The scientist who raced against the publicly funded project to decode the human genome will soon be sequencing the genomes of all the microbes floating in New York City air.
The 鈥渁ir genome project鈥� was announced by Craig Venter of the J. Craig Venter Institute in Rockville, Maryland, US, on Monday. He says it could lead to the discovery of previously unknown organisms and aid biosecurity.
According to Venter, siphoning off vats of smoky New York City air each day and amplifying the DNA of the fungi, bacteria and viruses it contains is the only way to uncover the mysteries of airborne microbial life. Only 1% of the microbes in the air can be identified by growing cultures in the lab, he told the New York Times, yet 鈥渋t is important to understand this unseen world鈥�.
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While some scientists think the idea is 鈥渃razy鈥�, others are fascinated. 鈥淲henever you take on a project of this scale, you are going to discover new things 鈥� there is so much we still don鈥檛 know about microbiology,鈥� says Jeffrey Blanchard, a microbiologist at the University of Massachusetts, Amherst, US, who is currently decoding the genome of cyanobacteria in the Sargasso Sea, off Bermuda.
鈥淭his is one of those Venter adventures, but I can鈥檛 make up my mind whether something will come of this or not,鈥� says Eckard Wimmer of the State University of New York at Stony Brook, US. He points out that simply sequencing a microbe鈥檚 genome does not automatically reveal whether it is infectious.
Bioterror comparison
杏吧原创s say that sequencing the 鈥渁ir鈥檚鈥� genome is the natural progression from Venter鈥檚 current project that has already uncovered 1.2 million new genes from organisms living in the Sargasso Sea.
But unlike the waterborne project, the air genome may aid homeland security, say scientists. Comparing an air sample taken during a suspected bioterror attack to the normal genetic 鈥渇ingerprint鈥� of the air could confirm or rule out the presence of dangerous microbes.
鈥淭he air has been minimally explored,鈥� says Eddy Rubin, director of the Joint Genome Institute in Walnut Creek, California, US. 鈥淭his will provide a way to see what is blowing around and to see if we could use it to secure the air.鈥�
鈥淔urther knowledge of airborne microbes would indeed help pathogen defence programmes,鈥� agrees Tom Slezak of Lawrence Livermore National Laboratory in California, US, who helped to develop BioWatch, a US department of homeland security programme that currently monitors air in 30 cities in the US around the clock. 鈥淎ccurate background profiles of air in multiple locations at multiple times of the year would be best.鈥�
鈥淪hotgun鈥� approach
Venter has deployed just two clandestine metre-high filters, one from the roof of a forty-storey building, the other from inside an office air circulation system. Each gathers 1400 cubic metres of air per day. After filtering off the larger particles, just the micro-organisms are left behind and their DNA will be extracted and sequenced using a 鈥渟hotgun鈥� approach.
Invented by Venter in 2001 to decode the human genome, this involves smashing DNA into small, random fragments, inserting them into lab-grown bacteria which then replicate and then piecing the DNA back together inside a computer program using powerful software that assumes overlapping sections must have come from the same strand.
It is much faster than the painstaking traditional approach which breaks strands into smaller sections first but it can be less accurate because two strands can end up incorrectly stuck together.
But this should not matter for Venter鈥檚 project. 鈥淔or organisms where you just want a snapshot of the genes, the shotgun approach might work quite well,鈥� says Bob Waterston of the University of Washington in Seattle, US, who showed that the use of the shotgun approach had caused inaccuracies when sequencing the human genome.
