Jo Handelsman named director of Wisconsin Institute for Discovery

Tuesday, November 29th, 2016

The Wisconsin Institute for Discovery (WID) will usher in a new year with a new director: Jo Handelsman, a Yale University professor and the associate director for science in the White House Office of Science and Technology Policy.

“I’m thrilled to welcome Dr. Handelsman back to Madison. In addition to being a world class researcher, she is nationally renowned for her impact as a teacher, role model, mentor, and an advocate for women and minorities in science careers,” says Marsha Mailick, UW–Madison’s vice chancellor for research and graduate education. “Jo is an inspiring individual who brings creativity, a spirit of experimentation, exemplary leadership skills and a commitment to rigor, that make her a great fit for UW–Madison.”

Jo Handelsman

Jo Handelsman

Handelsman begins her position on Feb. 1 and will report to Mailick. In addition to being named WID director, Handelsman will be honored with a distinguished named chair.

At Yale, Handelsman is a Howard Hughes Medical Institute Professor, the Frederick Phineas Rose Professor in the Department of Molecular, Cellular and Developmental Biology, and founder of the Yale Center for Scientific Teaching. For the last two years, she also has held the White House position.

Mailick calls this an exciting time for WID as it begins a new chapter under Handelsman’s leadership.

“I’m confident that moving forward WID will be a catalyst for discovery at UW–Madison,” Mailick says. “Jo is committed to WID’s mission and was instrumental in developing it while at UW–Madison several years ago.”

Handelsman has a long history with UW–Madison, having earned her Ph.D. from the university in molecular biology in 1984. She has held several positions at UW–Madison, first as assistant professor in the Department of Plant Pathology from 1985 to 1991, then associate professor in the department from 1991 to 1995, and professor in the department from 1995 to 2007.

She became professor and chair of the UW–Madison Bacteriology Department in 2007 and served in that role until 2009.  She was co-founder of the Women in Science and Engineering Leadership Institute at UW–Madison and co-director from 2001 to 2007 and founded the Wisconsin Program for Scientific Teaching.

Among her many awards, she has received an Honorary Doctor of Science from Bard College in 2013, the American Society for Microbiology Graduate Microbiology Teaching Award in 2012, and was named one of the “Ten People Who Mattered this Year” by Nature in 2012. In 2011, President Obama awarded Handelsman the Presidential Award for Science Mentoring.

Her book Entering Mentoring: A Seminar to Train a New Generation of Scientists, and associated course, are used by more than 150 U.S. universities. She was editor-in-chief of the academic journal DNA and Cell Biology. She’s also nationally recognized for her work on understanding implicit biases that shape scientist attitudes and their behaviors towards other people.

Handelsman’s research interest lies in understanding the structure and function of microbial communities and the signals that govern them through the application of metagenomics, genetics and small molecule chemistry. Her areas of emphasis include biochemistry and genetic regulation of antibiotic production, microbial diversity, antibiotic resistance, and symbioses in communities in soil, on plant roots and in insect guts. Her integration of biology with computational sciences and chemistry reflect the interdisciplinary nature of WID’s mission.

Handelsman cites her commitment to UW–Madison as a land grant university and its mission to public education and the Wisconsin Idea as reasons to return to UW.

“I am thrilled to be returning to UW–Madison, one of the nation’s great public universities,” Handelsman says. “The high quality of the faculty, staff and students — as well as the extraordinary commitment of the university to the State of Wisconsin through the Wisconsin Idea — make UW a truly singular institution. It is one of the few universities with the breadth and versatility to address the challenges of the future.”

Handelsman says WID can be a catalytic force for innovative research in the lab, as well as entrepreneurship. She refers to WID’s potential as octopoid — allowing communities and culture to take over and allow for random collisions and inspiration that lead to big breakthroughs.

“I believe WID represents an essential piece of Wisconsin’s future — a showcase for the wonders of science and technology, an intersection for the public and the academic community, and a place for fusion of science and the arts — all of which can unite to fuel Wisconsin’s innovation economy,” Handelsman says.

“Jo brings an exceptional wealth of accomplishments in research, modern teaching methods and science policy from her diverse experience spanning academia to the White House,” says Paul Ahlquist, professor of molecular virology, oncology and plant pathology and an investigator of the Morgridge Institute for Research and the Howard Hughes Medical Institute. Ahlquist chaired the 10-member committee that chose finalists for the position. “The combination of these broad insights and outside experience with Jo’s inside knowledge of UW–Madison makes her return a major win for the entire campus.”

