'Whole-environment sequencing' will reveal bugs in urban air.
What next for the geneticist who seems to have sequenced everything? After piecing together DNA sequences from the oceans, his dog and of course, humans, the genome pioneer Craig Venter has announced his next plan - to find out what microbes are blowing around in New York's air.
The Air Genome Project will filter bugs from the air in midtown Manhattan, the United States' most densely populated area. Researchers from the J. Craig Venter Institute in Rockville, Maryland, will collect dozens of samples both indoors and outside, before sifting through them for fragments of microbial DNA.
The move follows a similar project by Venter's company to sequence genetic information from a region of ocean near Bermuda (see ""Genome pioneer sets sights on Sargasso Sea":http://www.nature.com/news/2003/030428/full/030428-8.html"). That project identified some 1.3 million new genes and at least 1,800 new species of marine microorganism.
The Air Genome Project will work in a similar way to its marine predecessor. Having filtered the air, Venter's team will use the 'shotgun' method, which involves analysing small segments of DNA and piecing them together into longer strings by matching up their overlapping ends.
“Many bacteria and viruses in the air elicit destructive immune responses and we would like to explore these. Craig Venter , president, J. Venter Institute, Rockville, Maryland”
The scientists thus hope to identify more organisms than the old-fashioned method of simply leaving a culture dish on a windowsill and then incubating it to see what grows. Many microbial species cannot be cultured in the lab, so this method would not reveal their presence.
Even with the help of shotgun sequencing, it will be difficult to piece together entire genome sequences for all but the most abundant organisms, comments Bruce Moffett, a microbial ecologist at the University of East London, UK.
His own approach is to look at certain genes that all bacteria share, albeit in slightly different versions, to work out what species are present in a sample.
To collect the samples, Venter's team has designed a filter that will sift through some 1,400 cubic metres of air each day. Having tested the device on top of their building in Rockville, the researchers have now installed it on a 40-storey office block in the Big Apple, although its precise whereabouts is a secret.
They hope that identifying the microbes that flit through our air and into our lungs could be a useful step towards combating urban diseases such as asthma. "Many bacteria and viruses in the air elicit destructive immune responses and we would like to explore these," Venter says.
The researchers plan to make their results public by depositing them in a new environmental genomics database run by the US National Institutes of Health.
What's more, Venter says, if New York's bugs can make it there, they can make it anywhere. Urban areas across the world are likely to harbour many of the same species. "If it's as successful as our ocean sequencing we think it will have a large number of global applications," he told email@example.com.
president, J. Venter Institute, Rockville, Maryland