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The global microbiome

Written by Kayt Sukel

The Earth is home to billions of different bacteria and archaea—yet, to date, there has been no way to catalog the planet’s immense microbial diversity. Now an international consortium of scientists announce the first results from the Earth Microbiome Project.

Experts estimate that there are approximately a trillion species of microbes on Earth—in fact, there are more bacteria present in today’s oceans than there are stars in the known universe. These bacteria live almost anywhere: from the mouth of a migrating bird to the inside of the human gut to a small ground plant in the Amazonian jungle. Historically, characterizing the biological natures of these different organisms has been a challenge for a variety of reasons.

“I’m a soil microbiologist. The majority of microbes in the soil were unidentified. We couldn’t cultivate them. We didn’t understand their functions,” said Janet Jansson from Pacific Northwest National Laboratory. “We lacked the ability to understand not only the compositions of the micro-organisms in the soil I’m interested in, but also the ability to compare those communities to other communities from a variety of different kinds of sample types and habitats across the planet.”

To address those issues, Jansson partnered with colleagues from the University of California San Diego (UCSD), the University of Chicago, and Argonne National Laboratory to found the Earth Microbiome Project (EMP), a global undertaking to explore and catalog the diversity of microbial life on our planet. The founding project members developed a standard protocol for sampling and analyzing samples, as well as an open data-sharing platform so that other scientists, near and far, can continue to add to the collection with the goal of answering fundamental questions regarding the composition, distribution, and relationships among the Earth’s bacterial and archaeal communities. To date, the project has collected and analyzed over 27,000 samples.

“The collaborative nature of this project is really exciting. We have over 500 researchers from over 40 countries who have already contributed samples and data. We’ve got samples related to drinking water quality and oil spills. We’ve got skin samples from dolphins, seals, fish, birds, bats, cats, rats, rattlesnakes, and Komodo dragons,” said Luke Thompson from the National Oceanic and Atmospheric Administration (NOAA), which helped found the project. “And that’s just scratching the surface. There are many layers to this, and it will be exciting to see how people will use this data in the future.”

Today, the consortium published their first report in Nature, detailing 16S rRNA sequencing for each sample. Across those samples, the researchers identified approximately 300,000 unique 16S rRNA sequences—the majority of which were not present in existing databases—and discovered that such sequences appear to be specific to the type of environments from which the individual bacteria hails.

“There’s much more to learn,” said Jack Gilbert from the University of Chicago and Argonne National Laboratory. “So we invite the scientific community at large to expand the EMP by using our standardized protocols to contribute their data and samples via the data infrastructure we have here at UCSD.”