“We had a very strong pool of candidates for the WID director position,” says Mailick. “I’d like to thank the search committee for its generous donation of time and commitment to the process, and Christopher Bradfield, who has served as interim director of the Wisconsin Institute for Discovery.”

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

Gut’s microbial community shown to influence host gene expression

Friday, November 25th, 2016
Nacho Vivas

Nacho Vivas, lab manager at the Rey Lab in the Bacteriology Department at the University of Wisconsin-Madison, checks on a group of germ-free mice inside a sterile lab environment. Photo: Bryce Richter

In our guts, and in the guts of all animals, resides a robust ecosystem of microbes known as the microbiome. Consisting of trillions of organisms — bacteria, fungi and viruses — the microbiome is essential for host health, providing important services ranging from nutrient processing to immune system development and maintenance.

Now, in a study comparing mice raised in a “germ free” environment and mice raised under more typical lab conditions, scientists have identified yet another key role of the microbes that live within us: mediator of host gene expression through the epigenome, the chemical information that regulates which genes in cells are active.

John Denu

John Denu

Writing online Nov. 23 in the journal Molecular Cell, a team of researchers from the University of Wisconsin–Madison describes new research helping tease out the mechanics of how the gut microbiome communicates with the cells of its host to switch genes on and off. The upshot of the study, another indictment of the so-called Western diet (high in saturated fats, sugar and red meat), reveals how the metabolites produced by the bacteria in the stomach chemically communicate with cells, including cells far beyond the colon, to dictate gene expression and health in its host.

“The bugs are somehow driving gene expression in the host through alteration of the epigenome,” explains John Denu, a UW–Madison professor of biomolecular chemistry and a senior researcher at the Wisconsin Institute for Discovery, and a co-author of the new study. “We’re starting to understand the mechanism of how and why diet and the microbiome matter.”

The study, which was led by Kimberly Krautkramer, an MD/Ph.D. student in the UW School of Medicine and Public Health, revealed key differences in gene regulation in conventionally raised mice and mice raised in a germ-free environment. The mice were provided with two distinct diets:  one rich in plant carbohydrates similar to fruits and vegetables humans consume; the other mimicking a Western diet, high in simple sugars and fat.

Kimberly Krautkramer

Kimberly Krautkramer. Photo: Patricia Pointer/Wisconsin Institute for Discovery

A plant-based diet, according to Federico Rey, a UW–Madison professor of bacteriology and also a co-corresponding author of the new report, yields a richer microbiome: “A good diet translates to a beautifully complex microbiome,” Rey says.

“And we see that the gut microbiome affects the host epigenome in a diet-dependent manner. A plant-based diet seems to favor host-microbe communication.”

The new Wisconsin study shows that a small set of short-chain fatty acids produced as the gut bacteria consume, metabolize and ferment nutrients from plants are important chemical messengers, communicating with the cells of the host through the epigenome. “One of the findings here is that microbial metabolism or fermentation of plant fiber results in the production of short-chain fatty acids. These molecules, and potentially many others, are partially responsible for the communication” with the epigenome, says Denu.

In the study, the gut microbiota of the animals that were fed a diet rich in sugar and fat have a diminished capacity to communicate with host cells. According to the Wisconsin team, that may be a hint that the template for a healthy human microbiome was set in the distant past, when food from plants made up a larger portion of diet and sugar and fat were less available than in contemporary diets with more meat and processed foods.

Federico Rey

Federico Rey

“As we move away from plant-based diets, we may be losing some of that communication between microbes and host,” notes Rey. “With a Western-type diet, it seems like the communication between microbes and host gets lost.”

Foods rich in fat and sugar, especially processed foods, are more easily digested by the host, but are not necessarily a good source of food for the flora inhabiting the gut. The result is a less diverse microbiome and less communication to the host, according to the researchers.

A surprising finding in the study is that the chemical communication between the microbiome and host cells is far reaching. In addition to talking to cells in the colon, the microbiome also seems to be communicating with cells in the liver and in fatty tissue far removed from the gut. That, says Denu, is more evidence of the importance of the microbiome to the well-being of its host.

