J. Craig Venter Institute

A genetically transformed strain of bacteria takes on a bluish cast as a signal that synthetic coding was incorporated into the cell's genetic machinery.

Someday, microbiomes just might give us a world where crude oil is grown like a crop, where vaccines for new flu strains can be produced in days instead of months, and where physicians can tweak the bacteria in your gut to cure what ails you. At least that's the promise held out by genomics pioneer Craig Venter and others at a symposium conducted this week at Seattle's Institute for Systems Biology.

A decade ago, Venter was among a cadre of researchers who first decoded the human genome — in Venter's case, his own. Today, as the head of the J. Craig Venter Institute, he's among a cadre of researchers who are not only working out the implications of that genetic code for our daily lives, but also studying how to tweak the genetic codes of the myriad microbes that surround us — and in some cases, live within us. The makeup of those microbial communities is what scientists refer to a "microbiome."

A decade ago, the main challenge facing geneticists was to translate the "analog" information of cellular chemistry into a digital database, Venter told attendees. Today, the main challenge is to reverse course and make the "digital to analog" conversion, so that innovations in genetic code can be applied to the real world.

How's that done? Venter and his colleagues made a start on that task just a few years ago, by pioneering a process to synthesize DNA and insert it into a strain of bacteria. The daughter cells reflected the artificially altered programming instead of their forebears' natural genetic code.

Now Venter and others are putting synthetic biology to work. Here are just a few of the examples cited at the Seattle symposium, titled "Systems Biology and the Microbiome":

• Novartis, a major pharmaceutical company, is working with Venter on techniques to crack the genetic code of an influenza virus strain and pass it along to the vaccine-makers within five days. A quick turnaround is the key to containing the spread of deadly flu strains like the one that killed tens of millions in 1918. "We think we're actually pandemic-ready," Venter said.
• Several commercial ventures, including Sapphire Energy, are tweaking algae to produce oil-like compounds at a price that's cheaper than the cost of crude oil. Sapphire CEO Jason Pyle pointed out that based purely on commodity costs, corn is a cheaper energy source than oil (though not as cheap as natural gas). If genetically modified algae could be grown in mass quantities as cheaply as corn, it could become a renewable energy source that's much closer to carbon-neutral than fossil fuels. Carbon dioxide could come to be seen as "the raw material of the future," Venter said.

• Algae strains could also be reprogrammed to produce foodstuffs, Venter said. Such genetic twists could outpace today's chemical-heavy agricultural methods, which are increasingly being seen as too wasteful for the planet's rising population. "Ultimately, the elimination of agriculture as we know it should be a goal of modern science," Venter said. However, harnessing synthetic algae cells is "not a short-term project," he cautioned.
• Unraveling the human microbiome, particularly in our digestive system,. ranks among the top priorities for microbiologists. Physicians are already experimenting with "fecal transplants" — a gross-sounding procedure that involves injecting material from a donor's intestines into the gut of a patient who needs a healthier bacterial community. Having your digestive bacteria analyzed, and tweaked if necessary, may someday become part of a routine physical. (However, MIT's Eric Alm noted that it wouldn't have to be done annually, because your gut's microbiome doesn't usually change that quickly.)
• The bacteria in our bowels may even play a role in space exploration: If we ever get to the point of sending astronauts to Mars, Venter said one of the first items on the agenda should be to replace the astronauts' Earth-centric gut bacteria with a selection more suited to the Mars trip. Venter has said other bacteria cold be engineered to create fuel and food from raw materials on Mars, including the carbon dioxide in its atmosphere.

This all sounds like a science-fiction utopia, but some believe there's the potential for a sci-fi nightmare instead. Last month, an international environmental consortium called for a moratorium on the commercial use of synthetic organisms, and an outright ban on the application of synthetic biology to the human genome or the human microbiome.

"It is our obligation to safeguard the future, to be wise in our development and use of technologies which could threaten humans and the Earth," said Carolyn Raffensperger, executive director of the Science and Environmental Health Network. The results of an online survey on synthetic biology are due to be released next month.

What do you think about the idea using genetically altered microbes to produce fuel, food and medicine? Is it a panacea, a Pandora's Box, or something in between? Feel free to register your opinion in the online poll above, or in the comment space below.

More about the microbiome and synthetic biology:

• Scientists map the world's microbes
• What's living on your smartphone?
• Bacteria prefer prime real estate
• Renewable rubber highlights new economy
• One-third of Americans back ban on synthetic biology

Home Microbiome Study

A graph charts the relative proportions of different types of bacteria on shoes (odd-numbered columns) and cell phones (even-numbered columns). For a detailed breakdown, check the Home Microbiome Study website.

