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  • richardmitnick 12:48 pm on December 14, 2017 Permalink | Reply
    Tags: , , Earth Microbiome Project, ,   

    From PNNL: “Scientists create unprecedented catalog of microbial life on planet Earth” 

    PNNL BLOC
    PNNL Lab

    November 01, 2017[ Now in social media]
    Tom Rickey
    tom.rickey@pnnl.gov
    (509) 375-3732

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    Microbiome expert Janet Jansson. Credit: Andrea Starr / PNNL

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    Credit: UC San Diego Center for Microbiome Innovation

    Scientists have taken the most extensive snapshot ever of the vast microbial life on Earth.

    By drawing on more than 27,000 samples of soil, tissue, and water from the Arctic to Antarctica, more than 300 scientists at scores of institutions worldwide have created the first reference database of bacteria inhabiting the planet. The findings were published Nov. 1 in the journal Nature.

    The study is the latest result from the Earth Microbiome Project, which is led by a trio of scientists including Janet Jansson of the Department of Energy’s Pacific Northwest National Laboratory and colleagues at the University of California San Diego, the University of Chicago and DOE’s Argonne National Laboratory.

    Microbes are tiny, but the goal of Jansson and her colleagues from the outset in 2010 was anything but: To sample as many of the Earth’s microbial communities as possible to advance scientific understanding of microbes and their relationships with their environments, including plants, animals and humans. So far the project has spanned seven continents and 43 countries, with scientists analyzing more than 2 billion DNA sequences from bacteria and other microbes.

    The team so far has identified around 300,000 unique sequences of the 16S rRNA gene, a genetic marker specific for bacteria and their relatives, archaea. The 16S rRNA sequences serve almost like barcodes — unique identifiers that allow researchers to track bacteria across samples from around the world.

    For more information about the work by Jansson and the team, view the full news release.

    See the full article here .

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    Pacific Northwest National Laboratory (PNNL) is one of the United States Department of Energy National Laboratories, managed by the Department of Energy’s Office of Science. The main campus of the laboratory is in Richland, Washington.

    PNNL scientists conduct basic and applied research and development to strengthen U.S. scientific foundations for fundamental research and innovation; prevent and counter acts of terrorism through applied research in information analysis, cyber security, and the nonproliferation of weapons of mass destruction; increase the U.S. energy capacity and reduce dependence on imported oil; and reduce the effects of human activity on the environment. PNNL has been operated by Battelle Memorial Institute since 1965.

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  • richardmitnick 1:35 pm on November 2, 2017 Permalink | Reply
    Tags: , , , Earth Microbiome Project, , Mapping the Microbiome of … Everything, Massive global research collaboration known as the Earth Microbiome Project catalogues planet’s microbial diversity at unprecedented scale,   

    From UCSD: “Mapping the Microbiome of … Everything” 

    UC San Diego bloc

    UC San Diego

    November 01, 2017
    Heather Buschman

    Massive global research collaboration known as the Earth Microbiome Project catalogues planet’s microbial diversity at unprecedented scale.

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    From left, Berkeley Lab researchers Eric Dubinsky, Shi Wang (on left), and Neslihan Tas contributed to the Earth Microbiome Project. LBNL.

    ​In the Earth Microbiome Project, an extensive global team co-led by researchers at University of California San Diego, Pacific Northwest National Laboratory, University of Chicago and Argonne National Laboratory collected more than 27,000 samples from numerous, diverse environments around the globe. They analyzed the unique collections of microbes — the microbiomes — living in each sample to generate the first reference database of bacteria colonizing the planet. Thanks to newly standardized protocols, original analytical methods and open data-sharing, the project will continue to grow and improve as new data are added.

    The paper describing this effort, published November 1 in Nature, was co-authored by more than 300 researchers at more than 160 institutions worldwide.

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    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 Earth Microbiome Project was founded in 2010 by Rob Knight, PhD, professor at UC San Diego School of Medicine and director of the Center for Microbiome Innovation at UC San Diego; Jack Gilbert, PhD, professor and faculty director of The Microbiome Center at University of Chicago and group leader in Microbial Ecology at Argonne National Laboratory; Rick Stevens, PhD, associate laboratory director at Argonne National Laboratory and professor and senior fellow at University of Chicago; and Janet Jansson, PhD, chief scientist for biology and laboratory fellow at Pacific Northwest National Laboratory. Knight, Gilbert and Jansson are also co-senior authors of the Nature paper and Stevens is a co-author.

