Nature Reviews Microbiology 3, 489-498 (June 2005) | doi:10.1038/nrmicro1157

Focus on: Metagenomics

Community genomics in microbial ecology and evolution

Eric E. Allen1 & Jillian F. Banfield2  About the authors


It is possible to reconstruct near-complete, and possibly complete, genomes of the dominant members of microbial communities from DNA that is extracted directly from the environment. Genome sequences from environmental samples capture the aggregate characteristics of the strain population from which they were derived. Comparison of the sequence data within and among natural populations can reveal the evolutionary processes that lead to genome diversification and speciation. Community genomic datasets can also enable subsequent gene expression and proteomic studies to determine how resources are invested and functions are distributed among community members. Ultimately, genomics can reveal how individual species and strains contribute to the net activity of the community.

Author affiliations

  1. Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, California 94720, USA
  2. Department of Earth and Planetary Sciences, University of California, Berkeley, Berkeley, California 94720, USA

Correspondence to: Jillian F. Banfield2 Email:


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