Scientists: Harnessing microbes could help solve hunger, health, chemical and energy problems

Thursday, October 29th, 2015

While scientists learn more with each passing study about the way the invisible lives of fungi, bacteria, viruses and other microscopic organisms intersect with much larger plants and animals as well as the planet, Tim Donohue and a group of prominent scientists want to make sure researchers don’t miss the giant forest for the tiny trees.

Donohue, a UW–Madison bacteriology professor and director of the Great Lakes Bioenergy Research Center, joined 17 other scientists from around the world and representing a wide range of disciplines on Oct. 28 to lay out a case for an organized approach to harnessing the power of microbes to tackle many of the world’s most pressing problems.

Tim Donohue, professor of bacteriology

Tim Donohue

Led by Jeff F. Miller, a microbiology professor at the University of California, Los Angeles, in the journal Science, and microbiologist Nicole Dubilier of Germany’s Max Planck Institute for Marine Microbiology, in Nature, the authors proposed a Unified Microbiome Initiative to supply key knowledge and techniques to address sustainable agriculture, chemical and energy production, climate change, disease and more.

Discoveries ancient and modern illustrate the importance of microbes.

The geological record provides evidence of how ancestors of today’s microbes helped shape our planet. Microbes provide the oxygen we breathe, break down contaminants in water, help us digest and absorb nutrients in our food, and pass nitrogen in soil to hungry plants.

Yeast leavens bread and ferments beer, but also has a hand in the production of insulin, vaccines and industrial chemicals. Viruses may help guide normal development in animals, are a source of gene exchange in the oceans, and have stepped up as powerful tools for the study of genetics and delivery of gene therapies.

But much of what researchers have learned about the specific workings of the ubiquitous little “bugs” remains walled up within each microbe or group of microbes’ home range — or the particular branch of science practiced by the experts, according to Donohue.

“A variety of people in the academic community, the private sector and the federal government really feel it’s time to take the analysis of microbial communities to the next level,” he says. “That means moving beyond using genome sequences to obtain a census of which microbes are where, and tackling the next big challenge: understanding what communities of microbes are doing in different environments.”

A Unified Microbiome Initiative could help collect and process enormous amounts of information about dozens or hundreds or thousands of types of microbes that are born, eat, excrete, fight, die and evolve together — all the while making a fundamental difference in the environment they inhabit.

“What we need is an influx of people from other fields to work with the biochemists and microbiologists and engineers who have typically studied microbes in isolation,” Donohue says.

If scientists could accurately model communities of microbes, and anticipate how changes at the microscopic level make for changes visible on the human scale, they can anticipate problems and use microbes to create next-generationsolutions to grand societal problems.

“That has enormous potential for the health of the planet and the health of people. It could make personalized medicine work. It could create new energy sources and be the catalyst for next-generation bio-based manufacturing. It could grow food and provide clean water,” Donohue says. “Twenty years from now we may look back at this as a watershed time where we began to take information on microbes and use them as predictors of human health and influencers of planetary activities on a new scale.”

That would require organization and support for research that develops tools for exploring microbial communities and put those tools in the hands of multidisciplinary teams of scientists and engineers, according to the researchers writing in Nature and Science.

Donohue sees enthusiasm from U.S. governmental agencies and major private research philanthropic organizations for a collective push like the BRAIN Initiative, launched in 2013 by the White House’s Office of Science and Technology Policy (OSTP) to advance neuroscience. The initiative incorporates hundreds of millions of dollars in research supported by federal agencies, the pharmaceutical and medical imaging industries, and nonprofits like the Kavli Foundation.

OSTP and the Kavli Foundation have separately organized recent meetings where scientists fleshed out a vision of a Unified Microbiome Initiative.

“It’s important that this be an international effort,” Donohue says. “This is a problem the United States has the brain power and the resources to be a leader in. But to do it right, it is critical that we take advantage of the expertise that exists around the globe. Because these are problems — medicine, energy, food — we face collectively.”