    “The potential applications for this database and the types of research questions we can now ask are almost limitless,” Knight said. “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.’”

    The goal of the Earth Microbiome Project is to sample as many of the Earth’s microbial communities as possible in order to advance scientific understanding of microbes and their relationships with their environments, including plants, animals and humans. This task requires the help of scientists from all over the globe. So far, the project has spanned seven continents and 43 countries, from the Arctic to the Antarctic, and more than 500 researchers have contributed to the sample and data collection. Project members are using this information as part of approximately 100 studies, half of which have been published in peer-reviewed journals.

    “Microbes are everywhere,” said first author Luke Thompson, PhD, who took on the role of project manager while a postdoctoral researcher in Knight’s lab and is currently a research associate at the National Oceanic and Atmospheric Administration (NOAA). “Yet prior to this massive undertaking, changes in microbial community composition were identified mainly by focusing on one sample type, one region at a time. This made it difficult to identify patterns across environments and geography to infer generalized principles.”

    Project members analyze bacterial diversity among various environments, geographies and chemistries by sequencing the 16S rRNA gene, a genetic marker specific for bacteria and their relatives, archaea. The 16S rRNA sequences serve as “barcodes” to identify different types of bacteria, allowing researchers to track them across samples from around the world. Earth Microbiome Project researchers also used a new method to remove sequencing errors in the data, allowing them to get a more accurate picture of the number of unique sequences in the microbiomes.

    Within this first release of data, the Earth Microbiome Project team identified around 300,000 unique microbial 16S rRNA sequences, almost 90 percent of which don’t have exact matches in pre-existing databases.

    Pre-existing 16S rRNA sequences are limited because they were not designed to allow researchers to add data in a way that’s useful for the future. Project co-author Jon Sanders, PhD, a postdoctoral researcher in Knight’s lab, compares the difference between these other databases and the Earth Microbiome Project to the difference between a phone book and Facebook. “Before, you had to write in to get your sequence listed, and the listing would contain very little information about where the sequence came from or what other sequences it was found with,” he said. “Now, we have a framework that supports all that additional context, and which can grow organically to support new kinds of questions and insights.”

    “There are large swaths of microbial diversity left to catalogue. And yet we’ve ‘recaptured’ about half of all known bacterial sequences,” Gilbert said. “With this information, patterns in the distribution of the Earth’s microbes are already emerging.”

    According to Gilbert, one of the most surprising observations is that unique 16S sequences are far more specific to individual environments than are the typical units of species used by scientists. 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.

    “These global ecological patterns offer just a glimpse of what is possible with coordinated and cumulative sampling,” Jansson said. “More sampling is needed to account for factors such as latitude and elevation, and to track environmental changes over time. The 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.”

    For more about the Earth Microbiome Project, visit earthmicrobiome.org and follow @earthmicrobiome on Twitter. For the complete list of co-authors and institutions participating in the Earth Microbiome Project, view the full Nature paper .

    The project was funded, in part, by the John Templeton Foundation, W. M. Keck Foundation, Argonne National Laboratory, Australian Research Council, and Extreme Science and Engineering Discovery Environment, which is supported by National Science Foundation (ACI-1053575).

    See the full article here .

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    UC San Diego Campus

    The University of California, San Diego (also referred to as UC San Diego or UCSD), is a public research university located in the La Jolla area of San Diego, California, in the United States.[12] The university occupies 2,141 acres (866 ha) near the coast of the Pacific Ocean with the main campus resting on approximately 1,152 acres (466 ha).[13] Established in 1960 near the pre-existing Scripps Institution of Oceanography, UC San Diego is the seventh oldest of the 10 University of California campuses and offers over 200 undergraduate and graduate degree programs, enrolling about 22,700 undergraduate and 6,300 graduate students. UC San Diego is one of America’s Public Ivy universities, which recognizes top public research universities in the United States. UC San Diego was ranked 8th among public universities and 37th among all universities in the United States, and rated the 18th Top World University by U.S. News & World Report ‘s 2015 rankings.

     
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