansson J et al. (2010a) The Earth Microbiome Project: meeting report of the “1 EMP meeting on sample selection and acquisition” at Argonne National Laboratory October 6 2010. Stand Genomic Sci 3: 249253.
  • Gilbert JA, Field D, Swift P et al. (2010b) The taxonomic and functional diversity of microbes at a temperate coastal site: a “multi-omic” study of seasonal and diel temporal variation. PLoS ONE 5: e15545.
  • Giovannoni SJ, Tripp HJ, Givan S et al. (2005) Genome streamlining in a cosmopolitan oceanic bacterium. Science 309: 12421245.
  • Gleason HA (1926) The individualistic concept of the plant association. Bull Torrey Bot Club 1: 726.
  • Goss CH & Burns JL (2007) Exacerbations in cystic fibrosis. 1: epidemiology and pathogenesis. Thorax 62: 360367.
  • Green JL, Bohannan BJ & Whitaker RJ (2008) Microbial bio-geography: from taxonomy to traits. Science 320: 10391043.
  • Gudelj I, Weitz JS, Ferenci T, Claire Horner-Devine M, Marx CJ, Meyer JR & Forde SE (2010) An integrative approach to understanding microbial diversity: from intracellular mechanisms to community structure. Ecol Lett 13: 10731084.
  • Halary S, Leigh JW, Cheaib B, Lopez P & Bapteste E (2010) Network analyses structure genetic diversity in independent genetic worlds. P Natl Acad Sci USA 107: 127132.
  • Handelsman J, Rondon MR, Brady SF, Clardy J & Goodman RM (1998) Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. Chem Biol 5: R245R249.
  • Hanson CA, Fuhrman JA, Horner-Devine MC & Martiny JB (2012) Beyond biogeographic patterns: processes shaping the microbial landscape. Nat Rev Microbiol 10: 497506.
  • Hao W & Golding GB (2006) The fate of laterally transferred genes: life in the fast lane to adaptation or death. Genome Res 16: 636643.
  • Harrison E & Brockhurst MA (2012) Plasmid-mediated horizontal gene transfer is a coevolutionary process. Trends Microbiol 20: 262267.
  • Helling RB, Vargas CN & Adams J (1987) Evolution of Escherichia coli during growth in a constant environment. Genetics 116: 349358.
  • Hemme CL, Deng Y, Gentry TJ et al. (2010) Metagenomic insights into evolution of a heavy metal-contaminated groundwater microbial community. ISME J 4: 660672.
  • Hibbing ME, Fuqua C, Parsek MR & Peterson SB (2010) Bacterial competition: surviving and thriving in the microbial jungle. Nat Rev Microbiol 8: 1525.
  • Hilario E & Gogarten JP (1993) Horizontal transfer of ATPase genes–the tree of life becomes a net of life. Biosystems 31: 111119.
  • Hiller NL, Ahmed A, Powell E et al. (2010) Generation of genic diversity among Streptococcus pneumoniae strains via horizontal gene transfer during a chronic polyclonal pediatric infection. PLoS Pathog 6: e1001108.
  • Hollingshead SK, Becker R & Briles DE (2000) Diversity of PspA: mosaic genes and evidence for past recombination in Streptococcus pneumoniae. Infect Immun 68: 58895900.
  • Holloway C & Beiko RG (2010) Assembling networks of microbial genomes using linear programming. BMC Evol Biol 10: 360.
  • Hooper SD, Mavromatis K & Kyrpides NC (2009) Microbial co-habitation and lateral gene transfer: what transposases can tell us. Genome Biol 10: R45.
  • Hug LA, Beiko RG, Rowe AR, Richardson RE & Edwards EA (2012) Comparative metagenomics of three Dehalococcoides-containing enrichment cultures: the role of the non-dechlorinating community. BMC Genomics 13: 327.
  • Hugenholtz P, Goebel BM & Pace NR (1998) Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J Bacteriol 180: 47654774.
  • Hull D (1980) Individuality and selection. Annu Rev Ecol Syst 11: 311332.
  • Human Microbiome Project Consortium (2012) Structure, function and diversity of the healthy human microbiome. Nature 486: 207214.
  • Huse SM, Ye Y, Zhou Y & Fodor AA (2012) A core human microbiome as viewed through 16S rRNA sequence clusters. PLoS ONE 7: e34242.
  • Hutchinson GE (1957) The multivariate niche. Cold Spring Harb Symp Quant Biol 22: 415421.
  • Ivanova N, Tringe SG, Liolios K, Liu WT, Morrison N, Hugenholtz P & Kyrpides NC (2010) A call for standardized classification of metagenome projects. Environ Microbiol 12: 18031805.
  • Jain R, Rivera MC & Lake JA (1999) Horizontal gene transfer among genomes: the complexity hypothesis. P Natl Acad Sci USA 96: 38013806.
  • Jain R, Rivera MC, Moore JE & Lake JA (2003) Horizontal gene transfer accelerates genome innovation and evolution. Mol Biol Evol 20: 15981602.
  • Jeffery IB, Claesson MJ, O'Toole PW & Shanahan F (2012) Categorization of the gut microbiota: enterotypes or gradients? Nat Rev Microbiol 10: 591592.