Your cell phone and your shoes have whole communities of microbes living on them, as distinctive as the germs on your fingers and in your mouth.

Among the bacteria that typically live in your pocket are the relatives of nasty bugs that can cause pneumonia, meningitis and gonorrhea. In contrast, the soles of your shoes could harbor bacteria related to E. coli, salmonella and the microscopic critters that cause pink eye.

Eww, right? Maybe a more appropriate reaction would be "Wow!" At least that's the way I see it, as a participant in what could be the world's first comparative study of smartphones and shoes.

"We've never actually done this stunt before," said Jack Gilbert, a microbial ecologist at Argonne National Laboratory and the University of Chicago. He and his colleagues had yours truly and 30 other journalists swab their phones and their shoes to collect the microbial samples last weekend in Vancouver, Canada, during a news briefing at the annual meeting of the American Association for the Advancement of Science. The results of the DNA tests, conducted under the auspices of the Earth Microbiome Project, were distributed today.

Jonathan Eisen, a microbiologist at the University of California at Davis, said today's gene-sequencing technologies makes it possible to process genetic samples for mere hundreds of dollars, as opposed to millions of dollars, in a fraction of the time it used to take. "Five years ago, this would have taken our lab six months or more," he said.

That technological quantum leap is opening up new scientific frontiers. "For the first time, we're able to do surveys of places quickly and cheaply," Eisen said. "It's like we're kids in a candy store."

Last year, researchers turned up the "eww" factor by analyzing the microbial communities in public restrooms, which include germs linked to staph and diarrhea. Some of the researchers involved in the Earth Microbiome Project charted the microbial signatures of toilet seats, restroom floors and sink surfaces, and found that the flush handles and seats were "relatively enriched" with bacteria from our bowels.

Home Microbiome Study

Genetic markers distinguish between the samples taken from shoes (in blue) and the samples taken from cell phones (in red).

Compared to those findings, the results from the phone-vs.-shoe study are positively tame. "We found nothing that was pathogenic ... which means all of you are healthy. That's a good thing," Gilbert said.

There was a clear difference between the bacterial signatures of our shoes and our phones, although a couple of the samples look as if they were switched — suggesting that journalists don't always follow directions.

The researchers couldn't take samples from our bodies, because that would have run counter to the privacy guidelines for their experiments. But the fact that the cellphone samples were so similar suggests that we nurture those microbial communities with the germs from our hands. And we're not talking just about phones.

"One of the reporters in the room didn't have a phone on him, and said, 'Could you sample my wallet instead?' The sample from his wallet looks exactly like the smartphones," Gilbert said.

As for those nasty-sounding bacterial types, Gilbert said we shouldn't worry too much. These bacteria are almost certainly benign cousins to the bad sort of bugs. "The hypothesis is that the good bacteria are out-competing the bad bacteria," Gilbert said. "If they weren't there, the pathogens may be able to take root."

Our shoes reflected a wider diversity of microbes than the cell phones did — which makes sense when you consider how much we had to walk through to get to the news briefing in Vancouver. "There was one pair of shoes which was a significant outlier to the rest of the data," Gilbert observed. "We don't know why. It could have been that the person who owned those shoes may have stepped in some mud or something. ... If the person's been walking in a different environment from everybody else, we could potentially trace where someone is walking."

Which raises the question: Could your microbes serve as diagnostic tool, or even a detective tool? Researchers have talked about being able to figure out what ails you by analyzing your personal microbiome, but they're not there yet. Eventually, it may even be possible to read your whole history by checking exactly which bacteria you've picked up from which places.

"There's enough to suggest that this might be a tool, but the robustness of that tool would have to be seriously investigated," Gilbert said.

That's what the Earth Microbiome Project is all about.

"Anybody out there who is interested in microbes in the water, microbes in the air, microbes on skin, microbes on pets ... anybody can participate in the Earth Microbiome Project," Eisen said. "I can imagine scaling up to millions and millions of samples. If a citizen science project or a high-school class has an interesting quest, they can do this now."

Is that something that makes you go eww, wow ... or uh-oh? Please feel free to make your opinion known by registering a vote above, or leaving a comment below.

More about microbes:

• Scientists map the world's microbes
• Bacteria's slimy biofilm could help humans
• Scientists study belly-button bacteria
• Soap isn't always as clean as it seems
• Bacteria prefer prime real estate

For more about the phone-vs.-shoe experiment, check out the Home Microbiome Study's website and Facebook page.

Alan Boyle is msnbc.com's science editor. Connect with the Cosmic Log community by "liking" the log's Facebook page, following @b0yle on Twitter or following the Cosmic Log Google+ page. You can also check out "The Case for Pluto," my book about the controversial dwarf planet and the search for new worlds.