Functional Metagenomics: Recent Advances and Future Challenges

References

• Brulc , J.M. , Antonopoulos , D.A. , Miller , M.E. , Wilson , M.K. , Yannarell , A.C. , Dinsdale , E.A. , Edwards , R.E. , Frank , E.D. , Emerson , J.B. , Wacklin , P. , Coutinho , P.M. , Henrissat , B. , Nelson , K. E. and White , BA. 2009 . Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases . Proceedings of National Academy of Sciences USA , 106 : 1948 – 1953 .
   PubMed Web of Science ®Google Scholar
• Dinsdale , E.A. , Edwards , R.A. , Hall , D. , Angly , F. , Breitbart , M. , Brulc , J.M. , Furlan , M. , Desnues , C. , Haynes , M. , Li , L. , McDaniel , L. , Moran , M.A. , Nelson , K.E. , Nilsson , C. , Olson , R. , Paul , J. , Brito , B.R. , Ruan , Y. , Swan , B.K. , Stevens , R. , Valentine , D.L. , Thurber , R.V. , Wegley , L. , White , B.A. and Rohwer , F. 2008 . Functional metagenomic profiling of nine biomes . Nature , 452 : 629 – 632 .
   PubMed Web of Science ®Google Scholar
• Edward , R.A. , Rodriguez-Brito , B. , Wegley , L. , Haynes , M. , Breitbart , M. , Peterson , D.M. , Saar , M.O. , Alexander , S. , Alexander , E.C. Jr. and Rohwer , F. 2006 . Using pyrosequencing to shed light on deep mine microbial ecology . BMC Genomics , 7 : 57
   PubMedGoogle Scholar
• Frias-Lopez , J. , Shi , Y. , Tyson , G.W. , Coleman , M.L. , Schuster , S.C. , Chisholm , S.W. and Delong , E.F. 2008 . Microbial community gene expression in ocean surface waters . Proceedings of National Academy of Sciences USA , 105 : 3805 – 3810 .
   PubMed Web of Science ®Google Scholar
• Friedrich , M.W. 2006 . Stable-isotope probing of DNA: insights into the function of uncultivated microorganisms from isotopically labeled metagenomes . Current Opinion in Biotechnology , 17 : 59 – 66 .
   PubMedGoogle Scholar
• García Martín , H. , Ivanova , N. , Kunin , V. , Warnecke , F. , Barry , K.W. , McHardy , A.C. , Yeates , C. , He , S. , Salamov , A.A. , Szeto , E. , Dalin , E. , Putnam , N.H. , Shapiro , H.J. , Pangilinan , J.L. , Rigoutsos , I. , Kyrpides , N.C. , Blackall , L.L. , McMahon , K.D. and Hugenholtz , P. 2006 . Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities . Nature Biotechnology , 24 : 1263 – 1269 .
   PubMedGoogle Scholar
• Gilbert , J.A. , Field , D. , Huang , Y. , Edwards , R. , Li , W. , Gilna , P. and Joint , I. 2008 . Detection of large numbers of novel sequences in the metatranscriptomes of complex marine microbial communities . PLoS ONE , 3 : e3042
   PubMed Web of Science ®Google Scholar
• Hallam , S.J. , Konstantinidis , K.T. , Putnam , N. , Schleper , C. , Watanabe , Y. , Sugahara , J. , Preston , C. , de la Torre , J. , Richardson , P. M. and DeLong , E.F. 2006 . Genomic analysis of the uncultivated marine crenarchaeote Cenarchaeum symbiosum . Proceedings of National Academy of Sciences USA , 103 : 18296 – 18301 .
   PubMed Web of Science ®Google Scholar
• Handelsman , J. 2004 . Metagenomics: application of genomics to uncultured microorganisms . Microbiology and Molecular Biology Reviews , 68 : 669 – 685 .
   PubMed Web of Science ®Google Scholar
• Handelsman , J. , Rondon , M.R. , Brady , S.F. , Clardy , J. and Goodman , R.M. 1998 . Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products . Chemistry and Biology , 5 : R245 – 249 .
