This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow An author's correction has been published
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Right arrow Citation Map
Services
Right arrow E-mail this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrowReprints and Permissions
Right arrow Copyright Information
Right arrow Books from ASM Press
Right arrow MicrobeWorld
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Handelsman, J.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Handelsman, J.

 Previous Article  |  Next Article 

Microbiology and Molecular Biology Reviews, December 2004, p. 669-685, Vol. 68, No. 4
1092-2172/04/$08.00+0     DOI: 10.1128/MMBR.68.4.669-685.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.

Metagenomics: Application of Genomics to Uncultured Microorganisms

Jo Handelsman*

Department of Plant Pathology, University of Wisconsin-Madison, Madison, Wisconsin

Metagenomics (also referred to as environmental and community genomics) is the genomic analysis of microorganisms by direct extraction and cloning of DNA from an assemblage of microorganisms. The development of metagenomics stemmed from the ineluctable evidence that as-yet-uncultured microorganisms represent the vast majority of organisms in most environments on earth. This evidence was derived from analyses of 16S rRNA gene sequences amplified directly from the environment, an approach that avoided the bias imposed by culturing and led to the discovery of vast new lineages of microbial life. Although the portrait of the microbial world was revolutionized by analysis of 16S rRNA genes, such studies yielded only a phylogenetic description of community membership, providing little insight into the genetics, physiology, and biochemistry of the members. Metagenomics provides a second tier of technical innovation that facilitates study of the physiology and ecology of environmental microorganisms. Novel genes and gene products discovered through metagenomics include the first bacteriorhodopsin of bacterial origin; novel small molecules with antimicrobial activity; and new members of families of known proteins, such as an Na+(Li+)/H+ antiporter, RecA, DNA polymerase, and antibiotic resistance determinants. Reassembly of multiple genomes has provided insight into energy and nutrient cycling within the community, genome structure, gene function, population genetics and microheterogeneity, and lateral gene transfer among members of an uncultured community. The application of metagenomic sequence information will facilitate the design of better culturing strategies to link genomic analysis with pure culture studies.

* Mailing address: Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI 53706. Phone: (608) 263-8783. Fax: (608) 265-5289. E-mail: joh{at}plantpath.wisc.edu.

Microbiology and Molecular Biology Reviews, December 2004, p. 669-685, Vol. 68, No. 4
1092-2172/04/$08.00+0     DOI: 10.1128/MMBR.68.4.669-685.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.



This article has been cited by other articles:

  • Rattei, T., Tischler, P., Gotz, S., Jehl, M.-A., Hoser, J., Arnold, R., Conesa, A., Mewes, H.-W. (2010). SIMAP--a comprehensive database of pre-calculated protein sequence similarities, domains, annotations and clusters. Nucleic Acids Res 38: D223-D226 [Abstract] [Full Text]  
  • Zengler, K. (2009). Central Role of the Cell in Microbial Ecology. Microbiol. Mol. Biol. Rev. 73: 712-729 [Abstract] [Full Text]  
  • The NIH HMP Working Group, , Peterson, J., Garges, S., Giovanni, M., McInnes, P., Wang, L., Schloss, J. A., Bonazzi, V., McEwen, J. E., Wetterstrand, K. A., Deal, C., Baker, C. C., Di Francesco, V., Howcroft, T. K., Karp, R. W., Lunsford, R. D., Wellington, C. R., Belachew, T., Wright, M., Giblin, C., David, H., Mills, M., Salomon, R., Mullins, C., Akolkar, B., Begg, L., Davis, C., Grandison, L., Humble, M., Khalsa, J., Little, A. R., Peavy, H., Pontzer, C., Portnoy, M., Sayre, M. H., Starke-Reed, P., Zakhari, S., Read, J., Watson, B., Guyer, M. (2009). The NIH Human Microbiome Project. Genome Res 19: 2317-2323 [Abstract] [Full Text]  
  • Flier, J. S., Mekalanos, J. J. (2009). Gut Check: Testing a Role for the Intestinal Microbiome in Human Obesity. Sci Transl Med 1: 6ps7-6ps7 [Full Text]  
  • Siqueira, J.F. Jr., Rocas, I.N. (2009). Diversity of Endodontic Microbiota Revisited. JDR 88: 969-981 [Abstract] [Full Text]  
  • Yung, P. Y., Burke, C., Lewis, M., Egan, S., Kjelleberg, S., Thomas, T. (2009). Phylogenetic screening of a bacterial, metagenomic library using homing endonuclease restriction and marker insertion. Nucleic Acids Res 37: e144-e144 [Abstract] [Full Text]  
  • Kosakovsky Pond, S., Wadhawan, S., Chiaromonte, F., Ananda, G., Chung, W.-Y., Taylor, J., Nekrutenko, A., The Galaxy Team, (2009). Windshield splatter analysis with the Galaxy metagenomic pipeline. Genome Res 19: 2144-2153 [Abstract] [Full Text]  
  • Martinez, J. L. (2009). The role of natural environments in the evolution of resistance traits in pathogenic bacteria. Proc R Soc B 276: 2521-2530 [Abstract] [Full Text]  
  • Kovatcheva-Datchary, P., Zoetendal, E. G., Venema, K., de Vos, W. M., Smidt, H. (2009). Review: Tools for the tract: understanding the functionality of the gastrointestinal tract. Therapeutic Advances in Gastroenterology 2: s9-s22 [Abstract]  
  • Jogler, C., Lin, W., Meyerdierks, A., Kube, M., Katzmann, E., Flies, C., Pan, Y., Amann, R., Reinhardt, R., Schuler, D. (2009). Toward Cloning of the Magnetotactic Metagenome: Identification of Magnetosome Island Gene Clusters in Uncultivated Magnetotactic Bacteria from Different Aquatic Sediments. Appl. Environ. Microbiol. 75: 3972-3979 [Abstract] [Full Text]  
  • van Doorn, R., Slawiak, M., Szemes, M., Dullemans, A. M., Bonants, P., Kowalchuk, G. A., Schoen, C. D. (2009). Robust Detection and Identification of Multiple Oomycetes and Fungi in Environmental Samples by Using a Novel Cleavable Padlock Probe-Based Ligation Detection Assay. Appl. Environ. Microbiol. 75: 4185-4193 [Abstract] [Full Text]  
  • Aoi, Y., Kinoshita, T., Hata, T., Ohta, H., Obokata, H., Tsuneda, S. (2009). Hollow-Fiber Membrane Chamber as a Device for In Situ Environmental Cultivation. Appl. Environ. Microbiol. 75: 3826-3833 [Abstract] [Full Text]  
  • Simon, C., Herath, J., Rockstroh, S., Daniel, R. (2009). Rapid Identification of Genes Encoding DNA Polymerases by Function-Based Screening of Metagenomic Libraries Derived from Glacial Ice. Appl. Environ. Microbiol. 75: 2964-2968 [Abstract] [Full Text]  
  • Waschkowitz, T., Rockstroh, S., Daniel, R. (2009). Isolation and Characterization of Metalloproteases with a Novel Domain Structure by Construction and Screening of Metagenomic Libraries. Appl. Environ. Microbiol. 75: 2506-2516 [Abstract] [Full Text]  
  • Kaneshiro, E. S., Dei-Cas, E. (2009). Why the International Workshops on Opportunistic Protists?. Eukaryot Cell 8: 426-428 [Full Text]  
  • Fraser, C., Alm, E. J., Polz, M. F., Spratt, B. G., Hanage, W. P. (2009). The Bacterial Species Challenge: Making Sense of Genetic and Ecological Diversity. Science 323: 741-746 [Abstract] [Full Text]  