  • Jehmlich N, Hübschmann T, Gesell Salazar M, Völker U, Benndorf D, Müller S, von Bergen M & Schmidt F (2010) Advanced tool for characterization of microbial cultures by combining cytomics and proteomics. Appl Microbiol Biotechnol 88: 575584.
  • Jiao Y, D'haeseleer P, Dill BD, Shah M, Verberkmoes NC, Hettich RL, Banfield JF & Thelen MP (2011) Identification of biofilm matrix-associated proteins from an acid mine drainage microbial community. Appl Environ Microbiol 77: 52305237.
  • Johnson MA & Winquist RJ (2011) Island biogeography effects on microbial evolution may contribute to Crohn's disease. Biochem Pharmacol 82: 18011806.
  • Johnston C, Martin B, Granadel C, Polard P & Claverys J-P (2013) Programmed protection of foreign DNA from restriction allows pathogenicity island exchange during pneumococcal transformation. PLoS Pathog 9: e1003178.
  • Kastenmüller G, Schenk ME, Gasteiger J & Mewes HW (2009) Uncovering metabolic pathways relevant to phenotypic traits of microbial genomes. Genome Biol 10: R28.
  • Kelkar YD & Ochman H (2013) Genome reduction promotes increase in protein functional complexity in bacteria. Genetics 193: 303307.
  • Kim HD, Shay T, O'Shea EK & Regev A (2009) Transcriptional regulatory circuits: predicting numbers from alphabets. Science 325: 429432.
  • Kim M, Ashida H, Ogawa M, Yoshikawa Y, Mimuro H & Sasakawa C (2010) Bacterial interactions with the host epithelium. Cell Host Microbe 8: 2035.
  • Klenk HP & Göker M (2010) En route to a genome-based classification of Archaea and Bacteria? Syst Appl Microbiol 33: 175182.
  • Knietsch A, Bowien S, Whited G, Gottschalk G & Daniel R (2003) Identification and characterization of coenzyme B12-dependent glycerol dehydratase- and diol dehydratase-encoding genes from metagenomic DNA libraries derived from enrichment cultures. Appl Environ Microbiol 69: 30483060.
  • Knight R, Jansson J, Field D et al. (2012) Unlocking the potential of metagenomics through replicated experimental design. Nat Biotechnol 30: 513520.
  • Knights D, Costello EK & Knight R (2011) Supervised classification of human microbiota. FEMS Microbiol Rev 35: 343359.
  • Kobayashi I (2001) Behavior of restriction-modification systems as selfish mobile elements and their impact on genome evolution. Nucleic Acids Res 29: 37423756.
  • Kocher TD, Conroy JA, McKaye KR & Stauffer JR (1993) Similar morphologies of cichlid fish in Lakes Tanganyika and Malawi are due to convergence. Mol Phylogenet Evol 2: 158165.
  • Konopka A (2009) What is microbial community ecology? ISME J 3: 12231230.
  • Konstantinidis KT & Tiedje JM (2004) Trends between gene content and genome size in prokaryotic species with larger genomes. P Natl Acad Sci USA 101: 31603165.
  • Konstantinidis KT & Tiedje JM (2005) Towards a genome-based taxonomy for prokaryotes. J Bacteriol 187: 62586264.
  • Konstantinidis KT, Ramette A & Tiedje JM (2006) The bacterial species definition in the genomic era. Philos Trans R Soc Lond B Biol Sci 361: 19291940.
  • Koonin EV & Wolf YI (2008) Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world. Nucleic Acids Res 36: 66886719.
  • Koren O, Knights D, Gonzalez A, Waldron L, Segata N, Knight R, Huttenhower C & Ley RE (2013) A guide to enterotypes across the human body: meta-analysis of microbial community structures in human microbiome datasets. PLoS Comput Biol 9: e1002863.
  • Koskiniemi S, Sun S, Berg OG & Andersson DI (2012) Selection-driven gene loss in bacteria. PLoS Genet 8: e1002787.
  • Kreuzer-Martin HW (2007) Stable isotope probing: linking functional activity to specific members of microbial communities. Soil Sci Soc Am J 71: 611.
  • Kuczynski J, Liu Z, Lozupone C, McDonald D, Fierer N & Knight R (2010) Microbial community resemblance methods differ in their ability to detect biologically relevant patterns. Nat Methods 7: 813819.
  • Kuenen JG (1983) The role of specialists and generalists in microbial population interactions. Foundations of Biochemical Engineering: Kinetics and Thermodynamic in Biological Systems, Vol. 207, chapter 10 (Blanch HW, Papoutsakis ET & Stephanopoulos G, eds), pp. 229251. ACS Symposium Series.
  • Kunin V, Goldovsky L, Darzentas N & Ouzounis CA (2005) The net of life: reconstructing the microbial phylogenetic network. Genome Res 15: 954959.
  • Kuo CH, Moran NA & Ochman H (2009) The consequences of genetic drift for bacterial genome complexity. Genome Res 19: 14501454.
  • Kuramitsu HK, He X, Lux R, Anderson MH & Wenyuan S (2007) Interspecies interactions within oral microbial communities. Microbiol Mol Biol Rev 71: 46534670.
