Earth & Conservation

Massive International Project Maps the World’s Microbes

More than 500 scientists contributed 27,000-plus samples of the world’s microbes, ranging from soil in Antarctica to the human gut.

A screenshot of the Earth Microbiome Project's Microbial Cartographies interactive map | Earth Microbiome Project
A screenshot of the Earth Microbiome Project's Microbial Cartographies interactive map | Earth Microbiome Project

Want to know where a type of bacteria originated? Now there’s a map for that.

After a massive, multi-year effort, scientists have assembled a detailed chart of where the world’s microbes live. The project linked more than 300,000 species to the environments that nurture them across the globe, from the soil of Antarctica to the human gut. The gene sequences were drawn from 27,000-plus samples, contributed by more than 500 scientists. 

“We’re finding out on an unprecedented scale where all the microbes are and how they’re assembled into communities,” Rob Knight, director of the Center for Microbiome Innovation at the University of California, San Diego, told Seeker.

The findings were published Nov. 1 in the research journal Nature, in a paper with more than 300 co-authors. Knight’s group, along with the University of Chicago, the Argonne National Laboratory, and the Pacific Northwest National Laboratory, pulled together the map over seven years.

“Right at the beginning, some of our colleagues were every skeptical that anyone would be willing to give up something as precious as control over their samples and data to create this free and open resource,” Knight said. But he said the response from researchers was “incredibly rewarding.”

Earth Microbiome Project collaborators collect and analyze samples from diverse environments around the world. Top left: Hiking through the rain forest of Puerto Rico to sample soils with students (credit: Krista McGuire, University of Oregon). Top middle: Colobine monkeys in China, whose fecal microbiomes were sampled for this study (credit: Kefeng Niu). Top right: Bat in Belize, whose fecal microbiome was sampled for this study (credit: Angelique Corthals and Liliana Davalos). Bottom Left: Researcher sampling a stream in the Brooks Mountain Range, Alaska (credit: Byron Crump). Bottom middle: Swabbing bird eggshells from Spain (credit: Juan Peralta-Sanchez). Bottom right: Researcher sampling the southernmost geothermal soils on the planet, at summit of Mt. Erebus, Ross Island, Antarctica (credit: S. Craig Cary, Univ. of Waikato, New Zealand).

The collaboration, called the Earth Microbiome Project, catalogues bacteria using a genetic marker known as 16S rRNA, a common technique for distinguishing species from each other. Almost 90 percent of the bacteria hadn’t been sequenced using that technique, the researchers reported. They also found the varieties of environmental bacterial increased closer to the equator, and that many complex communities of microbes have formed from smaller, simpler communities — like Russian nesting dolls, Knight said.

Earth Microbiome Project

Though the full results are just being released, researchers have already used data assembled through the project in studies of drinking water and wine grapes, the Deepwater Horizon oil spil,l and the human microbiome. 

“We can tell you from these data how much the microbes represent different samples from around the world — different types of soils, different types of water samples, different types of animals and so forth,” Knight said. “You may be able to tell where on the planet a particular sample has come from, which obviously has a lot of interesting applications.”

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Those might include as trace evidence in court cases — or identifying an emerging illness.

“In terms of trying to understand where organisms live in the environment, where reservoirs of disease are, we have a much better view globally of where a lot of kinds of microbes are,” Knight said. “If a bacterium becomes of interest as a pathogen, we can very quickly ask what kind of sample group is it in, and can we say anything about what it is it about those samples that allow it to hang out there.”

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