Quantitative phylogenetic assessment of microbial communities in diverse environments

Science. 2007 Feb 23;315(5815):1126-30. doi: 10.1126/science.1133420. Epub 2007 Feb 1.


The taxonomic composition of environmental communities is an important indicator of their ecology and function. We used a set of protein-coding marker genes, extracted from large-scale environmental shotgun sequencing data, to provide a more direct, quantitative, and accurate picture of community composition than that provided by traditional ribosomal RNA-based approaches depending on the polymerase chain reaction. Mapping marker genes from four diverse environmental data sets onto a reference species phylogeny shows that certain communities evolve faster than others. The method also enables determination of preferred habitats for entire microbial clades and provides evidence that such habitat preferences are often remarkably stable over time.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Animals
  • Bacteria / classification*
  • Bacteria / genetics
  • Biological Evolution
  • Bone and Bones / microbiology
  • Ecosystem*
  • Environmental Microbiology*
  • Genes, Bacterial
  • Genes, rRNA
  • Genetic Markers
  • Genomics*
  • Likelihood Functions
  • Mining
  • Phylogeny*
  • Seawater / microbiology
  • Soil Microbiology
  • Water Microbiology
  • Whales / microbiology


  • Genetic Markers