  • Langille MGI, Zaneveld J, Caporaso JG, McDonald D, Knights D, Reyes JA, Clemente JC, Knight R, Beiko RG & Huttenhower C (2013) Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat Biotechnol (in press).
  • Larsen PE, Field D & Gilbert JA (2012) Predicting bacterial community assemblages using an artificial neural network approach. Nat Methods 9: 621625.
  • Lawley TD, Clare S, Walker AW et al. (2012) Targeted restoration of the intestinal microbiota with a simple, defined bacteriotherapy resolves relapsing Clostridium difficile disease in mice. PLoS Pathog 8: e1002995.
  • Layeghifard M, Peres-Neto PR & Makarenkov V (2012) Using directed phylogenetic networks to retrace species dispersal history. Mol Phylogenet Evol 64: 190197.
  • Lederberg J & McCray AT (2001) ‘Ome Sweet ‘Omics—a genealogical treasury of words. Scientist 15: 8.
  • Leibold MA, Holyoak M, Mouquet N et al. (2004) The metacommunity concept: a framework for multi-scale community ecology. Ecol Lett 7: 601613.
  • Leibold MA, Economo EP & Peres-Neto P (2010) Metacommunity phylogenetics: separating the roles of environmental filters and historical biogeography. Ecol Lett 13: 12901299.
  • Leininger S, Urich T, Schloter M, Schwark L, Qi J, Nicol GW, Prosser JI, Schuster SC & Schleper C (2006) Archaea predominate among ammonia-oxidizing prokaryotes in soils. Nature 442: 806809.
  • Lennon JT & Jones SE (2011) Microbial seed banks: the ecological and evolutionary implications of dormancy. Nat Rev Microbiol 9: 119130.
  • Lercher MJ & Pál C (2008) Integration of horizontally transferred genes into regulatory interaction networks takes many million years. Mol Biol Evol 25: 559567.
  • Ley RE, Turnbaugh P, Klein S & Gordon JI (2006) Microbial ecology: human gut microbes associated with obesity. Nature 444: 10221023.
  • Lima-Mendez G, Van Helden J, Toussaint A & Leplae R (2008) Reticulate representation of evolutionary and functional relationships between phage genomes. Mol Biol Evol 25: 762777.
  • Links MG, Dumonceaux T, Hemmingsen SM & Hill JE (2012) The chaperonin-60 universal target is a barcode for Bacteria that enables de novo assembly of metagenomic sequence data. PLoS ONE 7: e49755.
  • Little AEF, Robinson CJ, Peterson SB, Raffa KF & Handelsman J (2008) Rules of engagement: interspecies interactions that regulate microbial communities. Annu Rev Microbiol 62: 375401.
  • Löffler FE, Yan J, Ritalahti KM, Adrian L, Edwards EA, Konstantinidis KT, Müller JA, Fullerton H, Zinder SH & Spormann AM (2012) Dehalococcoides mccartyi gen. nov., sp. nov., obligately organohalide-respiring anaerobic bacteria relevant to halogen cycling and bioremediation, belong to a novel bacterial class, Dehalococcoidia classis nov., order Dehalococcoidales ord. nov. and family Dehalococcoidaceae fam. nov., within the phylum Chloroflexi. Int J Syst Evol Microbiol 63: 625635.
  • Loper JE, Hassan KA, Mavrodi DV et al. (2012) Comparative genomics of plant-associated Pseudomonas spp.: insights into diversity and inheritance of traits involved in multitrophic interactions. PLoS Genet 8: e1002784.
  • Lozupone CA, Hamady M, Kelley ST & Knight R (2007) Quantitative and qualitative β diversity measures lead to different insights into factors that structure microbial communities. Appl Environ Microbiol 73: 15761585.
  • Lynch M (2006) Streamlining and simplification of microbial genome architecture. Annu Rev Microbiol 60: 327349.
  • MacDonald NJ & Beiko RG (2010) Efficient learning of microbial genotype-phenotype association rules. Bioinformatics 26: 18341840.
  • MacDonald NJ, Parks DH & Beiko RG (2012) Rapid identification of high-confidence taxonomic assignments for metagenomic data. Nucleic Acids Res 40: e111.
  • Maidak BL, Cole JR, Lilburn TG, Parker CT Jr, Saxman PR, Farris RJ, Garrity GM, Olsen GJ, Schmidt TM & Tiedje JM (2001) The RDP-II (Ribosomal Database Project). Nucleic Acids Res 29: 173174.
  • Malcom JW (2011) Gene networks and metacommunities: dispersal differences can override adaptive advantage. PLoS ONE 6: e21541.
  • Mandel MJ (2010) Models and approaches to dissect host-symbiont specificity. Trends Microbiol 18: 504511.
  • Mariat D, Firmesse O, Levenez F, Guimarăes V, Sokol H, Doré J, Corthier G & Furet JP (2009) The Firmicutes/Bacteroidetes ratio of the human microbiota changes with age. BMC Microbiol 9: 123.
  • Martin AP (2002) Phylogenetic approaches for describing and comparing the diversity of microbial communities. Appl Environ Microbiol 68: 36733682.
  • Martinez-Garcia M, Brazel DM, Swan BK et al. (2012) Capturing single cell genomes of active polysaccharide degraders: an unexpected contribution of Verrucomicrobia. PLoS ONE 7: e35314.