   PubMed Web of Science ®Google Scholar
• Kalyuzhnaya , M.G. , Lapidus , A. , Ivanova , N. , Copeland , A.C. , McHardy , A.C. , Szeto , E. , Salamov , A. , Grigoriev , I.V. , Suciu , D. , Levine , S.R. , Markowitz , V.M. , Rigoutsos , I. , Tringe , S.G. , Bruce , D.C. , Richardson , P. M. , Lidstrom , M. E. and Chistoserdova , L. 2008 . High-resolution metagenomics targets specific functional types in complex microbial communities . Nature Biotechnology , 26 : 1029 – 1034 .
   PubMed Web of Science ®Google Scholar
• Kunin , V. , Copeland , A. , Lapidus , A. , Mavromatis , K. and Hugenholtz , P. 2008 . A bioinformatician's guide to metagenomics . Microbiology and Molecular Biology Reviews , 72 : 557 – 578 .
   PubMed Web of Science ®Google Scholar
• Lapidus , A. 2009 . “ Genome sequence databases (overview): sequencing and assembly ” . In The Encyclopedia of Microbiology , Edited by: Schaechter , M. 196 – 210 . New York : Elsevier .
   Google Scholar
• Li , L.L. , McCorkle , S.R. , Monchy , S. , Taghavi , S. and van der Lelie , D. 2009 . Bioprospecting metagenomes: glycosyl hydrolases for converting biomass . Biotechnology for Biofuels , 2 : 10
   PubMed Web of Science ®Google Scholar
• Liolios , K. , Mavromatis , K. , Tavernarakis , N. and Kyrpides , N.C. 2008 . The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata . Nucleic Acids Research , 36 : D475 – 479 .
   Google Scholar
• Markowitz , V.M. , Ivanova , N.N. , Szeto , E. , Palaniappan , K. , Chu , K. , Dalevi , D. , Chen , I.M. , Grechkin , Y. , Dubchak , I. , Anderson , I. , Lykidis , A. , Mavromatis , K. , Hugenholtz , P. and Kyrpides , N.C. 2008 . IMG/M: a data management and analysis system for metagenomes . Nucleic Acids Research , 36 : D534 – 538 .
   Google Scholar
• Mou , X. , Sun , S. , Edwards , R.A. , Hodson , R.E. and Moran , M.A. 2008 . Bacterial carbon processing by generalist species in the coastal ocean . Nature , 451 : 708 – 711 .
   PubMed Web of Science ®Google Scholar
• Pelletier , E. , Kreimeyer , A. , Bocs , S. , Rouy , Z. , Gyapay , G. , Chouari , R. , Rivière , D. , Ganesan , A. , Daegelen , P. , Sghir , A. , Cohen , G.N. , Médigue , C. , Weissenbach , J. and Le Paslier , D. 2008 . “Candidatus Cloacamonas acidaminovorans”: genome sequence reconstruction provides a first glimpse of a new bacterial division . Journal of Bacteriology , 190 : 2572 – 2579 .
   PubMed Web of Science ®Google Scholar
• Poretsky , R.S. , Hewson , I. , Sun , S. , Allen , A.E. , Zehr , J.P. and Moran , M.A. 2009 . Comparative day/night metatranscriptomic analysis of microbial communities in the North Pacific subtropical gyre . Environmental Microbiology , 11 : 1358 – 1375 .
   PubMedGoogle Scholar
• Preidis , G.A. and Versalovic , J. 2009 . Targeting the human microbiome with antibiotics, probiotics, and prebiotics: gastroenterology enters the metagenomics era . Gastroenterology , 136 : 2015 – 2031 .
   PubMed Web of Science ®Google Scholar
• Ram , R.J. , Verberkmoes , N.C. , Thelen , M.P. , Tyson , G.W. , Baker , B.J. , Blake , R.C. 2nd , Shah , M. , Hettich , R.L. and Banfield , J.F. 2005 . Community proteomics of a natural microbial biofilm . Science , 308 : 1915 – 1920 .
