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Scientists map the world's microbes

Nathan Shaner / MBARI

This tropical postcard consists of a petri dish containing an artistic arrangement of bacteria that have been genetically engineered to incorporate fluorescent proteins.

Microbiologists are starting to make sense of tens of thousands of samples they've collected from around the world, undoubtedly containing legions upon legions of different kinds of microorganisms. How many kinds? That's just the point: Nobody knows.

The microbial world is "Earth's dark matter," says Janet Jansson, a senior staff scientist at Lawrence Berkeley National Laboratory in California. By that, Jansson means that the varieties of bacteria and other microorganisms are as mysterious as the unseen stuff that makes up 85 percent of the matter in the universe.

Jansson held up a spoon of soil during a news conference Friday at annual meeting of the American Association for the Advancement of Science, held in Vancouver, Canada — and noted that there were more organisms in that spoonful than there were stars in the Milky Way galaxy (100 billion).

Talk about big numbers: Scientists estimate that there are 10 trillion microbes in every kilogram (2.2 pounds) of soil on Earth. Our planet is home about a nonillion cells (that's a 1 with 30 zeroes after it). Most of those are microbes. Each human body is thought to consist of 10 trillion cells, harboring microbial communities that amount to 100 trillion cells. From a microbe's point of view, we're all just lumps of flesh that are convenient places to hang out, said Jack Gilbert, a microbiologist at Argonne National Laboratory and the University of Chicago.

"Without them, you'd be dead," he told reporters at an AAAS meeting. "Without us, they'd just move onto something else."

Earth Microbiome Project
The problem is that far less than 10 percent of the world's varieties of microbes have ever been cultivated in the lab. The rest are out there in the world, beyond the reach of the traditional methods for categorizing and analyzing life forms. That's where the Earth Microbiome Project is aiming to make a big difference.

Over the past year, more than 100 researchers have been collecting samples from locales as far-flung as the Antarctic Dry Valleys, the Great Indian Desert, Yellowstone's hot springs and a Merlot grape vineyard on Long Island. Swabs have been sent in to document the microbial communities living within ants, iguanas and other animals. The effort meshes with the Human Microbiome Project, a longer-running, federally financed campaign to study the microbes living in us and on us.

Jansson said about 60,000 samples have been collected during the first year of the Earth Microbiome Project, and about 10,000 of those samples have been processed. Rather than trying to culture individual bacteria, the microbe-hunters are doing wholesale DNA sequencing to piece together as many genomes as they can. Eventually, the project's organizers hope to analyze hundreds of thousands of samples.

A few more samples are being sent in this week, courtesy of the journalists attending Friday's news briefing. Following the researchers' instructions, we swabbed our smartphones as well as the soles of our shoes, popped the swabs in collection vials, and handed them over to students for analysis over the next few weeks. I'll let you know if I find out anything interesting about the microbial communities living in my pants pocket or on my slip-ons.

Eventually, the project plans to produce a microbial gene atlas as well as a "field guide" to microbes from regions around the world, said Jonathan Eisen, a microbiologist at the University of California at Davis.

What's this have to do with us?
Insights into Earth's microbial dark matter could yield all sorts of benefits for science and our well-being. First of all, shedding light on the planet's microbial dark matter will give scientists a better sense of how Earth's "tree of life" is laid out. Just in the first year, the project has covered 82 percent of the currently known global diversity of microbes, Gilbert reported.

Charting the human microbiome should be a particularly fruitful exercise. Rob Knight, a researcher at the University of Colorado at Boulder, showed off some visualizations illustrating how the microbial communities on our fingertips, our face and in our mouths have distinct characteristics that can be charted over time — theoretically revealing where our fingers have been. "This raises all kinds of ethical concerns," he said, only half-jokingly.

Studies have shown that babies delivered vaginally and through Caesarian section have significantly different microbiomes 20 minutes after birth, Knight said. That could mean that those babies face different prospects for immune responses and allergies later in life — prospects that could be changed by postnatal "inoculations" with the right kind of bacteria.

Gilbert said fecal samples could reveal how our gut bacteria are doing, and whether we need to have our microbiomes adjusted for better health. As icky as it might sound, fecal transplants have already become an accepted therapy for some types of intestinal infections.

Even the microbiomes that have nothing directly to do with humans could be important. Take that Merlot vineyard, for example. "We're doing the microbiome of a 'good year,'" Gilbert said. If for some reason the wine made from the vineyard's grapes becomes less tasty, it might be possible to load up the soil with the good-year bacteria and restore the vintage to its glory days.

Gilbert would like to see the Earth Microbiome Project get to a point where it's possible to predict future changes in the ecosystem — including climate change impacts — by checking something like a microbial "weather report." But to do that, researchers will have to manage massive amounts of genomic and environmental data. That's a challenge that Rick Stevens, the Argonne Lab's associate director, compared to unraveling the secrets of subatomic particles with the Large Hadron Collider.

To study the smallest life forms on the planet, "we need bigger, better computers," he said.

Is this a job worth doing? The scientists leading the Earth Microbiome Project definitely think so. "I think people should be excited about this," Gilbert said. Are you excited? Feel free to weigh in with your comments below.

More from the AAAS meeting in Vancouver:


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