title: Quantitative phylogenetic assessment of microbial communities in diverse environments.
abstract: 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.
authors.affiliation: European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
authors.forename: C
authors.initials: C
authors.lastname: von Mering
authors.forename: P
authors.initials: P
authors.lastname: Hugenholtz
authors.forename: J
authors.initials: J
authors.lastname: Raes
authors.forename: S G
authors.initials: SG
authors.lastname: Tringe
authors.forename: T
authors.initials: T
authors.lastname: Doerks
authors.forename: L J
authors.initials: LJ
authors.lastname: Jensen
authors.forename: N
authors.initials: N
authors.lastname: Ward
authors.forename: P
authors.initials: P
authors.lastname: Bork
mesh_terms: D000818:Animals; D001419:Bacteria / Q000145:classification* / Q000235:genetics; D005075:Biological Evolution; D001842:Bone and Bones / Q000382:microbiology; D017753:Ecosystem; D004783:Environmental Microbiology; D005798:Genes, Bacterial; D020459:Genes, rRNA; D005819:Genetic Markers; D023281:Genomics; D016013:Likelihood Functions; D008906:Mining; D010802:Phylogeny; D012623:Seawater / Q000382:microbiology; D012988:Soil Microbiology; D014871:Water Microbiology; D014907:Whales / Q000382:microbiology
chemical_list: D005819:Genetic Markers