title: Comparative metagenomics of microbial communities.
abstract: The species complexity of microbial communities and challenges in culturing representative isolates make it difficult to obtain assembled genomes. Here we characterize and compare the metabolic capabilities of terrestrial and marine microbial communities using largely unassembled sequence data obtained by shotgun sequencing DNA isolated from the various environments. Quantitative gene content analysis reveals habitat-specific fingerprints that reflect known characteristics of the sampled environments. The identification of environment-specific genes through a gene-centric comparative analysis presents new opportunities for interpreting and diagnosing environments.
authors.affiliation: Department of Energy (DOE) Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA.
authors.forename: Susannah Green
authors.initials: SG
authors.lastname: Tringe
authors.forename: Christian
authors.initials: C
authors.lastname: von Mering
authors.forename: Arthur
authors.initials: A
authors.lastname: Kobayashi
authors.forename: Asaf A
authors.initials: AA
authors.lastname: Salamov
authors.forename: Kevin
authors.initials: K
authors.lastname: Chen
authors.forename: Hwai W
authors.initials: HW
authors.lastname: Chang
authors.forename: Mircea
authors.initials: M
authors.lastname: Podar
authors.forename: Jay M
authors.initials: JM
authors.lastname: Short
authors.forename: Eric J
authors.initials: EJ
authors.lastname: Mathur
authors.forename: John C
authors.initials: JC
authors.lastname: Detter
authors.forename: Peer
authors.initials: P
authors.lastname: Bork
authors.forename: Philip
authors.initials: P
authors.lastname: Hugenholtz
authors.forename: Edward M
authors.initials: EM
authors.lastname: Rubin
mesh_terms: D000818:Animals; D001105:Archaea / Q000145:classification / Q000235:genetics / Q000378:metabolism; D001419:Bacteria / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D044822:Biodiversity; D018441:Biofilms; D001842:Bone and Bones / Q000382:microbiology; D019295:Computational Biology; D017753:Ecosystem; D004734:Energy Metabolism; D005057:Eukaryotic Cells / Q000378:metabolism; D015723:Gene Library; D005796:Genes; D005798:Genes, Bacterial; D016678:Genome; D016680:Genome, Bacterial; D023281:Genomics; D008969:Molecular Sequence Data; D009876:Operon; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D011506:Proteins / Q000235:genetics / Q000378:metabolism; D020543:Proteome; D012623:Seawater / Q000382:microbiology*; D017422:Sequence Analysis, DNA; D012988:Soil Microbiology; D014907:Whales / Q000382:microbiology*
chemical_list: D001426:Bacterial Proteins; D011506:Proteins; D020543:Proteome