UW–Madison — where researchers are investigating the roles microbes play in lifelong health, plant productivity, wastewater treatment, manufacturing and more — is uniquely positioned to play a role in a concerted effort to broaden the way science studies and makes use of microbes.

“We have expertise in every arena that needs to be pulled in to contribute, beginning with a world-class cadre of microbiologists and a spirit of collaboration,” Donohue says. “Our medical school, veterinary school, strong engineering, agricultural experts, leaders in oceanography — if we can find a way here to connect teams of these people with researchers in analytics and computation, we can be a model for the country and the world.”

This story was originally published on the UW News site.

Mycologist says our close relatives break the bounds of biology

Monday, October 26th, 2015

The mushroom nicknamed “death cap” made headlines this summer when it poisoned Syrian refugees fleeing through Eastern Europe.

But it was cooperation, not toxicity, that attracted Anne Pringle to Amanita phalloides. The fungus consumes carbon compounds released by tree roots, says the UW-Madison associate professor of botany and bacteriology, and in return helps the roots absorb soil nutrients. “I was interested in the evolution of cooperation,” she says, “and fungi and plants are models for understanding how symbiotic species interact — how the relationship is policed and maintained.”


The European Amanita phalloides (“death cap”) mushroom. Photo: Archenzo/Creative Commons. Banner photo: The hallucinogenic toadstool Amanita muscaria is also invading new terrain. Photo courtesy of Rytas Vilgalys.

Long before the Syrian refugees were poisoned, Pringle says, immigrants in California were dying as the death cap expanded its range along the West Coast. “A. phalloides poisoning is a really unpleasant way to go,” she says. “There’s intestinal distress, diarrhea. Then you feel fine during a ‘honeymoon’ that lasts several hours or more. Death can come through liver and kidney failure.”

In large swaths of California, she says, “the mushrooms are so abundant, it’s hard to believe they’re simply a neutral addition to the landscape.”

Fungi are essential recyclers of material and members of ecosystems, but they are “a cryptic part of biodiversity, largely hidden in the soil,” Pringle says. “We don’t have a fungicide that is species specific, and if you drenched its habitat with fungicide, would that be effective and safe for the environment?”

Fungi as a group are poorly known, says Pringle, who was an associate professor of organismic and evolutionary biology at Harvard University before coming to Wisconsin. “The fungi are basically a jungle of species. There are an estimated one to 10 million species, and we have names for 100,000, which suggests how little we know. You can go outside and pick up some soil, put it in a gene sequencer, and you will see a heck of a lot of species that do not match anything seen before.”

Pringle’s studies of spore dispersal show that fungi actually have some mobility. “Typically, people think fungi just release spores passively to the wind or water,” she says, “but it seems that they have evolved a mechanism to make sure the spores are released when they are most likely to spread.”

Pringle, along with Damon Smith and Mehdi Kabbage, two UW-Madison assistant professors of plant pathology, is studying the spring-like mechanism that parasitic soybean fungi use to catapult their spores into the wind. Such a mechanism, she says, “challenges the idea of fungi as passive entities.”


Anne Pringle

Pringle says fungi are puzzling. “If there is a rule in biology, I can think about how it does not apply to fungi. They challenge our preconceptions of how biology works.”

The overall oddness of fungi appears in the genes. In almost all organisms, every cell contains identical genes — it is a difference in gene activation that distinguishes a blood cell from a nerve cell. “But in fungi, one part looks very different genetically from another,” Pringle says, “so the entity you call an individual from a physical perspective encompasses many different genetic individuals. What is going on?”

Cooperation, not competition, is the archetypal relationship between fungi and many of their hosts, especially plants, Pringle says. “How you think about biology is shaped by the organisms you work with. If you think about fungi, you start with symbiosis.”

The goal of her ecological studies, she says, “is to slowly chip away at this overwhelming amount of not-knowledge. How does the pattern of fungal biodiversity vary across regions, and across the planet? How are species being moved? What does extinction look like in the fungal kingdom?”

