Comparative metagenomics of microbial communities

Science

Volumn 308, Issue 5721, 2005, Pages 554-557

  Tringe, Susannah Green ^a,b   Von Mering, Christian ^c   Kobayashi, Arthur ^a   Salamov, Asaf A ^a   Chen, Kevin ^d   Chang, Hwai W ^e   Podar, Mircea ^e   Short, Jay M ^e   Mathur, Eric J ^e   Detter, John C ^a   Bork, Peer ^c   Hugenholtz, Philip ^a   Rubin, Edward M ^a,b  

^a DOE JOINT GENOME INSTITUTE   (United States)

^b LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^c EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^d UNIVERSITY OF CALIFORNIA   (United States)

^e DIVERSA CORPORATION   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DIAGNOSING ENVIRONMENTS; METAGENOMICS; MICROBIAL COMMUNITIES;

BIODIVERSITY; DNA; GENETIC ENGINEERING; METABOLISM; MICROBIOLOGY;

GENES;

MICROBIAL COMMUNITY; MICROBIAL ECOLOGY;

ARTICLE; DNA CONTENT; DNA DETERMINATION; DNA ISOLATION; GENE SEQUENCE; LAND BIOME; MARINE ENVIRONMENT; METABOLISM; MICROFLORA; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS;

ANIMALS; ARCHAEA; BACTERIA; BACTERIAL PROTEINS; BIODIVERSITY; BIOFILMS; BONE AND BONES; COMPUTATIONAL BIOLOGY; ECOSYSTEM; ENERGY METABOLISM; EUKARYOTIC CELLS; GENE LIBRARY; GENES; GENES, BACTERIAL; GENOME; GENOME, BACTERIAL; GENOMICS; MOLECULAR SEQUENCE DATA; OPERON; PHYLOGENY; POLYMERASE CHAIN REACTION; PROTEINS; PROTEOME; SEAWATER; SEQUENCE ANALYSIS, DNA; SOIL MICROBIOLOGY; WHALES;

EID: 20244376755     PISSN: 00368075     EISSN: None     Source Type: Journal    
DOI: 10.1126/science.1107851     Document Type: Article

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24. This work was performed under the auspices of the DOE'S Office of Science, Biological and Environmental Research Program; the University of California, Lawrence Livermore National Laboratory, under contract no. W-7405-Eng-48; Lawrence Berkeley National Laboratory under contract no. DE-AC03-76SF00098; and Los Alamos National Laboratory under contract no. W-7405-ENG-36. S.G.T. was supported by grant no. THL007279F, an NIH National Research Service Award (NRSA) Training and Fellowship grant to E.R. K.C. was supported by NSF grant no. EF 03-31494. Sequencing of the environmental libraries was performed under a license agreement with Diversa (J. R. Short, U.S. patent no. 6455254). We gratefully acknowledge the efforts of C. Baptista, L. Christoffersen, J. Garcia, K. Li, J. Ritter, P. Sammon, S. Wells, D. Whitney, J. Eads, T. Richardson, M. Noordewier, and L. Bibbs. We thank C. Smith for providing the whale fall samples; K. Remington for providing Sargasso Sea sample information; N. Ivanova, N. Kyrpides, and members of the Rubin laboratory for helpful comments on the manuscript; and J. Chapman, I. Grigoriev, E. Szeto, J. Korbel, T. Doerks, K. Foerstner, E. Harrington, and M. Krupp for assistance with data processing and analysis. These Whole Genome Shotgun projects have been deposited with the DNA Data Bank of Japan, the European Molecular Biology Laboratory (EMBL) Nucleotide Sequence Database, and the GenBank in collaboration (DDBJ/EMBL/GenBank) under the project accessions AAFX00000000 (soil), AAFY00000000 (whale fall 1), AAFZ00000000 (whale fall 2), and AAGA00000000 (whale fall 3). For each project, the version described in this paper is the first version, AAFX01000000, AAFY01000000, AAFZ01000000, and AAGA01000000. The 16S rRNA sequences from the soil and three whale fall samples have been deposited under GenBank accession nos. AY921654 to AY922252. The metagenomic data will also be incorporated into the U.S. Department of Energy Joint Genome Institute Integrated Microbial Genomes system (www.jgi.doe.gov/) to facilitate detailed comparative analysis of the data in the context of all publicly available complete microbial genomes.