The kicker experiment in the study, says Denu, was providing mice raised in a germ-free environment with three different short-chain fatty acids that the study showed to be important messengers to the epigenome. The supplement was enough to promote the kind of healthy interplay between microbiota and host cells seen in mice given a diet high in plant fiber.

“It helps show that the collection of three short-chain fatty acids produced in the plant-based diet are likely major communicators,” adds Denu. “We see that it is not just the microbe. It’s microbial metabolism.”

This research was funded by the National Institutes of Health under grants F30 DK108494 and GM059789-15/P250VA. Additional support was provided by the Clinical and Translational Science Award program through the NIH National Center for Advancing Translational Sciences grants UL1TR000427, KL2TR000428, DK108259, and DK101573.

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

Beyond genes: Protein atlas scores nitrogen fixing duet

Tuesday, October 18th, 2016

Of the many elusive grails of agricultural biotechnology, the ability to confer nitrogen fixation into non-leguminous plants such as cereals ranks near the very top.

Doing so is a huge challenge because legumes partner with bacteria called rhizobia in a symbiotic waltz that enables plants to draw sustenance from the air and transcend the need for environmentally harmful chemical fertilizers. The natural process is central to the practice of crop rotation, widely used to prevent exhaustion of soil from crops such as corn, which depend on the application of synthetic fertilizers.

Flowerleafstem1

Flowering Medicago truncatula. Photo: Dhileepkumar Jayaraman and Shanmugam Rajasekar/Ane lab

The fact that two distinct and very distantly related organisms — a plant and a bacterium — can partner to perform the feat of drawing life-sustaining nitrogen from the atmosphere is just one of the challenges plant engineers face as they seek to confer this quality on other important crops.

The answer to the challenge, however, may be one big step closer with the publication Oct. 17 of a massive atlas of plant and bacterial proteins at play as the symbiotic process plays out between plant and microbe.

Writing in the current Nature Biotechnology, a group from the University of Wisconsin–Madison details more than 23,000 plant and bacterial proteins and the molecular controls by which they execute the beneficial relationship. The atlas, possibly the most exhaustive proteomic inventory of any kind to date, shows in minute detail the interplay of proteins as rhizobia colonize root nodules on the model legume Medicago truncatula.

“We can see deeper into the proteome than ever before,” explains Joshua Coon, a UW–Madison professor of biomolecular chemistry and chemistry, and a corresponding author of the new atlas. “We’re able to use technology to provide an unprecedented view of these proteins.”

Joshua Coon

Joshua Coon

That new picture, he says, takes our understanding of the mechanics of nitrogen fixation to an unprecedented level of detail. Because proteins are regulated by genes, the new atlas could ultimately help inform a strategy for engineering the nitrogen-fixing ability of legumes into other plants.

“Linking the protein information with the genetic networks is important,” notes Jean-Michel Ane, a UW–Madison professor of bacteriology, also a corresponding author of the new report. “It allows us to see patterns by correlating gene expression with proteins.”

The new atlas was compiled using potent new mass spectroscopy technology, says Coon, a leading authority on the technique that permits scientists to parse a sample into its many constituent components and measure them in exquisite detail. “The complexity of measuring the number of proteins in a sample is mind-boggling,” Coon says. “Knowing the genes isn’t enough. There are millions and billions of ways proteins can be modified to give them a new mission. All of this information at the protein level is novel, and we can look globally at all these molecules and how they are modified and make some predictions about function.”

Jean-Michel Ane

Jean-Michel Ane

The new study, supported mostly by grants from the National Science Foundation, was led by Harald Marx, a postdoctoral fellow in the UW–Madison Genome Center; and Catherine Minogue, a former graduate student in the UW–Madison Department of Chemistry. Michael Sussman, a UW–Madison professor of biochemistry, and Sushmita Roy, a professor of biostatistics and medical informatics, also contributed to the study.

The Wisconsin researchers stress that while the new protein atlas will be an important cipher for decoding the molecular details of nitrogen fixation symbiosis, the goal of conferring the trait on plants other than legumes remains in the distant future.

The Wisconsin work was conducted using the model legume Medicago truncatula and its rhizobial symbiont Sinorhizobium meliloti, a system developed for genetics research about 20 years ago.

“It is a very close relative to alfalfa,” says Ane, referencing the legume widely used in agriculture as part of crop rotation systems.