Many people are surprised to find that the genomes of fungi and people are so closely related, Pringle observes. “If biology is to be true, we have to build rules that work for the whole of life. Maybe there are no general rules, and if that’s true, that’s also interesting. Understanding these issues is a critical part of our job, and it gets me up every day. If we are going to search for life on other planets, we need to think about how the entire spectrum of life works.”

This story was originally published on the UW-Madison News site.

Ancestors of land plants were wired to make the leap to shore

Tuesday, October 6th, 2015
liverworts, moss, fern

Liverwort plants, pictured here with moss and a fern, are an ancient lineage of land plant. Fossils suggest they may have been some of the first plants to colonize land 450 million years ago. Photo: Jean-Michel Ane lab, UW-Madison.

When the algal ancestor of modern land plants made the transition from aquatic environments to an inhospitable shore 450 million years ago, it changed the world by dramatically altering climate and setting the stage for the vast array of terrestrial life.

The genetic and developmental innovations plants used to make the leap to land have been enduring secrets of nature. Now, an international team of researchers, writing in the Proceedings of the National Academy of Sciences (PNAS), reveals that the aquatic algae from which terrestrial plant life first arose were genetically pre-adapted to form the symbiotic relationships with microorganisms that most land plants need to acquire nutrients from the soil.

The finding is important because it begins to flesh out the story of how the first land plants evolved from freshwater algae, formed critical symbiotic partnerships with microorganisms like fungi and bacteria, and made the world’s land masses habitable. What’s more, it could help with the development of biofuels. Understanding the genetic pathways involved could allow agronomists to unlock similar genes that are likely conserved in plants such as cereals and green algae, which are promising biofuel stock but require substantial amounts of chemical fertilizer.

“We were expecting that these mechanisms arose with land plants,” explains Jean-Michel Ane, a University of Wisconsin-Madison professor of bacteriology and agronomy and the senior author of the PNAS report. “The surprise was finding in algae the mechanisms we know allow plants to interact with symbiotic fungi.”

The discovery shows that the algae knew how to interact with beneficial microbes while it was still in the water, observes Pierre-Marc Delaux, who conducted the research as a postdoctoral fellow at UW-Madison and is now at the John Innes Centre in the U.K. “Without the development of this pre-adapted capability in algae, the Earth would be a very different place today,” says Delaux.

Jean-Michel Ane

Jean-Michel Ane

Many plant species depend on symbiotic relationships with microorganisms to thrive. The most famous are legumes and their beneficial association with nitrogen-fixing bacteria. Other plant species depend on relationships with fungi to chemically convert minerals in soil to forms that benefit the plant, notes Ane.

The efficient acquisition of mineral nutrients, says Ane, was likely one of the primary challenges for the earliest land plants.

“The association between plants, algae and fungi probably played a really important role in the ability of plants to colonize land,” he says. “In fact, many of us think early plants were able to colonize lands because they evolved the ability to associate with beneficial fungi.”

The genes required to encourage symbiosis between plants and microbes likely arose in a common ancestor of green algae and land plants, says Ane.

Prior to the new study, little was know about the associations between algae and fungi. The genetic pathways plants use to form a symbiosis with fungi were known in land plants called liverworts and hornworts, ancient lineages sister to all other land plant lineages. Liverworts thrive in damp environments worldwide and the oldest known liverwort fossils provide the earliest evidence of plants colonizing land.

“We had found these mechanisms in liverworts, but not algae previously,” explains Ane.

And while microorganisms had been found before in association with algae, they were believed to be pathogens, not symbionts. “Nobody had studied associations in these freshwater algae. We think some of these associations may be beneficial.”

Genetic features in plants, animals and microbes tend to be preserved and repurposed through evolutionary history. Discovering these pathways allowing associations with beneficial microbes in green algae and in cereals, which now require significant amounts of chemical fertilizer, could enable the engineering in plants of more efficient nutrient acquisition — significantly reducing the need for chemical fertilizers for food and bioenergy production.

The study was supported by grants from the National Science Foundation, UW-Madison and the Bill & Melinda Gates Foundation.

This story was originally published on the UW-Madison News site.