  • Martiny JB, Bohannan BJ, Brown JH et al. (2006) Microbial biogeography: putting microorganisms on the map. Nat Rev Microbiol 4: 102112.
  • Martiny AC, Tai AP, Veneziano D, Primeau F & Chisholm SW (2009) Taxonomic resolution, ecotypes and the biogeography of Prochlorococcus. Environ Microbiol 11: 823832.
  • Martiny AC, Treseder K & Pusch G (2013) Phylogenetic conservatism of functional traits in microorganisms. ISME J 7: 830838.
  • May RM (1973) Stability and Complexity in Model Ecosystems. Princeton Univ, Press.
  • Mayr E (1942) Systematics and the Origin of Species. Columbia Univ, Press, New York.
  • McBride BC & Van der Hoeven JS (1981) Role of interbacterial adherence in colonization of the oral cavities of gnotobiotic rats infected with Streptococcus mutans and Veillonella alcalescens. Infect Immun 33: 467472.
  • McCutcheon JP & von Dohlen CD (2011) An interdependent metabolic patchwork in the nested symbiosis of mealybugs. Curr Biol 21: 13661372.
  • McDonald D, Clemente JC, Kuczynski J et al. (2012) The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome. GigaScience 1: 7.
  • McGill BJ, Enquist BJ, Weiher E & Westoby M (2006) Rebuilding community ecology from functional traits. Trends Ecol Evol 21: 178185.
  • McGinty SE, Rankin DJ & Brown SP (2011) Horizontal gene transfer and the evolution of bacterial cooperation. Evolution 65: 2132.
  • McHardy AC & Rigoutsos I (2007) What's in the mix: phylogenetic classification of metagenome sequence samples. Curr Opin Microbiol 10: 499503.
  • McInerney JO, Pisani D, Bapteste E & O'Connell MJ (2011) The Public Goods Hypothesis for the evolution of life on Earth. Biol Direct 6: 41.
  • McNab BK (2009) Physiological convergence amongst ant-eating and termite-eating mammals. J Zool 203: 485510.
  • McNulty NP, Yatsunenko T, Hsiao A et al. (2011) The impact of a consortium of fermented milk strains on the gut microbiome of gnotobiotic mice and monozygotic twins. Sci Transl Med 3: 106ra106.
  • Medini D, Donati C, Tettelin H, Masignani V & Rappuoli R (2005) The microbial pan-genome. Curr Opin Genet Dev 15: 589594.
  • Meehan CJ & Beiko RG (2012) Lateral gene transfer of an ABC transporter complex between major constituents of the human gut microbiome. BMC Microbiol 12: 248.
  • Menge BA (1995) Indirect effects in marine rocky intertidal interaction webs: patterns and importance. Ecol Monogr 65: 2174.
  • Mikesková H, Novotný C & Svobodová K (2012) Interspecific interactions in mixed microbial cultures in a biodegradation perspective. Appl Microbiol Biotechnol 95: 861870.
  • Mirete S, de Figueras CG & González-Pastor JE (2007) Novel nickel resistance genes from the rhizosphere metagenome of plants adapted to acid mine drainage. Appl Environ Microbiol 73: 60016011.
  • Mishler BD & Donoghue MJ (1982) Species concepts: a case for pluralism. Syst Zool 31: 491503.
  • Moran MA, Satinsky B, Gifford SM et al. (2013) Sizing up metatranscriptomics. ISME J 7: 237243.
  • Morris RM, Rappe MS, Connon SA, Vergin KL, Siebold WA, Carlson CA & Giovannoni SJ (2002) SAR11 clade dominates ocean surface bacterioplankton communities. Nature 420: 806810.
  • Morris JJ, Johnson ZI, Szul MJ, Keller M & Zinser ER (2011) Dependence of the cyanobacterium Prochlorococcus on hydrogen peroxide scavenging microbes for growth at the ocean's surface. PLoS ONE 6: e16805.
  • Morris JJ, Lenski RE & Zinser ER (2012) The Black Queen Hypothesis: evolution of dependencies through adaptive gene loss. MBio 3: e0003612.
  • Mouillot D, Graham NA, Villéger S, Mason NW & Bellwood DR (2013) A functional approach reveals community responses to disturbances. Trends Ecol Evol 28: 167177.
  • Muegge BD, Kuczynski J, Knights D, Clemente JC, González A, Fontana L, Henrissat B, Knight R & Gordon JI (2011) Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans. Science 332: 970974.
  • Müller S, Hübschmann T, Kleinsteuber S & Vogt C (2012) High resolution single cell analytics to follow microbial community dynamics in anaerobic ecosystems. Methods 57: 338349.
  • Nemergut DR, Costello EK, Hamady M et al. (2011) Global patterns in the biogeography of bacterial taxa. Environ Microbiol 13: 135144.
  • Nogueira T, Rankin DJ, Touchon M, Taddei F, Brown SP & Rocha EPC (2009) Horizontal gene transfer of the secretome drives the evolution of bacterial cooperation and virulence. Curr Biol 19: 16831691.
