Nav: Home

PNNL helps lead national microbiome initiative

May 27, 2016

RICHLAND, Wash. - Scientists at the U.S. Department of Energy's Pacific Northwest National Laboratory are playing a central role as the nation devotes more than $500 million to understand communities of microorganisms and their role in climate science, food production and human health.

Scientists Janet Jansson and Ljiljana Paša-Toli are part of a core group of scientists advising the White House on issues related to research around the microbiome, a term that describes a community of microbes in a given environment.

Both Jansson and Paša-Toli are leaders of broader scientific teams at PNNL. Jansson is chief scientist for biology in the Earth and Biological Sciences Directorate at PNNL, while Paša-Toli is lead scientist for mass spectrometry at EMSL, the Environmental Molecular Sciences Laboratory, a DOE Office of Science User Facility at PNNL.

Earlier this month, the two took part in a White House briefing as the president's advisers announced more than $121 million in new funding from federal agencies for the National Microbiome Initiative. That's in addition to more than $400 million from foundations such as the Gates and Kavli foundations, organizations such as the American Chemical Society and the American Physical Society, and companies, universities, and other laboratories.

That's big money to study tiny organisms with a big impact.

Microorganisms have huge sway over environmental happenings in soil, groundwater, the ocean, the atmosphere, and our own bodies. They determine in large part how the planet stores carbon, when and how carbon is released into the environment, and what happens to contaminants and other compounds. They're important for knowing how plants take up nutrients, for helping crops sustain or develop resistance to conditions like drought, and for overall crop productivity.

Microorganisms also play a huge role in human health and disease - not just infections but in conditions like obesity, inflammatory bowel disease and diabetes. In toto, the little buggers make up an estimated one-third of all the biomass on Earth.

A lot to learn

Just a teaspoon of soil has tens of thousands of different microbial species present. While scientists have made strides sorting out which species are present in such complex samples, how those species interact remains a hugely daunting problem.

Jansson and Paša-Toli ask the same sorts of questions that an anthropologist might ask when encountering a new community. Who is present? What business do they transact with each other? What is the currency they use to get things done? What does their trash tell us about their way of life?

"We want to know not just who's there, but what they're doing," said Jansson, an expert on the role of microbes in the environment.

"We are getting pretty good at identifying some of the microorganisms present in samples, and some of what they do, but completely understanding a single microbial community, even a tiny one, is a future challenge to solve," added Jansson, president of the International Society of Microbial Ecology.

Think of an analyst confronted with the following disparate array of data: Loud buses, thousands of people, ubiquitous fast food, diesel fuel, cars, loud noises, and lots of bickering and jockeying for position. What does it all mean? The scene might be - an airport, a sporting event, a concert, an ordinary big-city work day, or an evacuation after a major disaster.

So, too, scientists like Jansson and Paša-Toli are presented an array of data about complex microbial communities, but it's very difficult to put the information together to create a coherent picture of the activity they're seeing. They can identify some microbial species; they can detect microbial nutrients and their byproducts; they see signs of their molecular doings; but putting together the big picture remains tremendously difficult.

PNNL colleague Richard Allen White III, who is working with Jansson on a project to disentangle the information about microbes that live in soil from the Kansas prairie, puts it this way:

"Imagine taking a thick book written in hundreds of different languages, chopping the book up into pieces the size of grains of rice, and then having to put it back together again," said White. "That's not unlike the challenge we face when we try to understand what's going on in even a handful of soil."

Past successes and a roadmap

Last year, Jansson and Paša-Toli were part of an elite team of scientists who, in a paper in the journal Science, called for a Unified Microbiome Initiative to understand and harness the capabilities of Earth's microbial ecosystems - a call that has largely been answered with the new White House initiative.

Last year, Jansson used an array of technologies to show the versatility of microbes that live in permafrost, which is a reservoir for a huge amount of carbon. The fate of that carbon as the climate warms and permafrost thaws is a huge issue for scientists trying to understand the planet's future. The work, published in Nature, yielded one of the most detailed looks ever at the microbes active in permafrost.

Earlier this year, Jansson and PNNL colleague Aaron Wright were among the authors of a paper in ACS Nano that discussed the technologies needed to explore the world's microbiomes. Among the technological challenges are several related to understanding the "omics" of organisms - information related to genes, protein coding and activity, and metabolism. While DNA sequencing has become very quick and relatively inexpensive, the other measurements currently take longer and are more costly.

