Metagenomics
• The study of metagenomes, genetic material
recovered directly from environmental
samples.
• Term: Coined in 1998 to refer to the idea that
a collection of genes sequenced from the
environment could be analyzed in a way
analogous to the study of a single genome.
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ssDNA template hybridized with primer & mix
One of 4 dNTPs added to reaction; if complementary, incorporated into growing strand
Pyrophosphate (PPi) released & converted to ATP by sulfurylase
ATP serves as substrate for luciferase causing photon emission
History
• Norman Pace: Studied the diversity of rRNA sequences;
first to propose cloning DNA directly from
environmental samples (1985).
• Mya Breitbart & Forest Rohwer: Used environmental
shotgun sequencing to show that 200 liters of seawater
contains over 5000 different viruses (2002).
• Craig Venter: Led the Global Sampling Expedition (GOS)
that circumnavigated the globe collecting
metagenomic samples; sample from the Sargasso Sea
foung DNA from nearly 2000 species, including 200
bacteria never seen before (2003).
• Stephan Schuster: First to publish sequences of an
environmental sample generated with high-throughput
sequencing (2005).
Bioinformatics
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Shotgun sequencing (454 pyrosequencing)
Assembly (Phrap or Celera)
Gene prediction (MEGAN & GLIMMER)
Species diversity (BLAST & MEGAN)
Data integration (MG-RAST)
Comparative metagenomics (COG & KEGG)