  • O'Connor TJ, Boyd D, Dorer MS & Isberg RR (2012) Aggravating genetic interactions allow a solution to redundancy in a bacterial pathogen. Science 338: 14401444.
  • Ohta T (1992) The nearly neutral theory of molecular evolution. Annu Rev Ecol Syst 23: 263286.
  • Pál C, Papp B & Lercher MJ (2005) Adaptive evolution of bacterial metabolic networks by horizontal gene transfer. Nat Genet 37: 13721375.
  • Parks DH & Beiko RG (2012) Measuring community similarity with phylogenetic networks. Mol Biol Evol 29: 39473958.
  • Parks DH & Beiko RG (2013) Measures of phylogenetic differentiation provide robust and complementary insights into microbial communities. ISME J 7: 173183.
  • Patel PV, Gianoulis TA, Bjornson RD, Yip KY, Engelman DM & Gerstein MB (2010) Analysis of membrane proteins in metagenomics: networks of correlated environmental features and protein families. Genome Res 20: 960971.
  • Patel V, Jain S & Madamwar D (2012) Naphthalene degradation by bacterial consortium (DV-AL) developed from Alang-Sosiya ship breaking yard, Gujarat, India. Bioresour Technol 107: 122130.
  • Pearson T, Giffard P, Beckstrom-Sternberg S et al. (2009) Phylogeographic reconstruction of a bacterial species with high levels of lateral gene transfer. BMC Biol 7: 78.
  • Petrof EO, Gloor GB, Vanner SJ, Weese SJ, Carter D, Daigneault MC, Brown EM, Schroeter K & Allen-Vercoe E (2013) Stool substitute transplant therapy for the eradication of Clostridium difficile infection: ‘RePOOPulating’ the gut. Microbiome 1: 3.
  • Pfeiffer T & Bonhoeffer S (2004) Evolution of cross-feeding in microbial populations. Am Nat 163: E126E135.
  • Phillips J (1935) Succession, development, the climax and the complex organism: an analysis of concepts. J Ecol 23: 488508.
  • Poretsky RS, Bano N, Buchan A, LeCleir G, Kleikemper J, Pickering M, Pate WM, Moran MA & Hollibaugh JT (2005) Analysis of microbial gene transcripts in environmental samples. Appl Environ Microbiol 71: 41214126.
  • Porwollik S, Boyd EF, Choy C, Cheng P, Florea L, Proctor E & McClelland M (2004) Characterization of Salmonella enterica Subspecies I genovars by use of microarrays. J Bacteriol 186: 58835898.
  • Prakash T & Taylor TD (2012) Functional assignment of metagenomic data: challenges and applications. Brief Bioinform 13: 711727.
  • Preidis GA & Versalovic J (2009) Targeting the human microbiome with antibiotics, probiotics, and prebiotics: gastroenterology enters the metagenomics era. Gastroenterology 136: 20152031.
  • Prosser JI, Bohannan BJ, Curtis TP et al. (2007) The role of ecological theory in microbial ecology. Nat Rev Microbiol 5: 384392.
  • Puigbò P, Wolf YI & Koonin EV (2009) Search for a ‘Tree of Life’ in the thicket of the phylogenetic forest. J Biol 8: 59.
  • Qin J, Li Y, Cai Z et al. (2012) A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature 490: 5560.
  • Radivojac P, Clark WT, Oron TR et al. (2013) A large-scale evaluation of computational protein function prediction. Nat Methods 10: 221227.
  • Raes J, Letunic I, Yamada T, Jensen LJ & Bork P (2011) Toward molecular trait-based ecology through integration of biogeochemical, geographical and metagenomic data. Mol Syst Biol 7: 473.
  • Ragan MA, Harlow TJ & Beiko RG (2006) Do different surrogate methods detect lateral genetic transfer events of different relative ages? Trends Microbiol 14: 48.
  • Ram RJ, Verberkmoes NC, Thelen MP, Tyson GW, Baker BJ, Blake RC 2nd, Shah M, Hettich RL & Banfield JF (2005) Community proteomics of a natural microbial biofilm. Science 308: 19151920.
  • Rankin DJ, Rocha EPC & Brown SP (2011) What traits are carried on mobile genetic elements, and why? Heredity 106: 110.
  • Redfield RJ (2001) Do bacteria have sex? Nat Rev Genet 2: 634639.
  • Reim A, Lüke C, Krause S, Pratscher J & Frenzel P (2012) One millimetre makes the difference: high-resolution analysis of methane-oxidizing bacteria and their specific activity at the oxic–anoxic interface in a flooded paddy soil. ISME J 6: 21282139.
  • Relman DA (2002) New technologies, human-microbe interactions, and the search for previously unrecognized pathogens. J Infect Dis 186: S254S258.
  • Reno ML, Held NL, Fields CJ, Burke PV & Whitaker RJ (2009) Biogeography of the Sulfolobus islandicus pan-genome. P Natl Acad Sci USA 106: 86058610.
  • Ricklefs RE (2008) Disintegration of the ecological community. Am Nat 172: 741750.
  • Rodríguez-Valera F (2004) Environmental genomics, the big picture? FEMS Microbiol Lett 231: 153158.
  • Rusch DB, Halpern AL, Sutton G et al. (2007) The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific. PLoS Biol 5: e77.