Banner photo: Nodules on the roots of the model legume Medicago truncatula. The root nodules are where the process of nitrogen fixation takes place. The plant and its bacterial symbiont were used in a landmark University of Wisconsin–Madison study to detail the proteins involved in the process of nitrogen fixation, where plant nutrients are drawn from the atmosphere. Photo: Matthew Crook/Ane lab

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

Bacteriology professor Jade Wang named HHMI Faculty Scholar

Thursday, September 22nd, 2016
Jue Wang HHMI


Jue “Jade” Wang (right), associate professor of bacteriology, works with student Christina Johnson in Wang’s lab in the Microbial Sciences Building. Wang is the recipient of a Howard Hughes Medical Institute Faculty Scholar award. Photo: Bryce Richter

Jue “Jade” Wang, an associate professor of bacteriology at the University of Wisconsin–Madison, has been named a Howard Hughes Medical Institute (HHMI) Faculty Scholar.

The recognition comes with research funding for Wang and her laboratory each year for the next five years, as well as support for the institution in order to help cover the administrative costs associated with her work.

“We’re very happy that she’s gotten this award,” says Rick Gourse, professor of bacteriology and a colleague of Wang’s in the bacteriology department.

The Faculty Scholars Program, created through a partnership between HHMI, the Bill and Melinda Gates Foundation and the Simons Foundation, is intended to boost the work of promising early-career scientists who have already demonstrated excellence in their fields.

Wang is one of 84 Faculty Scholars recognized at 43 institutions across the U.S, according to HHMI. This is the first time it has been awarded. Wang was chosen from among 1,400 applicants at 220 institutions.

This year’s program will invest around $83 million in research support for recipients and their institutions. Grant awards range from $600,000 up to $1.8 million.

“Support for outstanding early-career scientists is essential for continued progress in science in future years,” Marian Carlson, director of life sciences at the Simons Foundation, said in a statement issued by the philanthropies.

Wang, who has been at UW–Madison since 2012, studies the physical conflicts between the machinery in bacterial cells responsible for making copies of DNA and the machinery responsible for creating RNA from DNA. She is interested in how such conflicts, in the form of collisions, have shaped the evolution of microbial genomes and how bacterial cells avoid them by coordinating cellular responses to stress.

Stress on bacterial cells such as nutrient deprivation or exposure to antibiotics can exacerbate these conflicts.

“DNA-RNA polymerase collisions are a big problem because they can result in mutations in the bacterial genome,” says Gourse, who originally helped recruit Wang to UW–Madison. These mutations can lead to the development of antibiotic resistance.

According to the Faculty Scholars website, the trajectory for early-career scientists has become much less certain as the competition for grant support has intensified in recent years. In the last two decades, the National Institutes of Health research award success rate for scientists in the U.S. has declined dramatically. The average age at which an investigator receives his or her first major research grant has, meanwhile, increased.

“Basic science has not fared well in our current funding climate,” says Gourse. “This award will allow her to do things she would not be able to do otherwise.”

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

Collisions during DNA replication and transcription contribute to mutagenesis

Wednesday, June 29th, 2016

When a cell makes copies of DNA and translates its genetic code into proteins at the same time, the molecular machinery that carries on replication and the one that transcribes the DNA to the mRNA code move along the same DNA double strand as their respective processes take place. Sometimes replication and transcription proceed on the same direction, but sometimes the processes are in a collision course. Researchers at Baylor College of Medicine and the University of Wisconsin-Madison have determined that these collisions can significantly contribute to mutagenesis. Their results appear today (June 29) in Nature.

Jue Wang

Jue D. Wang

“We first developed a laboratory assay that would allow us to detect a wide range of mutations in a specific gene in the bacteria Bacillus subtilis,” said corresponding author Jue D. Wang, who was an associate professor of molecular & human genetics at Baylor when a portion of the work was completed. She is currently an associate professor of bacteriology at the University of Wisconsin-Madison. “In some bacteria, we introduced the gene so the processes of replication and transcription would proceed on the same direction. In other bacteria the gene was engineered so the processes would collide head-on.”

The researchers discovered that when replication and transcription were oriented toward a head-on collision path the mutation rate was higher than when their paths followed the same direction. Furthermore, most of the mutations caused by replication transcription conflicts were either insertions/deletions or substitutions in the promoter region of the gene, the region that controls gene expression.