“Happy Days Study” meets the microbiome

Thursday, August 6th, 2015
Members of the Wisconsin Longitudinal Study (WLS) class of 1957

Members of the Wisconsin Longitudinal Study class of 1957 during a 50th reunion held in 2007. The WLS has evolved to become one of the longest-running social science studies ever undertaken and now provides valuable information about the group’s ongoing education, employment, health, family life and aging status. Photo: Jeff Miller

For almost 60 years, the Wisconsin Longitudinal Study (WLS) has closely followed the life course of roughly a third of Wisconsin high school graduates from the class of 1957.

Subjects of the project known as the “Happy Days Study” — one of the most consistent, comprehensive and expansive studies of aging and health in America — have contributed their time for repeated, highly detailed surveys of health, family life and employment. They have given access to medical and life histories, including diseases, health-related behaviors, cognitive status, psychological and physical well-being, and detailed geographical data showing where subjects have lived over the course of their lives. As new molecular assays have been developed, the WLS cohort has also contributed biological samples such as saliva, which can be genotyped.

Now, with the advent of new high-throughput genetic sequencing technologies, a new frontier beckons: the microbiome.

In our gut, each of us has a unique ecosystem composed of hundreds of species of microorganisms, acquired since birth from the environment, our food and the people closest to us. Together with their genes, this collection of microorganisms is known as the microbiome. Humans and other animals are utterly dependent on these microbial hitchhikers to do things like digest food, process nutrients, modulate the immune system and outcompete the pathogenic microbes that sometimes infect us.

Pamela Herd

Pamela Herd

“We know relatively little about the gut microbiome,” explains Pamela Herd, a professor in the University of Wisconsin-Madison’s Robert M. La Follette School of Public Affairs and the principal investigator of the WLS. “But one of the things that is so interesting about it is its plasticity. The broader environment seems to influence its composition.”

To date, studies of human gut microbiota have been limited. The largest study, conducted in 2012 and supported by the National Institutes of Health, sampled “healthy” human microbiomes from 256 people selected non-randomly from St. Louis and Houston. Researchers are also hamstrung by limited environmental information from their subjects. Things like diet, social interaction and where people live are known to influence the composition of the gut’s resident colony of microbes. There is also little known about the microbial communities that colonize the elderly. It is known that gut microbiota in the elderly are more varied from person to person, and that those differences can be associated with health, including frailty, inflammation and obesity.

Federico Rey

Federico Rey

To begin to address some of these limitations, Herd and her WLS colleagues have embarked on a novel collaboration with the lab of UW-Madison bacteriology Professor Federico Rey. With the help of the University of Wisconsin Survey Center, the WLS researchers have collected fecal samples from more than 400 participants in the WLS to begin to map out the health implications of the microbes that live in our gut as we grow old.

“This is not easy data to collect,” notes Rey, who participated in a landmark study while at Washington University showing that the composition of the microbes in the gut can significantly influence metabolism and obesity.

In that study, human microbiota samples were transplanted into germ-free mice to see, among other things, if the mouse recipients would mirror the metabolism or obesity of the human donor, which they in fact did.

“People who are obese have a different microbiome,” says Rey, “and we can colonize mice with human fecal samples to reflect aspects of that phenotype.”

The new effort by WLS and the collaboration with Rey is a rare marriage of biology and social science. The fact that the subjects of the WLS have been intensively tracked for almost 60 years, means the information found in their microbiomes can be correlated with where they lived, who they lived with, their health and employment histories, and even their psychological well-being. Such things as where someone has lived, for example, may be reflected in the gut microbiome because the germs we accumulate in our gut can come from things like soil.

germ-free mice

Nacho Vivas, lab manager at the Rey Lab in the Bacteriology Department at the University of Wisconsin-Madison, tends to the individual enclosures of a group of germ-free mice in their sterile environment and provides them with fresh food. Photo: Bryce Richter

Observations drawn from WLS data can be tested in the context of the microbiome. For example, WLS data suggest that growing up poor can have a “sustained influence on health and mortality across the life course.” In another context, being raised on a farm — as 20 percent of the WLS sample were — seems to have a significant positive influence on health and longevity.