  • Sabehi G, Massana R, Bielawski JP, Rosenberg M, Delong EF & Béjà O (2003) Novel Proteorhodopsin variants from the Mediterranean and Red Seas. Environ Microbiol 5: 842849.
  • Sage RF, Christin PA & Edwards EJ (2011) The C(4) plant lineages of planet Earth. J Exp Bot 62: 31553169.
  • Sale PF (1978) Coexistence of coral reef fishes — a lottery for living space. Environ Biol Fish 3: 85102.
  • Salimi F, Zhuang K & Mahadevan R (2010) Genome-scale metabolic modeling of a clostridial co-culture for consolidated bioprocessing. Biotechnol J 5: 726738.
  • Salyers AA, Gupta A & Wang Y (2004) Human intestinal bacteria as reservoirs for antibiotic resistance genes. Trends Microbiol 12: 412416.
  • Sapp J (2005) The Bacterium's Place in Nature. Microbial Phylogeny and Evolution, pp. 152. Oxford University Press, New York, NY.
  • Schellenberg J, Links MG, Hill JE, Dumonceaux TJ, Peters GA, Tyler S, Ball TB, Severini A & Plummer FA (2009) Pyrosequencing of the chaperonin-60 universal target as a tool for determining microbial community composition. Appl Environ Microbiol 75: 28892898.
  • Schellenberg J, Links MG, Hill JE, Hemmingsen SM & Dumonceaux TJ (2011) Pyrosequencing of chaperonin-60 (cpn60) amplicons as a means of determining microbial community composition. Methods Mol Biol 733: 143158.
  • Schink B (2002) Synergistic interactions in the microbial world. Antonie Van Leeuwenhoek 81: 257261.
  • Schloissnig S, Arumugam M, Sunagawa S et al. (2013) Genomic variation landscape of the human gut microbiome. Nature 493: 4550.
  • Schloss PD & Handelsman J (2003) Biotechnological prospects from metagenomics. Curr Opin Biotechnol 14: 303310.
  • Schloss PD & Handelsman J (2005) Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl Environ Microbiol 71: 15011506.
  • Schneiker S, Perlova O, Kaiser O et al. (2007) Complete genome sequence of the myxobacterium Sorangium cellulosum. Nat Biotechnol 25: 12811289.
  • Schnoes AM, Brown SD, Dodevski I & Babbitt PC (2009) Annotation error in public databases: misannotation of molecular function in enzyme superfamilies. PLoS Comput Biol 5: e1000605.
  • Schouls LM, Schot CS & Jacobs JA (2003) Horizontal transfer of segments of the 16S rRNA genes between species of the Streptococcus anginosus group. J Bacteriol 185: 72417246.
  • Shade A & Handelsman J (2012) Beyond the Venn diagram: the hunt for a core microbiome. Environ Microbiol 14: 412.
  • Shen K, Sayeed S, Antalis P et al. (2006) Extensive genomic plasticity in Pseudomonas aeruginosa revealed by identification and distribution studies of novel genes among clinical isolates. Infect Immun 74: 52725283.
  • Sher D, Thompson JW, Kashtan N, Croal L & Chisholm SW (2011) Response of Prochlorococcus ecotypes to co-culture with diverse marine bacteria. ISME J 5: 11251132.
  • Sibley CD & Surette MG (2011) The polymicrobial nature of airway infections in cystic fibrosis: Cangene Gold Medal Lecture. Can J Microbiol 57: 6977.
  • Siezen RJ, Tzeneva VA, Castioni A, Wels M, Phan HTK, Rademaker JLW, Starrenburg MJC, Kleerebezem C, Molenaar D & Van Hylckama Vlieg JET (2010) Phenotypic and genomic diversity of Lactobacillus plantarum strains isolated from various environmental niches. Environ Microbiol 12: 758773.
  • Skippington E & Ragan MA (2011) Lateral genetic transfer and the construction of genetic exchange communities. FEMS Microbiol Rev 35: 707735.
  • Smidt H & de Vos WM (2004) Anaerobic microbial dehalogenation. Annu Rev Microbiol 58: 4373.
  • Smillie CS, Smith MB, Friedman J, Cordero OX, David LA & Alm EJ (2011) Ecology drives a global network of gene exchange connecting the human microbiome. Nature 480: 241244.
  • Smith J (2001) The social evolution of bacterial pathogenesis. Proc Biol Sci 268: 6169.
  • Smith MI, Yatsunenko T, Manary MJ et al. (2013) Gut microbiomes of Malawian twin pairs discordant for kwashiorkor. Science 339: 548554.
  • Sokal RR & Sneath PHA (1963) Principles of numerical taxonomy. Freeman, San Francisco, WH.
  • Souza V, Rocha M, Valera A & Eguiarte LE (1999) Genetic structure of natural populations of Escherichia coli in wild hosts on different continents. Appl Environ Microbiol 65: 33733385.
  • Staley JT & Konopka A (1985) Measurement of in situ activities of nonphotosynthetic microorganisms in aquatic and terrestrial habitats. Annu Rev Microbiol 39: 321346.
  • Stams AJ (1994) Metabolic interactions between anaerobic bacteria in methanogenic environments. Antonie Van Leeuwenhoek 66: 271294.