  • Kim, E.-Y., Oh, K.-H., Lee, M.-H., Kang, C.-H., Oh, T.-K., Yoon, J.-H. (2009). Novel Cold-Adapted Alkaline Lipase from an Intertidal Flat Metagenome and Proposal for a New Family of Bacterial Lipases. Appl. Environ. Microbiol. 75: 257-260 [Abstract] [Full Text]  
  • Schipper, C., Hornung, C., Bijtenhoorn, P., Quitschau, M., Grond, S., Streit, W. R. (2009). Metagenome-Derived Clones Encoding Two Novel Lactonase Family Proteins Involved in Biofilm Inhibition in Pseudomonas aeruginosa. Appl. Environ. Microbiol. 75: 224-233 [Abstract] [Full Text]  
  • Suzuki, H., Sota, M., Brown, C. J., Top, E. M. (2008). Using Mahalanobis distance to compare genomic signatures between bacterial plasmids and chromosomes. Nucleic Acids Res 36: e147-e147 [Abstract] [Full Text]  
  • Zoetendal, E G, Rajilic-Stojanovic, M, de Vos, W M (2008). High-throughput diversity and functionality analysis of the gastrointestinal tract microbiota. Gut 57: 1605-1615 [Abstract] [Full Text]  
  • Mori, T., Mizuta, S., Suenaga, H., Miyazaki, K. (2008). Metagenomic Screening for Bleomycin Resistance Genes. Appl. Environ. Microbiol. 74: 6803-6805 [Abstract] [Full Text]  
  • Jones, B. V., Begley, M., Hill, C., Gahan, C. G. M., Marchesi, J. R. (2008). Functional and comparative metagenomic analysis of bile salt hydrolase activity in the human gut microbiome. Proc. Natl. Acad. Sci. USA 105: 13580-13585 [Abstract] [Full Text]  
  • Manichanh, C., Chapple, C. E., Frangeul, L., Gloux, K., Guigo, R., Dore, J. (2008). A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library. Nucleic Acids Res 36: 5180-5188 [Abstract] [Full Text]  
  • Northen, T. R., Lee, J.-C., Hoang, L., Raymond, J., Hwang, D.-R., Yannone, S. M., Wong, C.-H., Siuzdak, G. (2008). A nanostructure-initiator mass spectrometry-based enzyme activity assay. Proc. Natl. Acad. Sci. USA 105: 3678-3683 [Abstract] [Full Text]  
  • Ansong, C., Purvine, S. O., Adkins, J. N., Lipton, M. S., Smith, R. D. (2008). Proteogenomics: needs and roles to be filled by proteomics in genome annotation. Brief Funct Genomic Proteomic 0: eln010v1-eln010 [Abstract] [Full Text]  
  • Wommack, K. E., Bhavsar, J., Ravel, J. (2008). Metagenomics: Read Length Matters. Appl. Environ. Microbiol. 74: 1453-1463 [Abstract] [Full Text]  
  • Chung, E. J., Lim, H. K., Kim, J.-C., Choi, G. J., Park, E. J., Lee, M. H., Chung, Y. R., Lee, S.-W. (2008). Forest Soil Metagenome Gene Cluster Involved in Antifungal Activity Expression in Escherichia coli. Appl. Environ. Microbiol. 74: 723-730 [Abstract] [Full Text]  
  • Laybourn-Parry, J., Pearce, D. A (2007). The biodiversity and ecology of Antarctic lakes: models for evolution. Phil Trans R Soc B 362: 2273-2289 [Abstract] [Full Text]  
  • Bollmann, A., Lewis, K., Epstein, S. S. (2007). Incubation of Environmental Samples in a Diffusion Chamber Increases the Diversity of Recovered Isolates. Appl. Environ. Microbiol. 73: 6386-6390 [Abstract] [Full Text]  
  • Mirete, S., de Figueras, C. G., Gonzalez-Pastor, J. E. (2007). Novel Nickel Resistance Genes from the Rhizosphere Metagenome of Plants Adapted to Acid Mine Drainage. Appl. Environ. Microbiol. 73: 6001-6011 [Abstract] [Full Text]  
  • Taylor, M. W., Radax, R., Steger, D., Wagner, M. (2007). Sponge-Associated Microorganisms: Evolution, Ecology, and Biotechnological Potential. Microbiol. Mol. Biol. Rev. 71: 295-347 [Abstract] [Full Text]  
  • Gloux, K., Leclerc, M., Iliozer, H., L'Haridon, R., Manichanh, C., Corthier, G., Nalin, R., Blottiere, H. M., Dore, J. (2007). Development of High-Throughput Phenotyping of Metagenomic Clones from the Human Gut Microbiome for Modulation of Eukaryotic Cell Growth. Appl. Environ. Microbiol. 73: 3734-3737 [Abstract] [Full Text]  
  • Guan, C., Ju, J., Borlee, B. R., Williamson, L. L., Shen, B., Raffa, K. F., Handelsman, J. (2007). Signal Mimics Derived from a Metagenomic Analysis of the Gypsy Moth Gut Microbiota. Appl. Environ. Microbiol. 73: 3669-3676 [Abstract] [Full Text]  