In this month's issue of Nature Microbiology, Jansson and PNNL chemist Erin Baker discuss the importance of understanding such communities as whole entities. The pair calls for strides in technology, optimized protocols, improved databases, speedier analysis, larger sample sizes, and international collaborations.

Currently, Jansson is heading a major initiative at PNNL looking at Microbiomes in Transition, known as the MinT Initiative. More than two dozen researchers are involved in the five-year effort focusing on environmental issues, exposure science, and computational biology. Last year, one of the first actions of the MinT team, in conjunction with EMSL scientists including Paša-Toli, was to bring together nearly 200 microbiome experts from around the world to discuss the future of microbiome studies and the technologies necessary for scientists to develop to make further discoveries.
-end-


DOE/Pacific Northwest National Laboratory

Related Microbes Articles:

Microbes seen controlling action of host's genes
Duke researchers have shown that microbes can control their animal hosts by manipulating the molecular machinery of their cells, triggering patterns of gene expression that consequently contribute to health and disease.
Three-way dance between herbivores, plants and microbes unveiled
What looks like a caterpillar chewing on a leaf or a beetle consuming fruit is likely a three-way battle that benefits most, if not all of the players involved, according to a Penn State entomologist.
Vitamin B12: Power broker to the microbes
In the microbial world, vitamin B12 is a hot commodity.
Gut microbes and bird's breath from the U at #SICB2017
University of Utah researchers will be among the scientists convening in New Orleans for the 2017 Annual Meeting for the Society for Integrative and Comparative Biology Jan.
Gut microbes contribute to recurrent 'yo-yo' obesity
New research in mice may in the future help dieters keep the weight off.
Digital microbes for munching yourself healthy
A research team at the Luxembourg Centre for Systems Biomedicine (LCSB) of the University of Luxembourg has taken an important step in modelling the complexity of the human gut's bacterial communities -- the microbiome -- on the computer.
How gut microbes help chemotherapy drugs
Two bacterial species that inhabit the human gut activate immune cells to boost the effectiveness of a commonly prescribed anticancer drug, researchers report Oct.
Soil microbes flourish with reduced tillage
Microbes improve soil quality by cycling nutrients and breaking plant residues down into soil organic matter.
Microbes help plants survive in severe drought
Plants can better tolerate drought and other stressors with the help of natural microbes, University of Washington research has found.
Mix and match microbes to make probiotics last
Scientists have tried to alter the human gut microbiota to improve health by introducing beneficial probiotic bacteria.

Related Microbes Reading:

I Contain Multitudes: The Microbes Within Us and a Grander View of Life
by Ed Yong (Author)

New York Times Bestseller

New York Times Notable Book of 2016

NPR Great Read of 2016

Economist Best Books of 2016

Brain Pickings Best Science Books of 2016

Smithsonian Best Books about Science of 2016

Science Friday Best Science Book of 2016

A Mother Jones Notable Read of 2016

A Bill Gates “Gates Notes” Pick

MPR Best Books of... View Details


Teaming with Microbes: The Organic Gardener's Guide to the Soil Food Web, Revised Edition
by Jeff Lowenfels (Author), Wayne Lewis (Author)

The 2011 Garden Writers of America Gold Award for Best Writing/Book proves soil is anything but an inert substance. Healthy soil is teeming with life -- not just earthworms and insects, but a staggering multitude of bacteria, fungi, and other microorganisms. When we use chemical fertilizers, we injure the microbial life that sustains healthy plants, and thus become increasingly dependent on an arsenal of artificial substances, many of them toxic to humans as well as other forms of life. But there is an alternative to this vicious circle: to garden in a way that strengthens, rather than... View Details


Missing Microbes: How the Overuse of Antibiotics Is Fueling Our Modern Plagues
by Martin J. Blaser MD (Author)

"A critically important and startling look at the harmful effects of overusing antibiotics, from the field's leading expert Tracing one scientist's journey toward understanding the crucial importance of the microbiome, this revolutionary book will take readers to the forefront of trail-blazing research while revealing the damage that overuse of antibiotics is doing to our health: contributing to the rise of obesity, asthma, diabetes, and certain forms of cancer. In Missing Microbes, Dr. Martin Blaser invites us into the wilds of the human microbiome where for hundreds of thousands of years... View Details


