Applications
Metagenomics & Microbial Diversity
Overview
Metagenomics is the study of the genomic content in a complex sample. The two primary goals of this approach are to characterize the organisms present in a sample and identify what roles each organism has within a specific environment. Metagenomics samples are found nearly everywhere, including several microenvironments within the human body, soil samples, extreme environments such as deep mines and the various layers within the ocean.
The Genome Sequencer FLX System enables a comprehensive view into the diversity and metabolic profile of an environmental habitat. The system's long reads ensure the enormous specificity needed to compare sequenced reads against DNA or protein databases. The platform is ideal for counting environmental gene tags to analyze the relative abundance of microbial species under varying environmental conditions.
Publications:
- Palacios et al. A New Arenavirus in a Cluster of Fatal Transplant-Associated Diseases. New England Journal of Medicine 358: 991-8. March 6, 2008.
- Turnbaugh et al. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444: 1027-1031. December 21, 2006.
- Dinsdale et al. Microbial ecology of four coral atolls in the northern line islands. PLoS ONE 3: e1584. February 27 2008.
Click here to see all Metagenomics and Microbial Diversity publications.
Application Note:
Data Analysis tools:
Given the complexity of metagenomic samples, a number of publicly available bio-informatics tools have been created.
MEGAN: (www-ab.informatik.uni-tuebingen.de/software/megan/welcome.html), a Metagenome Analyzer, allows a single scientist to analyze large data sets and group sequencing reads into taxonomic units.
The SEED database (www.theseed.org/wiki/Main_Page) is a public resource of complete and draft genome sequences to help relate sequences to metabolic function.
IMG/M (http://img.jgi.doe.gov/m) provides tools for analyzing the functional capability of microbial communities based on their metagenomic sequence, in the context of reference isolate genomes, using a variety of public functional and pathway resources.
CAMERA (http://camera.calit2.net) is a user-driven site dedicated to providing the scientific community with metagenomic data and analysis tools.
CARMA (http://www.cebitec.uni-bielefeld.de/brf/carma/carma.html) is a software pipeline for analyzing metagenomes. The Ribosomal Database Project (http://rdp.cme.msu.edu) provides tools to analyze 16S rRNA sequences.
COGs (http://www.ncbi.nlm.nih.gov/COG), NCBI's non-redundant Clusters of Orthologs database provides phylogenetic classification of proteins encoded in complete genomes.
KEGG (http://www.genome.jp/kegg/), the Kyoto Encyclopedia of Genes and Genomes, is a reference data base for linking genomes to biological systems and environments.