  • Stearns JC, Lynch MD, Senadheera DB, Tenenbaum HC, Goldberg MB, Cvitkovitch DG, Croitoru K, Moreno-Hagelsieb G & Neufeld JD (2011) Bacterial biogeography of the human digestive tract. Sci Rep 1: 170.
  • Steele JA, Countway PD, Xia L et al. (2011) Marine bacterial, archaeal and protistan association networks reveal ecological linkages. ISME J 5: 14141425.
  • Stolyar S, Van Dien S, Hillesland KL, Pinel N, Lie TJ, Leigh JA & Stahl DA (2007) Metabolic modeling of a mutualistic microbial community. Mol Syst Biol 3: 92.
  • Sul WJ, Park J, Quensen JF 3rd, Rodrigues JL, Seliger L, Tsoi TV, Zylstra GJ & Tiedje JM (2009) DNA-stable isotope probing integrated with metagenomics for retrieval of biphenyl dioxygenase genes from polychlorinated biphenyl-contaminated river sediment. Appl Environ Microbiol 75: 55015506.
  • Suzuki MT, Béjà O, Taylor LT & Delong EF (2001) Phylogenetic analysis of ribosomal RNA operons from uncultivated coastal marine bacterioplankton. Environ Microbiol 3: 323331.
  • Teeling H, Fuchs BM, Becher D et al. (2012) Substrate-controlled succession of marine bacterioplankton populations induced by a phytoplankton bloom. Science 336: 608611.
  • Teles FR, Teles RP, Sachdeo A, Uzel NG, Song XQ, Torresyap G, Singh M, Papas A, Haffajee AD & Socransky SS (2012) Comparison of microbial changes in early redeveloping biofilms on natural teeth and dentures. J Periodontol 83: 11391148.
  • Tettelin H, Masignani V, Cieslewicz MJ et al. (2005) Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial “pan-genome”. P Natl Acad Sci USA 102: 1395013955.
  • Tettelin H, Riley D, Cattuto C & Medini D (2008) Comparative genomics: the bacterial pan-genome. Curr Opin Microbiol 11: 472477.
  • Treangen TJ & Rocha EP (2011) Horizontal transfer, not duplication, drives the expansion of protein families in prokaryotes. PLoS Genet 7: e1001284.
  • Trzesicka-Mlynarz D & Ward OP (1995) Degradation of polycyclic aromatic hydrocarbons (PAHs) by a mixed culture and its component pure cultures, obtained from PAH-contaminated soil. Can J Microbiol 41: 470476.
  • Turnbaugh PJ, Ley RE, Hamady M, Fraser-Liggett CM, Knight R & Gordon JI (2007) The human microbiome project. Nature 449: 804810.
  • Turnbaugh PJ, Hamady M, Yatsunenko T et al. (2009) A core gut microbiome in obese and lean twins. Nature 457: 480484.
  • Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ, Richardson PM, Solovyev VV, Rubin EM, Rokhsar DS & Banfield JF (2004) Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428: 3743.
  • Urban MC & Skelly DK (2006) Evolving metacommunities: toward an evolutionary perspective on metacommunities. Ecology 87: 16161626.
  • Van den Abbeele P, Belzer C, Goossens M, Kleerebezem M, De Vos WM, Thas O, De Weirdt R, Kerckhof FM & Van de Wiele T (2013) Butyrate-producing Clostridium cluster XIVa species specifically colonize mucins in an in vitro gut model. ISME J 7: 949961.
  • Van Valen L (1976) Ecological species, multispecies, and oaks. Taxon 25: 233239.
  • Venner S, Feschotte C & Biémont C (2009) Dynamics of transposable elements: towards a community ecology of the genome. Trends Genet 25: 317323.
  • Venter JC, Remington K, Heidelberg JF et al. (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science 304: 6674.
  • Vergin KL, Tripp HJ, Wilhelm LJ, Denver DR, Rappé MS & Giovannoni SJ (2007) High intraspecific recombination rate in a native population of Candidatus pelagibacter ubique (SAR11). Environ Microbiol 9: 24302440.
  • Viklund J, Ettema TJ & Andersson SG (2012) Independent genome reduction and phylogenetic reclassification of the oceanic SAR11 clade. Mol Biol Evol 29: 599615.
  • Violle C, Navas ML, Vile D, Kazakou E, Fortunel C, Hummel I & Garnier E (2007) Let the concept of trait be functional!. Oikos 116: 882892.
  • Ward DM, Weller R & Bateson MM (1990) 16S rRNA sequences reveal numerous uncultured microorganisms in a natural community. Nature 345: 6365.
  • Warnecke T & Rocha EP (2011) Function-specific accelerations in rates of sequence evolution suggest predictable epistatic responses to reduced effective population size. Mol Biol Evol 28: 23392349.
  • Watrous J, Hendricks N, Meehan M & Dorrestein PC (2010) Capturing bacterial metabolic exchange using thin film desorption electrospray ionization-imaging mass spectrometry. Anal Chem 82: 15981600.
  • Watrous JD, Alexandrov T & Dorrestein PC (2011) The evolving field of imaging mass spectrometry and its impact on future biological research. J Mass Spectrom 46: 209222. doi:10.1002/jms.1876.