“We have decades of information on social relationships,” says Herd, “and we’re wondering about things like how social relationships affect the microbiome. Every time we shake hands or kiss, we exchange microbes. Some studies have shown that people who are isolated are likely to die younger, but why?”

Exploring the microbiome in the context of the WLS data may help provide some answers because environment and social interaction seem to play such a large role in the composition and changes to the microbiome.

And like genetic information, it may be possible in the future to predict health or prescribe medical interventions based on what your microbiome says about you, says Rey.

“Environment matters,” he argues, “and the things we are going to be looking at promise to take our understanding of that to an entirely new level.”

The new work is being supported in part by a $90,000 interdisciplinary research award from the UW-Madison Office of the Vice Chancellor for Research and Graduate Education with funding from the Wisconsin Alumni Research Foundation.

This story was originally published on the UW-Madison News site.

Bugs to biofuels – Audio

Friday, June 26th, 2015

Bugs to biofuels

Gina Lewin, Research Assistant, Currie Lab
Department of Bacteriology
UW-Madison College of Agricultural and Life Sciences
Phone (608) 262-7538

3:05 – Total Time
0:17 – Challenge to break down biomass
0:49 – The leaf cutter ant
1:22 – Answers in ant trash
1:53 – Microbial communities
2:15 – Why this is different
2:47 – Ants with a Twitter account
2:58 – Lead out


Sevie Kenyon: The path to biofuels led by bugs, we’re visiting today with Gina Lewin, Department of Bacteriology University of Wisconsin-Madison in the College of Agricultural and Life Sciences, and I’m Sevie Kenyon. Gina, tell us what you’re doing with insects related to biofuels.
Gina Lewin: I’m interested in how we can breakdown plant biomass for making biofuels, so breaking down plant biomass is really important if we want to make biofuels from the non food parts of plants like the stalks of the corn, or from poplar trees or different prairie grasses. What I’m doing is looking at insect systems that have evolved to be really good at breaking down plant biomass into simple sugars. Continue reading

Drugs from bugs – Audio

Friday, June 12th, 2015
Ant worker covered in white bacterium. The bacterium produces antibiotics that protect the colony from pathogens. Photo by Don Parson

Ant worker covered in white bacterium. The bacterium produces antibiotics that protect the colony from pathogens. Photo by Don Parson

Heidi Horn, Research Assistant
Department of Bacteriology
UW-Madison College of Agricultural and Life Sciences
Phone (608) 890-0237

Drugs from bugs
3:03 – Total Time
0:15 – Connecting insects to medicine
0:46 – Antibiotics found in ant colonies
1:05 – Long time from the ant to the market
1:25 – About the ants
1:42 – Searching for ants
2:21 – Keeping Panama ants alive in Wisconsin
2:41 – For more information
2:55 – Lead out


Sevie Kenyon: Bugs and drugs, we are visiting today with Heidi Horn Department of Bacteriology University of Wisconsin-Madison in the College of Agricultural and Life Sciences, and I’m Sevie Kenyon.

Heidi, how do we connect bugs with medicine?

Heidi Horn: I know it seems like a strange, strange connection, but our lab is actually doing that every day. We actually study a tropical ant called leaf cutter ants, and they are very cool in many ways. They actually grow a fungus for their food so they are farmers, but it gets even cooler than that. They have an association with a bacterium that makes an antibiotic that protects them so we use antibiotics when we go to the doctor and so almost in the same sense the ants are using antibiotics. Continue reading

Exploring bugs and bioenergy: Gina Lewin’s path to the Currie Lab

Monday, April 6th, 2015

For many college students, summer provides a chance to test-drive future career paths. When Gina Lewin took advantage of such an opportunity, her test drive hit the jackpot.

In the summer of 2009, Lewin participated in a National Science Foundation-funded program called Research Experience for Undergraduates (REU), which invites college juniors and seniors to join research projects around the country.