   PubMed Web of Science ®Google Scholar
• Schloss , PD and Handelsman , J. 2005 . Metagenomics for studying unculturable microorganisms: cutting the Gordian knot . Genome Biology , 6 : 229
   PubMed Web of Science ®Google Scholar
• Schlüter , A. , Bekel , T. , Diaz , N.N. , Dondrup , M. , Eichenlaub , R. , Gartemann , K.H. , Krahn , I. , Krause , L. , Krömeke , H. , Kruse , O. , Mussgnug , J.H. , Neuweger , H. , Niehaus , K. , Pühler , A. , Runte , K.J. , Szczepanowski , R. , Tauch , A. , Tilker , A. , Viehöver , P. and Goesmann , A. 2008 . The metagenome of a biogas-producing microbial community of a production-scale biogas plant fermenter analysed by the 454-pyrosequencing technology . Journal of Biotechnology , 136 : 77 – 90 .
   PubMed Web of Science ®Google Scholar
• Schmidt , T.M. , DeLong , E.F. and Pace , N.R. 1991 . Analysis of a marine picoplankton community by 16S rRNA gene cloning and sequencing . Journal of Bacteriology , 173 : 4371 – 4378 .
   PubMed Web of Science ®Google Scholar
• Snyder , L.A. , Loman , N. , Pallen , M.J. and Penn , C.W. 2008 . Next-generation sequencingthe promise and perils of charting the great microbial unknown . Microbial Ecology , 57 : 1 – 3 .
   PubMedGoogle Scholar
• Staley , J.T. and Konopka , A. 1985 . Measurement of in situ activities of nonphotosynthetic microorganisms in aquatic and terrestrial habitats . Annual Review of Microbiology , 39 : 321 – 346 .
   PubMed Web of Science ®Google Scholar
• Strous , M. , Pelletier , E. , Mangenot , S. , Rattei , T. , Lehner , A. , Taylor , M.W. , Horn , M. , Daims , H. , Bartol-Mavel , D. , Wincker , P. , Barbe , V. , Fonknechten , N. , Vallenet , D. , Segurens , B. , Schenowitz-Truong , C. , MÉdigue , C. , Collingro , A. , Snel , B. , Dutilh , B.E. , den Camp , Op , van der Drift , H.J. , Cirpus , C. , van de Pas-Schoonen , I. , Harhangi , K.T. , van Niftrik , H.R. , Schmid , L. , Keltjens , M. , van de Vossenberg , J. , Kartal , J. , Meier , B. , Frishman , H. , Huynen , D. , Mewes , M.A. , Weissenbach , H.W. , Jetten , J. , Wagner , M.S. and Le Paslier , M.D. 2006 . Deciphering the evolution and metabolism of an anammox bacterium from a community genome . Nature , 440 : 790 – 794 .
   PubMed Web of Science ®Google Scholar
• Thurber , R.V. , Willner-Hall , D. , Rodriguez-Mueller , B. , Desnues , C. , Edwards , R.A. , Angly , F. , Dinsdale , E. , Kelly , L. and Rohwer , F. 2009 . Metagenomic analysis of stressed coral holobionts . Environmental Microbiology , 11 : 2148 – 2163 .
   PubMedGoogle Scholar
• Tringe , S.G. , von Mering , C. , Kobayashi , A. , Salamov , A.A. , Chen , K. , Chang , H.W. , Podar , M. , Short , J.M. , Mathur , E.J. , Detter , J.C. , Bork , P. , Hugenholtz , P. and Rubin , E.M. 2005 . Comparative metagenomics of microbial communities . Science , 308 : 554 – 557 .
   PubMed Web of Science ®Google Scholar
• Tringe , S.G. and Hugenholtz , P. 2008 . A renaissance for the pioneering 16S rRNA gene . Current Opinion in Microbiology , 11 : 442 – 446 .
   PubMed Web of Science ®Google Scholar
• Tyson , G.W. , Chapman , J. , Hugenholtz , P. , Allen , E.E. , Ram , R.J. , Richardson , P. M. , Solovyev , V. V. , Rubin , E. M. , Rokhsar , D. S. and Banfield , J.F. 2004 . Community structure and metabolism through reconstruction of microbial genomes from the environment . Nature , 428 : 37 – 43 .
