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.

[1]  G. G. Stokes.  "J." , 1890, The New Yale Book of Quotations.

[2]  Harold Barnes,et al.  Oceanography and Marine Biology , 1959 .

[3]  P. Olive.  Oceanography and marine biology: an annual review , 1994 .

[4]  R. Overbeek,et al.  The use of gene clusters to infer functional coupling. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[5]  김삼묘,et al.  “Bioinformatics” 특집을 내면서 , 2000 .

[6]  E. Koonin,et al.  Bacterial rhodopsin: evidence for a new type of phototrophy in the sea. , 2000, Science.

[7]  E. Delong,et al.  Environmental diversity of bacteria and archaea. , 2001, Systematic biology.

[8]  J. Hughes,et al.  Counting the Uncountable: Statistical Approaches to Estimating Microbial Diversity , 2001, Applied and Environmental Microbiology.

[9]  P. Hugenholtz.  Exploring prokaryotic diversity in the genomic era , 2002, Genome Biology.

[10]  L. Øvreås,et al.  Prokaryotic Diversity--Magnitude, Dynamics, and Controlling Factors , 2002, Science.

[11]  Jo Handelsman,et al.  A Census of rRNA Genes and Linked Genomic Sequences within a Soil Metagenomic Library , 2003, Applied and Environmental Microbiology.

[12]  P. Bork,et al.  Genome evolution reveals biochemical networks and functional modules , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[13]  Min Pan,et al.  Low-pass sequencing for microbial comparative genomics , 2004, BMC Genomics.

[14]  Darren A. Natale,et al.  The COG database: an updated version includes eukaryotes , 2003, BMC Bioinformatics.

[15]  O. White,et al.  Environmental Genome Shotgun Sequencing of the Sargasso Sea , 2004, Science.

[16]  Susumu Goto,et al.  The KEGG resource for deciphering the genome , 2004, Nucleic Acids Res..

[17]  Jizhong Zhou,et al.  Detection of Genes Involved in Biodegradation and Biotransformation in Microbial Communities by Using 50-Mer Oligonucleotide Microarrays , 2004, Applied and Environmental Microbiology.

[18]  Eric Mathur,et al.  Exploring Nitrilase Sequence Space for Enantioselective Catalysis , 2004, Applied and Environmental Microbiology.

[19]  J. Banfield,et al.  Community structure and metabolism through reconstruction of microbial genomes from the environment , 2004, Nature.

[20]  Rolf Daniel,et al.  The soil metagenome--a rich resource for the discovery of novel natural products. , 2004, Current opinion in biotechnology.

[21]  宁北芳,et al.  疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A , 2005 .

[22]  Christian von Mering,et al.  STRING: known and predicted protein–protein associations, integrated and transferred across organisms , 2004, Nucleic Acids Res..

[23]  BMC Bioinformatics , 2005 .