At the Great Lakes Bioenergy Research Center (GLBRC) at the University of Wisconsin–Madison, Lewin worked in the lab of chemical and biological engineering professor Brian Pfleger. She was tasked with coaxing a bacterium to produce diesel fuel compounds.

As summer progressed, Lewin’s interest in bioenergy and microbiology grew, but she also found herself falling in love with the big research campus of UW–Madison and the city that surrounds it.

“The REU was my first time doing microbiology research,” Lewin says. “I had been thinking about going to graduate school since the end of my freshman year, but being here definitely cemented that interest.”

ants_large horizontal

Ants from the Currie Lab. Photo: Wolfgang Hoffman

She applied for graduate school and joined UW–Madison’s microbiology doctoral training program in the fall of 2010.

Lewin, the daughter of two lawyers, grew up in a semi-rural part of central New Jersey. One of her favorite childhood memories is attending summer nature camps at a nearby environmental education center where she learned to identify the bugs she caught in the woods and streams.

After graduating from high school in 2006, Lewin moved across the country to Pomona College, some thirty miles east of Los Angeles, where she was drawn to science and majored in molecular biology.

But it was not until her REU at UW–Madison that Lewin discovered a connection between her childhood interest in bugs and bioenergy research.

In the lab of GLBRC researcher Cameron Currie, Lewin now studies how insects use microbes to break down cellulose, the sugars found in the cell walls of woody plants, in order to procure nutrient-enriched food. Understanding the insects’ process for breaking down cellulose could ultimately inform GLBRC’s own efforts to convert biomass to ethanol and other biofuels.

Lewin’s particular focus is on the insects’ powerful ability to partner with a community of microbes.

“Scientists have long studied how a single microbe in a flask degrades cellulose,” Lewin says. “But in the environment, organisms don’t exist in isolation; they have evolved to be part of a community. Our goal is to apply the power of these symbiotic relationships to biofuel production.”

Leaf-cutter ants found in tropical rainforests are a particularly impressive example of these mutually beneficial relationships.

Living as a highly organized society in colonies that can grow large enough to be visible from space, the vast majority of leaf-cutter ants work to support their queen. In return, the queen maintains the colony by laying up to 20,000 eggs a day for up to twenty years in the lab.

What is perhaps most remarkable, however, is that the leaf-cutter ants are miniature farmers who have perfected their agricultural activities — deconstructing biomass and cultivating a fungus — over the course of ten million years. Humans, in contrast, have spent a mere 12,000 years developing and fine-tuning their agricultural expertise.

Leaf-cutter ants collect and degrade large amounts of fresh leaves that the fungus converts to food.

“The fungus makes a fuzzy pearl-like structure that contains the nutrients the ants need,” Lewin says. “The larvae and the queen only eat these fungal structures, while the adult workers also feed on leaf sap and fruits.” Some species of leaf-cutter ants even grow a bacterium on their body that protects the fungus from pathogens.

Each colony’s fungus farm consists of a garden, where the plant material is first deposited and partially degraded, and a dump, a dedicated waste management site that may be located under- or aboveground, depending on the ant species.

“Seventy percent of the leaves’ cellulose is carried to the dump for final degradation. It turns out that the dump’s microbial community is much more efficient at degrading cellulose than any individual strain we have studied thus far,” Lewin summarizes her dissertation findings.

Gina Lewin_Cameron Currie

Gina Lewin and thesis advisor Cameron Currie present their research to then-Secretary of Energy Steven Chu. Photo: Matthew Wisniewski

Currie, Lewin’s advisor, is as pleased with these results as with Lewin’s success in obtaining external funding for her work.

“I teased Gina that the offer letter for the National Science Foundation’s predoctoral fellowship [dated around April 1, 2012] was probably an April Fool’s joke,” Currie recalls. “These fellowships are incredibly competitive. I’ve never even heard of anyone getting one in their second year.”

Graduate school clearly suits Lewin well, whether she peers through the microscope, gathers fungal samples in Costa Rica, or applies for a research fellowship.