   PubMed Web of Science ®Google Scholar
• Urich , T. , Lanzén , A. , Qi , J. , Huson , D.H. , Schleper , C. and Schuster , S.C. 2008 . Simultaneous assessment of soil microbial community structure and function through analysis of the meta-transcriptome . PLoS One , 3 : e2527
   PubMed Web of Science ®Google Scholar
• Venter , J.C. , Remington , K. , Heidelberg , J.F. , Halpern , A.L. , Rusch , D. , Eisen , J.A. , Wu , D. , Paulsen , I. , Nelson , K.E. , Nelson , W. , Fouts , D.E. , Levy , S. , Knap , A.H. , Lomas , M.W. , Nealson , K. , White , O. , Peterson , J. , Hoffman , J. , Parsons , R. , Baden-Tillson , H. , Pfannkoch , C. , Rogers , Y.H. and Smith , H.O. 2004 . Environmental genome shotgun sequencing of the Sargasso Sea . Science , 304 : 66 – 74 .
   PubMed Web of Science ®Google Scholar
• VerBerkmoes , N.C. , Denef , V.J. , Hettich , R.L. and Banfield , J.F. 2009 . Systems biology: Functional analysis of natural microbial consortia using community proteomics . Nature Reviews Microbiology , 7 : 196 – 205 .
   PubMed Web of Science ®Google Scholar
• VerBerkmoes , N.C. , Russell , A.L. , Shah , M. , Godzik , A. , Rosenquist , M. , Halfvarson , J. , Lefsrud , M.G. , Apajalahti , J. , Tysk , C. , Hettich , R.L. and Jansson , J.K. 2009 . Shotgun metaproteomics of the human distal gut microbiota . ISME Journal , 3 : 179 – 189 .
   PubMed Web of Science ®Google Scholar
• Warnecke , F. and Hess , M. 2009 . A perspective: metatranscriptomics as a tool for the discovery of novel biocatalysts . Journal of Biotechnology , 142 : 91 – 95 .
   PubMed Web of Science ®Google Scholar
• Warnecke , F. , Luginbühl , P. , Ivanova , N. , Ghassemian , M. , Richardson , T.H. , Stege , J.T. , Cayouette , M. , McHardy , A.C. , Djordjevic , G. , Aboushadi , N. , Sorek , R. , Tringe , S.G. , Podar , M. , Martin , H.G. , Kunin , V. , Dalevi , D. , Madejska , J. , Kirton , E. , Platt , D. , Szeto , E. , Salamov , A. , Barry , K. , Mikhailova , N. , Kyrpides , N.C. , Matson , E.G. , Ottesen , E.A. , Zhang , X. , Hernández , M. , Murillo , C. , Acosta , L.G. , Rigoutsos , I. , Tamayo , G. , Green , B.D. , Chang , C. , Rubin , E.M. , Mathur , E.J. , Robertson , D.E. , Hugenholtz , P. and Leadbetter , J.R. 2007 . Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite . Nature , 450 : 560 – 565 .
   PubMed Web of Science ®Google Scholar
• Wilmes , P. , Andersson , A.F. , Lefsrud , M.G. , Wexler , M. , Shah , M. , Zhang , B. , Hettich , R.L. , Bond , P.L. , VerBerkmoes , N. C. and Banfield , J.F. 2008 . Community proteogenomics highlights microbial strain-variant protein expression within activated sludge performing enhanced biological phosphorus removal . ISME Journal , 2 : 853 – 864 .
   PubMed Web of Science ®Google Scholar
• Woese , C.R. 1987 . Bacterial evolution . Microbiological Reviews , 51 : 221 – 271 .
   PubMedGoogle Scholar
• Woese , C.R. 1998 . A manifesto for microbial genomics . Current Biology , 8 : R781 – R783 .
   Google Scholar
• Wommack , K.E. , Bhavsar , J. and Ravel , J. 2008 . Metagenomics: read length matters . Applied and Environmental Microbiology , 74 : 1453 – 1463 .
   PubMedGoogle Scholar
• Woyke , T. , Teeling , H. , Ivanova , N.N. , Huntemann , M. , Richter , M. , Gloeckner , F.O. , Boffelli , D. , Anderson , I.J. , Barry , K.W. , Shapiro , H.J. , Szeto , E. , Kyrpides , N.C. , Mussmann , M. , Amann , R. , Bergin , C. , Ruehland , C. , Rubin , E.M. and Dubilier , N. 2006 . Symbiosis insights through metagenomic analysis of a microbial consortium . Nature , 443 : 950 – 955 .
   PubMed Web of Science ®Google Scholar