Comparative metagenomics of microbial communities.
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.
Tringe
Susannah Green
SG
Department of Energy (DOE) Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA.
von Mering
Christian
C
Kobayashi
Arthur
A
Salamov
Asaf A
AA
Chen
Kevin
K
Chang
Hwai W
HW
Podar
Mircea
M
Short
Jay M
JM
Mathur
Eric J
EJ
Detter
John C
JC
Bork
Peer
P
Hugenholtz
Philip
P
Rubin
Edward M
EM
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*
D001426:Bacterial Proteins; D011506:Proteins; D020543:Proteome