Issue 12.08 - August 2004
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Craig Venter's Epic Voyage to Redefine the Origin of the Species 

By James Shreeve Page 10 of 10 

How to Hunt Microbes

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Venter's team takes samples from ecosystems around the world and sends them to his gene-sequencing HQ at the Institute for Biological Energy Alternatives in Rockville, Maryland. Here's the way the microbes are snagged, bagged, and tagged.

1. Sampling
Every 200 miles, Sorcerer II's crew pumps 53 gallons of seawater on board, from a depth of about 5 feet. The water is strained through a series of three increasingly fine paper filters. The filters are sealed, labeled, frozen, and periodically airlifted to Rockville for analysis.

2. Shotgunning
Back in the US, the filter papers are cut up and chemically treated to strip away all but the organisms' DNA. This solution is then "shotgunned" - forced through a pinhole nozzle under high pressure - to break the long strands of DNA into millions of fragments.

3. Tagging
The fragments of DNA are copied, broken into smaller pieces, and tagged with fluorescent dyes corresponding to the four bases: A, C, T, and G. An electrical charge carries the pieces through capillaries - tubes about the width of a human hair.

4. Sequencing
As they move through the capillaries, DNA pieces arrange themselves by length. A laser then scans the ends of each tagged piece, creating rough sequences called "reads."

5. Assembling and Classifying
Computer algorithms assemble longer DNA sequences by joining segments where there are overlapping stretches of code. The number of species can be estimated by comparing the DNA in the sample to known species. Classification into species can be determined by similarity among samples.

6. Annotating
Data specialists "blast" stretches of DNA against databases of known genes - comparing them base letter by letter. If a novel gene has a sequence similar to a known gene, they are assumed to have similar functions.

James Shreeve ( is the author of The Genome War: How Craig Venter Tried to Capture the Code of Life and Save the World.
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