“In college, I had to choose between ecology and molecular biology,” Lewin remembers. “When I decided to major in molecular biology, I was a little sad to leave behind the outdoor activities we did in the ecology classes. But graduate school has allowed me to bring those two interests back together.”

Last but not least, Lewin has also contributed significantly to GLBRC’s education and outreach efforts.

In the summer of 2011, Lewin worked with high school science teacher Craig Kohn from Waterford, Wis., who participated in GLBRC’s Research Experience for Teachers (RET) program. Together they designed a classroom activity that adapted Lewin’s lab assay for demonstrating the breakdown of cellulose for a high school level.

“We figured out that Craig could make a cheap growth medium for microbes by mixing Miracle Gro fertilizer from a garden center with tap water,” Lewin explains.

To see if an environmental sample, such as a scoop of cow manure, contains microbes capable of growing on a piece of cellulosic filter paper, Kohn’s high school students put the sample, the paper, and the fertilizer in a test tube. The students then quantified cellulose degradation by counting the days until a complete tear was observed in the paper.

The following two summers, Lewin and John Greenler, director of GLBRC’s education and outreach program, presented the activity to teachers attending the Bioenergy Institute for Educators. And in the fall of 2014, the activity was expanded for UW–Madison freshmen and used in a First-Year Interest Group (FIG) course in bioenergy.

“In today’s world, just being a great researcher and doing teaching assistant duty for one semester is no longer enough to become a successful faculty member. Gina is a poster child for the importance of translating her research into engaging classroom material,” Greenler says.

“In the six years since her REU, Gina has grown into a real spokesperson for GLBRC,” Greenler adds.

The GLBRC is one of three Department of Energy Bioenergy Research Centers created to make transformational breakthroughs and build the foundation of new cellulosic biofuels technology. For more information on the GLBRC, visit

This story was originally published on the Great Lakes Bioenergy Research Center website.

Day in the life of a microbiology grad student

Monday, April 6th, 2015

Meet Gina Lewin, a graduate student in the Microbiology Doctoral Training Program. She conducts research in Cameron Currie’s bacteriology lab where she studies microbial communities and leafcutter ant systems. By studying these ants, scientists like Lewin can learn how to break down plants like corn stalks to convert them into biofuels.

Daniel Amador-Noguez engineers better bacteria for biofuels

Tuesday, March 3rd, 2015

In high school,” Daniel Amador-Noguez recalls, “I took a science class where one of the lectures was all about the future – where the research was taking us, what were some potential future discoveries – and I thought, ‘oh, all this sounds really cool, so how come it hasn’t happened yet?’”

Seventeen years later, it’s not at all difficult to square that eager young man with the energetic scientist Amador-Noguez has become. An assistant professor of bacteriology at the University of Wisconsin–Madison and researcher at the Great Lakes Bioenergy Research Center (GLBRC), Amador-Noguez emanates anticipation, for next week’s result, the future of his research, and the future of biofuels.


David Stevenson (left), research specialist, and Daniel Amador-Noguez examine a plate of microbes in the Microbial Sciences Building. Photos by Matthew Wisniewski.

“It’s difficult to come up with a biological process that isn’t affected by bacteria,” he says. “They are virtually everywhere, not just in the environment but also inside our bodies. And if we can improve our understanding of microbes we can do a lot of enormously important things, including improving biofuels.”

Amador-Noguez’s lab focuses on understanding metabolism in biofuel-producing bacteria with the goal of engineering microbes that can more efficiently convert plant biomass to energy. It’s exciting research, but it’s also the kind of data-driven work that Amador-Noguez hungered for from a very early age.

Growing up in Pachuca, a small city in central Mexico, in the 1980s Amador-Noguez struggled to find information on biology, the subject that interested him most. Science education in Mexico at that time was not strong, the Internet was not yet in widespread use, and bookstores were scarce, so Amador-Noguez found himself reading and re-reading the same encyclopedia periodical his mother had arranged to be sent to the house.

“I must have read that encyclopedia three or four times by the time I was nine or ten,” he says. “My favorite volume had a section on genetic mutations with all this classic imagery of flies, where you have all these different flies with three eyes or four wings. It’s a bit creepy but for a kid that’s really interesting!”

