By John Kerr 02/11/2017


A genetic database of over 27,000 bacterial samples from around the world – including New Zealand – will keep researchers busy for years to come.

Cataloging the bacterial diversity of the entire planet? Given that microbes are basically everywhere, this seems like an impossible task. But an international team of researchers is taking on the challenge.

EMP_logo_no_backgroundThe Earth Microbiome Project, co-founded by Dunedin-born microbiologist Prof Rob Knight in 2010, describes itself as “a massive crowd-sourced effort to analyze microbial communities across the globe.” The immense depth and breadth of the samples already collected by the Project is outlined in a new analysis published today in Nature.

More than 27,000 samples have been sourced from researchers around the world, including samples from volcanoes in Hawaii, mummified seals in Antarctica, monkey poo in China and good old New Zealand dirt. The Project team analysed the unique collections of microbes — the microbiomes — living in each sample to generate the first reference database of bacteria colonizing the planet. And they’ve made it freely available to all.

The infographic below gives an idea of the sheer scale of the project.

 

 

“The potential applications for this database and the types of research questions we can now ask are almost limitless,” says Knight, who is based at the University of California.

“Here’s just one example — we can now identify what kind of environment a sample came from in more than 90 percent of cases, just by knowing its microbiome, or the types and relative quantities of microbes living in it. That could be useful forensic information at a crime scene… think ‘CSI.’”

Read more about the research on Scimex.org.

 

Researcher sampling soil in an ice cave near the summit of Mt. Erebus, Ross Island, Antarctica. Mt. Erebus generates the most southern and isolated geothermal soils on the planet. (Photo by S. Craig Cary, Univ. of Waikato, New Zealand).

Microbial life on planet Earth

The diversity of environments sampled by the Earth Microbiome Project helps demonstrate just how much local environment shapes the microbiome. For example, the skin microbiomes of cetaceans (whales and dolphins) and fish are more similar to each other than they are to the water they swim in; conversely, the salt in saltwater microbiomes makes them distinct from freshwater, but they are still more similar to each other than to aquatic animal skin.

Overall, the microbiomes of a host, such as a human or animal, were quite distinct from free-living microbiomes, such as those found in water and soil. For example, the free-living microbiomes were far more diverse, in general, than host-associated microbiomes.

The future will be busy

Attempting to catalogue the extent of bacterial life on planet Earth is an inspirational challenge, but the research goes beyond mere microbial ‘stamp collecting’.

“These global ecological patterns offer just a glimpse of what is possible with coordinated and cumulative sampling,” says Project co-founder Janet Jansson.

“Earth Microbiome Project provides both a resource for the exploration of myriad questions, and a starting point for the guided acquisition of new data to answer them.”

Already the data from the Project has been used in studies covering topics as varied as obesity, oil spills and wine. Co-founder Jack Gilbert from the US Department of Energy previously explained how microbiomes are a surprisingly important factor in understanding climate change.

As the Arctic tundra heats up, carbon stored in its depths begins to move. If it joins the atmosphere, it could contribute to rising global levels of carbon dioxide. And microbes affect where it goes—whether it is released into the air or absorbed by lakes, the oceans or soil. Understanding what tundra microbes do during warming will let us get a better idea of how it might affect climate.

In a comment article published alongside the Nature paper Prof Jeroen Raes, a microbiologist at KU Leuven, agrees the value of the Earth Microbiome Project will extend far beyond what is reported in the latest paper.

“The project provides a resource that will keep microbial ecologists and evolutionary biologists busy for years”

You can find more information on the Earth Microbiome Project website, including an interactive map of where the samples have come from.

 

earth microbiome project
Just a few of the thousands of samples captured in the Earth Microbiome Project. Top left: Hiking through the rain forest of Puerto Rico to sample soils with students (photo credit: Krista McGuire, University of Oregon) Top middle: Trachypithecus francoisi adult female and infant, a colobine monkey from China, whose fecal microbiome was sampled for this study (photo credit: Kefeng Niu). Top right: Saccopteryx bilineata, an insectivorous bat from Lamanai, Belize, whose fecal microbiome was sampled for this study (photo credit: Angelique Corthals and Liliana Davalos). Bottom left: Researcher sampling a stream in the Brooks Mountain Range, Alaska (photo credit: Byron Crump). Bottom middle: Swabbing bird eggshells from Spain (photo credit: Juan M. Peralta-Sánchez). Bottom right: Researcher sampling the southernmost geothermal soils on the planet at the summit of Mt Erebus, Ross Island, Antarctica (photo credit: S. Craig Cary, Univ. of Waikato, New Zealand).