Metagenomics and Microbial Communities


Metagenomics is the genomic analysis of microbial communities. This new science provides access to organisms that are recalcitrant to culturing, as are the vast majority of microorganisms on Earth. Metagenomics thereby offers a first peek at the wide variety of life that has never been studied, thus providing new insight into the structure and function of ecosystems as diverse as the oceans and the human gastrointestinal tract.

Keywords: metagenomics; microbial ecology; microbial communities; unculturable; biotechnology

Figure 1.

Examples of services provided by microorganisms. Clockwise from top: microorganisms in the sea remove carbon dioxide from the atmosphere and produce oxygen; the ozone layer in the stratosphere, which protects Earth from harmful ultraviolet rays, was created by the reaction of oxygen molecules produced on the early Earth by microbes; the human body contains more bacterial cells than human cells and most of these live in the gastrointestinal tract; certain bacteria convert dinitrogen gas to ammonia in special structures on the roots of leguminous plants; soil bacteria are the source of most of the antibiotics and many other drugs used in medicine today; microbes ferment many foods; centre, microorganisms come in many shapes and sizes. Graphic: Nicolle Rager Fuller.

Figure 2.

Construction and analysis of metagenomic libraries. Graphic: Nicolle Rager Fuller.

Figure 3.

(a) Tube worms containing bacterial symbionts. Courtesy: National Science Foundation (Courtesy: National Science Foundation). (b) Bacterial symbionts inside the tube worm (Courtesy of Colleen M Cavanaugh). See also

Figure 4.

DNA cloned from soil confers many traits on E. coli. (a) Left plate contains no antibiotics, right plate contains β‐lactam antibiotic. Clone ‘C’ carries a gene from the soil metagenome that makes E. coli resistant to the β‐lactam antibiotic. (b) Clone on left contains no heterologous DNA. The other four clones carry DNA fragments from soil metagenomic that confer on E. coli the ability to produce pigments. Photos: Heather Allen and Lynn Williamson.



Bäckhed F, Ley RE, Sonnenburg JL, Peterson DA and Gordon JI (2005) Host‐bacterial mutualism in the human intestine. Science 307: 1915–1920.

Boetius A (2005) Microfauna–macrofauna interaction in the seafloor: lessons from the tubeworm. PLoS Biology 3: e102, doi:10.1371/journal.pbio.0030102.

Handelsman J, Rondon MR, Brady SF, Clardy J and Goodman RM (1998) Molecular biology provides access to the chemistry of unknown soil microbes: a new frontier for natural products. Chemistry Biology 5(10): R245–R249.

Madigan M and Martinko J (2005) Brock Biology of Microorganisms, Chaps. 1, 8 and 10. San Francisco, CA: Benjamin Cummings.

Moran NA and Degnan PH (2006) Functional genomics of Buchnera and the ecology of aphid hosts. Molecular Ecology 15(5): 1251–1261.

National Research Council (2007) New Science of Metagenomics Revealing the Secrets of Our Microbial Planet. Washington, DC: National Academies Press.

Pace NR, Stahl DA, Lane DJ and Olsen GJ (1985) Analyzing natural microbial populations by rRNA sequences. ASM News 51(1): 4–12.

Riesenfeld CS, Goodman RM and Handelsman J (2004) Uncultured soil bacteria are a reservoir of new antibiotic resistance genes. Environmental Microbiology 6: 981–989.

Stein JL, Marsh TL, Wu KY, Shizuya H and DeLong EF (1996) Characterization of uncultivated prokaryotes: isolation and analysis of a 40‐kilobase‐pair genome fragment from a planktonic marine archaeon. Journal of Bacteriology 178(3): 591–599.

Tyson GW, Chapman J, Hugenholtz P et al. (2004) Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428: 37–43.

Further Reading

Delong EF (2007) Sea change for metagenomics? Nature Reviews Microbiology 5: 326.

Handelsman J (2004) Metagenomics: application of genomics to uncultured microorganisms. Microbiology and Molecular Biology Reviews 68: 669–685.

Rohwer F (2007) Phage metagenomics. Annual Review of Genetics 41: doi:10.1146/annurev.genet.40.110405.090628.

Turnbaugh PJ, Ley RE, Mahowald MA et al. (2006) An obesity‐associated gut microbiome with increased capacity for energy harvest. Nature 444: 1027–1031.

Woyke T, Teeling H and Ivanova NN et al. (2006) Symbiosis insights through metagenomic analysis of a microbial consortium. Nature 443: 950–955.

Contact Editor close
Submit a note to the editor about this article by filling in the form below.

* Required Field

How to Cite close
Handelsman, Jo(Dec 2007) Metagenomics and Microbial Communities. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1002/9780470015902.a0020367]