  • Watrous J, Roach P, Alexandrov T et al. (2012) Mass spectral molecular networking of living microbial colonies. P Natl Acad Sci USA 109: E1743E1752.
  • Webb CT, Hoeting JA, Ames GM, Pyne MI & LeRoy Poff N (2010) A structured and dynamic framework to advance traits-based theory and prediction in ecology. Ecol Lett 13: 267283.
  • Weckwerth W (2003) Metabolomics in systems biology. Annu Rev Plant Biol 54: 669689.
  • Welch RA, Burland V, Plunkett G 3rd et al. (2002) Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli. P Natl Acad Sci USA 99: 1702017024.
  • Whitham TG, DiFazio SP, Schweitzer JA, Shuster SM, Allan GJ, Bailey JK & Woolbright SA (2008) Extending genomics to natural communities and ecosystems. Science 320: 492495.
  • Whittaker RH (1967) Gradient analysis of vegetation. Biol Rev 49: 207264.
  • Whitworth DE (2008) Genomes and knowledge – a questionable relationship? Trends Microbiol 16: 512519.
  • Wilhelm LJ, Tripp HJ, Givan SA, Smith DP & Giovannoni SJ (2007) Natural variation in SAR11 marine bacterioplankton genomes inferred from metagenomic data. Biol Direct 2: 27.
  • Wilmes P & Bond PL (2004) The application of two-dimensional polyacrylamide gel electrophoresis and downstream analyses to a mixed community of prokaryotic microorganisms. Environ Microbiol 6: 911920.
  • Wilmes P, Andersson AF, Lefsrud MG, Wexler M, Shah M, Zhang B, Hettich RL, Bond PL, VerBerkmoes NC & Banfield JF (2008a) Community proteogenomics highlights microbial strain-variant protein expression within activated sludge performing enhanced biological phosphorus removal. ISME J 2: 853864.
  • Wilmes P, Wexler M & Bond PL (2008b) Metaproteomics provides functional insight into activated sludge wastewater treatment. PLoS ONE 3: e1778.
  • Wintermute EH & Silver PA (2010) Dynamics in the mixed microbial concourse. Genes Dev 24: 26032614.
  • Woese CR, Olsen GJ, Ibba M & Söll D (2000) Aminoacyl-tRNA synthetases, the genetic code, and the evolutionary process. Microbiol Mol Biol Rev 64: 202236.
  • Wolcott R, Costerton JW, Raoult D & Cutler SJ (2013) The polymicrobial nature of biofilm infection. Clin Microbiol Infect 19: 107112.
  • Wu GD, Chen J, Hoffmann C et al. (2011) Linking long-term dietary patterns with gut microbial enterotypes. Science 334: 105108.
  • Xie Y, Luo Z, Li Z, Deng M, Liu H, Zhu B, Ruan B & Li L (2012) Structural shifts of fecal microbial communities in rats with acute rejection after liver transplantation. Microb Ecol 64: 546554.
  • Yamada T, Waller AS, Raes J, Zelezniak A, Perchat N, Perret A, Salanoubat M, Patil KR, Weissenbach J & Bork P (2012) Prediction and identification of sequences coding for orphan enzymes using genomic and metagenomic neighbours. Mol Syst Biol 8: 581.
  • Yatsunenko T, Rey FE, Manary MJ et al. (2012) Human gut microbiome viewed across age and geography. Nature 486: 222227.
  • Ye Y & Doak TG (2009) A parsimony approach to biological pathway reconstruction/inference for genomes and metagenomes. PLoS Comput Biol 5: e1000465.
  • Yelton AP, Thomas BC, Simmons SL, Wilmes P, Zemla A, Thelen MP, Justice N & Banfield JF (2011) A semi-quantitative, synteny-based method to improve functional predictions for hypothetical and poorly annotated bacterial and archaeal genes. PLoS Comput Biol 7: e1002230.
  • Yilmaz P, Kottmann R, Field D et al. (2011) Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Nat Biotechnol 29: 415420.
  • Yu K & Zhang T (2012) Metagenomic and metatranscriptomic analysis of microbial community structure and gene expression of activated sludge. PLoS ONE 7: e38183.
  • Yu NY, Wagner JR, Laird MR et al. (2010) PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes. Bioinformatics 26: 16081615.
  • Zarraonaindia I, Smith DP & Gilbert JA (2013) Beyond the genome: community-level analysis of the microbial world. Biol Philos 28: 261282.
  • Zhu P & Li M (2012) Recent progresses on AI-2 bacterial quorum sensing inhibitors. Curr Med Chem 19: 174186.
  • Zhuang K, Vemuri GN & Mahadevan R (2011) Economics of membrane occupancy and respiro-fermentation. Mol Syst Biol 7: 500.
  • Zhuang K, Ma E, Lovley DR & Mahadevan R (2012) The design of long-term effective uranium bioremediation strategy using a community metabolic model. Biotechnol Bioeng 109: 24752483.
  • Zomorrodi AR & Maranas CD (2012) OptCom: a multi-level optimization framework for the metabolic modeling and analysis of microbial communities. PLoS Comput Biol 8: e1002363.