  • Podar, M., Abulencia, C. B., Walcher, M., Hutchison, D., Zengler, K., Garcia, J. A., Holland, T., Cotton, D., Hauser, L., Keller, M. (2007). Targeted Access to the Genomes of Low-Abundance Organisms in Complex Microbial Communities. Appl. Environ. Microbiol. 73: 3205-3214 [Abstract] [Full Text]  
  • Zhu, Y., Pulukkunat, D. K., Li, Y. (2007). Deciphering RNA structural diversity and systematic phylogeny from microbial metagenomes. Nucleic Acids Res 35: 2283-2294 [Abstract] [Full Text]  
  • Nakatsu, C. H. (2007). Soil Microbial Community Analysis Using Denaturing Gradient Gel Electrophoresis. Soil Sci. 71: 562-571 [Abstract] [Full Text]  
  • Zwolinski, M. D. (2007). DNA Sequencing: Strategies for Soil Microbiology. Soil Sci. 71: 592-600 [Abstract] [Full Text]  
  • Huson, D. H., Auch, A. F., Qi, J., Schuster, S. C. (2007). MEGAN analysis of metagenomic data. Genome Res 17: 377-386 [Abstract] [Full Text]  
  • Bibiloni, R., Mangold, M., Madsen, K. L., Fedorak, R. N., Tannock, G. W. (2006). The bacteriology of biopsies differs between newly diagnosed, untreated, Crohn's disease and ulcerative colitis patients.. J Med Microbiol 55: 1141-1149 [Abstract] [Full Text]  
  • Cavaletti, L., Monciardini, P., Bamonte, R., Schumann, P., Rohde, M., Sosio, M., Donadio, S. (2006). New lineage of filamentous, spore-forming, gram-positive bacteria from soil.. Appl. Environ. Microbiol. 72: 4360-4369 [Abstract] [Full Text]  
  • Elend, C., Schmeisser, C., Leggewie, C., Babiak, P., Carballeira, J. D., Steele, H. L., Reymond, J.-L., Jaeger, K.-E., Streit, W. R. (2006). Isolation and biochemical characterization of two novel metagenome-derived esterases.. Appl. Environ. Microbiol. 72: 3637-3645 [Abstract] [Full Text]  
  • White, R. H. (2006). The difficult road from sequence to function.. J. Bacteriol. 188: 3431-3432 [Full Text]  
  • Moussard, H., Henneke, G., Moreira, D., Jouffe, V., Lopez-Garcia, P., Jeanthon, C. (2006). Thermophilic lifestyle for an uncultured archaeon from hydrothermal vents: evidence from environmental genomics.. Appl. Environ. Microbiol. 72: 2268-2271 [Abstract] [Full Text]  
  • Weng, L., Rubin, E. M., Bristow, J. (2006). Application of sequence-based methods in human microbial ecology. Genome Res 16: 316-322 [Abstract] [Full Text]  
  • DeLong, E. F., Preston, C. M., Mincer, T., Rich, V., Hallam, S. J., Frigaard, N.-U., Martinez, A., Sullivan, M. B., Edwards, R., Brito, B. R., Chisholm, S. W., Karl, D. M. (2006). Community Genomics Among Stratified Microbial Assemblages in the Ocean's Interior. Science 311: 496-503 [Abstract] [Full Text]  
  • Liolios, K., Tavernarakis, N., Hugenholtz, P., Kyrpides, N. C. (2006). The Genomes On Line Database (GOLD) v.2: a monitor of genome projects worldwide. Nucleic Acids Res 34: D332-D334 [Abstract] [Full Text]  
  • Lim, H. K., Chung, E. J., Kim, J.-C., Choi, G. J., Jang, K. S., Chung, Y. R., Cho, K. Y., Lee, S.-W. (2005). Characterization of a Forest Soil Metagenome Clone That Confers Indirubin and Indigo Production on Escherichia coli. Appl. Environ. Microbiol. 71: 7768-7777 [Abstract] [Full Text]  
  • Ricke, P., Kube, M., Nakagawa, S., Erkel, C., Reinhardt, R., Liesack, W. (2005). First Genome Data from Uncultured Upland Soil Cluster Alpha Methanotrophs Provide Further Evidence for a Close Phylogenetic Relationship to Methylocapsa acidiphila B2 and for High-Affinity Methanotrophy Involving Particulate Methane Monooxygenase. Appl. Environ. Microbiol. 71: 7472-7482 [Abstract] [Full Text]  
  • Williamson, L. L., Borlee, B. R., Schloss, P. D., Guan, C., Allen, H. K., Handelsman, J. (2005). Intracellular Screen To Identify Metagenomic Clones That Induce or Inhibit a Quorum-Sensing Biosensor. Appl. Environ. Microbiol. 71: 6335-6344 [Abstract] [Full Text]  
  • Visick, K. L., Fuqua, C. (2005). Decoding Microbial Chatter: Cell-Cell Communication in Bacteria. J. Bacteriol. 187: 5507-5519 [Full Text]  
  • Whitaker, R. J., Banfield, J. F. (2005). Population Dynamics Through the Lens of Extreme Environments. Reviews in Mineralogy and Geochemistry 59: 259-277 [Full Text]  


Copyright © 2010 by the American Society for Microbiology.   For an alternate route to Journals.ASM.org, visit: http://intl-journals.asm.org | More Info»