Tiny Creatures: The World of Microbes (Read and Wonder)
by Nicola Davies (Author), Emily Sutton (Illustrator)

"Sutton's large-scale illustrations help children to visualize microorganisms and processes that are too small to see. . . . A handsome and rewarding picture book." — Booklist (starred review) All around the world—in the sea, in the soil, in the air, and in your body—there are living things so tiny that millions could fit on an ant's antenna. They're busy doing all sorts of things, from giving you a cold and making yogurt to eroding mountains and helping to make the air we breathe. View Details


Planet of Microbes: The Perils and Potential of Earth's Essential Life Forms
by Ted Anton (Author)

We live in a time of unprecedented scientific knowledge about the origins of life on Earth. But if we want to grasp the big picture, we have to start small—very small. That’s because the real heroes of the story of life on Earth are microbes, the tiny living organisms we cannot see with the naked eye. Microbes were Earth’s first lifeforms, early anaerobic inhabitants that created the air we breathe. Today they live, invisible and seemingly invincible, in every corner of the planet, from Yellowstone’s scalding hot springs to Antarctic mountaintops to inside our very bodies—more than... View Details


Microbe Hunters
by Paul de Kruif (Author)

This science classic by Paul de Kruif chronicles the pioneering bacteriological work of the first scientists to see and learn from the microscopic world.

 

Paul de Kruif's Microbe Hunters is a timeless dramatization of the scientists, bacteriologists, doctors, and medical technicians who discovered microbes and invented the vaccines to counter them. De Kruif reveals the now seemingly simple but really fundamental discoveries of science—for instance, how a microbe was first viewed in a clear drop of rain water, and when, for the first time ever, Louis Pasteur... View Details


10% Human: How Your Body's Microbes Hold the Key to Health and Happiness
by Alanna Collen (Author)

You are just 10% human. For every one of the cells that make up the vessel that you call your body, there are nine impostor cells hitching a ride. You are not just flesh and blood, muscle and bone, brain and skin, but also bacteria and fungi. Over your lifetime, you will carry the equivalent weight of five African elephants in microbes. You are not an individual but a colony.

Until recently, we had thought our microbes hardly mattered, but science is revealing a different story, one in which microbes run our bodies; remaining a healthy human is impossible without them.

In this... View Details


Microbe
by Michele Swanson (Author), Gemma Reguera (Author), Moselio Schaechter (Author), Frederick C. Neidhardt (Author)

Brings the excitement, breadth, and power of the modern microbial sciences to the next generation of students and scientists.

This new edition of Microbe is an eloquent and highly readable introduction to microbiology that will engage and excite science majors and pre-health professionals. The authors, all prominent scientists, have carefully crafted this lively narrative to bring key microbiology concepts to life and promote a lifelong passion for the microbial sciences.

Far more than a comprehensive reference book, Microbe is replete with case... View Details


Pasteur's Fight Against Microbes (Science Stories)
by Beverly Birch (Author), Christian Birmingham (Author)

n 1856, when Louis Pasteur first began studying microbes in rotten sugarbeet juice, he put into motion a chain of events that saved France's wine industry, and revolutionized medicine and biology. View Details


Microbes: The Good, the Bad, and the Ugly (Amazing Human Body)
by Joanne Randolph (Editor)

Explores the bacteria that live in human intestines, including how they help digest food and how food affects the microbiota in the body. View Details

Best Science Podcasts 2017

We have hand picked the best science podcasts for 2017. Sit back and enjoy new science podcasts updated daily from your favorite science news services and scientists.
Now Playing: TED Radio Hour

Simple Solutions
Sometimes, the best solutions to complex problems are simple. But simple doesn't always mean easy. This hour, TED speakers describe the innovation and hard work that goes into achieving simplicity. Guests include designer Mileha Soneji, chef Sam Kass, sleep researcher Wendy Troxel, public health advocate Myriam Sidibe, and engineer Amos Winter.
Now Playing: Science for the People

#448 Pavlov (Rebroadcast)
This week, we're learning about the life and work of a groundbreaking physiologist whose work on learning and instinct is familiar worldwide, and almost universally misunderstood. We'll spend the hour with Daniel Todes, Ph.D, Professor of History of Medicine at The Johns Hopkins University, discussing his book "Ivan Pavlov: A Russian Life in Science."