After high school, Amador-Noguez headed to the Monterrey Institute of Technology in northern Mexico, where he had his first real exposure to science, including laboratory research. Since he hadn’t been able to find a good biology program in Mexico, he majored in chemistry.

After graduating from Monterrey in 2001, Amador-Noguez pursued a doctorate in molecular genetics at Baylor College of Medicine in Houston, Texas. While studying the molecular mechanisms of aging in the long-lived Ames Dwarf mice and Little mice, Amador-Noguez discovered that liver metabolism played a key role in the mice’s longevity. His research has focused on metabolism ever since.

He left Baylor with doctorate in hand in 2007 and headed to Joshua Rabinowitz’s lab at Princeton University to do a postdoctoral fellowship in cellular metabolism. He began using mass spectrometry, an analytical chemistry technique, to study the metabolism of bacteria related to biofuel production, and there his interest in biofuels was born.

After five years at Princeton, Amador-Noguez joined UW–Madison and GLBRC in the fall of 2013. To study bacteria in his lab, he now uses metabolomics, a relatively new, systems-level approach to understanding the behavior of metabolites and the regulation of metabolism in microorganisms.

Amador-Noguez uses analytical tools such as mass spectrometry and liquid chromatography, which enable him to identify and measure most of the metabolites inside bacteria, as well as determine the bacteria’s metabolic flux, or which of the bacteria’s metabolic pathways are the most active (or inactive) as the cell converts nutrients into the energy and building blocks it needs to grow.


The Amador-Noguez Lab

Metabolic flux, the extent to which carbon is passing through one metabolic pathway versus another, is of particular importance to biofuel production. Often, the way to engineer bacteria that are more efficient at converting biomass into biofuels is to maximize flux through pathways known to be involved in biofuel production.

The linked nature of metabolic pathways also makes inhibition of any one pathway a significant issue in studying bacteria; if one pathway is not working, a cell will simply shut down the rest of its metabolism.

In one recent GLBRC project, Amador-Noguez and his team sought to understand how a particular toxin inhibits the conversion of plant sugars into biofuels. The toxin in question is produced from lignin – the woody backbone of plants – during the process of breaking down plant biomass into its sugar components such as glucose.

Amador-Noguez discovered that, in general, these “lignotoxins” are powerful inhibitors of the enzymes the cell needs to synthesize nucleotides, which are essential to the cell’s DNA.

Now that Amador-Noguez knows which enzymes are affected, he and other researchers can find a way to direct those particular enzymes to be more resistant to lignotoxins. Or he can break the regulatory connections between nucleotide biosynthesis pathways and fermentation pathways so that the bacteria would simply remain unaware that a particular biosynthetic pathway was not functioning properly, and would thus continue to produce biofuels.

Looking to the future, Amador-Noguez is excited about the possibility of developing new metabolomics tools that could help reveal how metabolism is regulated within entire bacterial communities, and not just in isolated bacterial species. He says that much remains unknown about how bacteria play nice with one another but that gaining an understanding of the community’s rules could yield powerful results.

“If we could understand how different bacteria interact with each other metabolically in these complex bacterial communities we could do a lot of things,” he explains. “We could understand what shapes the bacterial communities living inside of our bodies, which would have important ramifications for human health, and we could engineer each bacteria in those communities to specialize in doing one thing, which could make the process of biofuel production much more efficient.”

“Biofuels,” he adds, “are an important solution for many of our energy issues. We’re always going to need fuel and we’re always going to need chemicals. And the biological production of biofuels and high-value chemicals from plant biomass is one of the most promising strategies for the sustainable generation of these essential commodities.”

Like many scientists working today on energy-related research, Amador-Noguez remains motivated by the impact his day-to-day research could have on the national and global energy picture, as well as by his long-burning desire to make important advances happen.

“The fact that what we’re doing can contribute to solving big problems in society, that is very motivational,” he says.

This story was originally published on the Great Lakes Bioenergy Research Center website.