“People have mostly been looking at mutations in the DNA sequence that codes for protein, but in this paper we found that the promoter, the regulatory element of gene expression, is very susceptible to mutagenesis,” said Wang, “and this susceptibility is facilitated by head-on transcription and DNA replication.”

Promoters control how much of a gene is transcribed, for instance, particular mutations in promoters may enhance or reduce the production of proteins, or silence them completely. These genetic changes in gene expression may affect an organism’s health.

“The mutation mechanism we identified is not just applicable to our experimental system, but can potentially contribute to mutations that alter gene expression in a genome-wide scale, from bacteria to human,” said Wang.

Other contributors to this work include T. Sabari Sankar, Brigitta Wastuwidyaningtyas, Yuexin Dong, and Sarah Lewis.

This work was supported by the National Institutes of Health Director’s New Innovator Award DP20D004433.

UW-Madison seeks to capitalize on push to harness helpful microbes

Tuesday, June 14th, 2016
Microbiome bacteria

In this scanning electron microscope image, the bacteria (Acetobacter xylinum) is producing cellulose nanofibers, which are incredibly strong for how light they are. Engineers use the nanofibers to create materials that have a wide range of uses, from strong composites to tissue engineering. Photo: Thomas Ellingham, UW-Madison mechanical engineering graduate student

Since the 17th century, when Antonie van  Leeuwenhoek first observed microorganisms through the lens of a rudimentary microscope, humans have slowly come to appreciate that ours is a germy world.

Through the ages with van Leeuwenhoek, Louis Pasteur and Robert Koch, the 19th century scientist who found that microorganisms could cause disease, human awareness of the microbial world and its importance has expanded to help underpin critical medical and agricultural discoveries, such as antibiotics and nitrogen-fixing bacteria, as well as to make us masters of the organisms that enrich our lives and diets through ordinary bread and wine.

In more recent years, microbes have proved their worth through things like polymerase chain reaction, a now common method to amplify DNA in the lab, in forensics and in medicine. The process depends on an enzyme from a bacterium retrieved from a hot spring in Yellowstone National Park in the 1960s and fuels billions of dollars in economic activity annually. In addition, the re-tasking of a natural microbial immune system, CRISPR, has enabled precise genome editing from microbes to plants and animals.

Tim_Donohue

Timothy Donohue. Photo: Great Lakes Bioenergy Research Center

Now, seeking to further harness microbes’ many uses, the federal government has launched the National Microbiome Initiative (NMI) to “foster the integrated study of microbiomes across different ecosystems.”

Microbiomes are defined as communities of microorganisms that live on or in people (and other animals), plants, soil, oceans and the atmosphere.

The initiative will put us in a position to better understand microbes in context and how they work, explains University of Wisconsin—Madison bacteriology Professor Timothy Donohue. Its resources will depend much on the next federal budget, but various funding agencies as well as private organizations have committed to finding new support to enhance budgets for work related to the initiative.

“It is a scientific fact that ‘microbes touch everything,’ from the food we eat, the air we breathe and the water we drink,” says Donohue. “They are the master chemists of the universe, responsible for the world around us, and are intimately linked to the future health and evolution of the planet and its inhabitants.”

UW-Madison, Donohue argues, has both strengths and challenges in terms of capitalizing on the initiative. “Wisconsin has a history of and currently benefits by having many of the global thought leaders in microbiology,” he says. “However, to realize the potential of the NMI, we can benefit from leaders from disciplines who traditionally have not worked in the microbial sciences.”

Trina McMahon

Trina McMahon. Photo: Bryce Richter

In addition to strong programs in microbiology, he lists Wisconsin’s disciplinary breadth and long history of interdisciplinary research as assets. Researchers in fields such as chemistry, engineering, business and ethics will work to demystify microbiomes, how they function and how they might be exploited for the benefit of human health, food and energy production, environmental remediation and basic discovery.

A challenge, he says, will be aligning the technologies necessary to be successful in what is sure to be a competitive market for both capital and intellectual resources.

“There are major technology areas of need in this arena, including data analysis, modeling, imaging, technology development, biodesign, materials science, biomanufacturing and others,” Donohue says. “Some of these are common to this initiative and others, so there is intense national and international competition for leaders in these emerging areas.”

Trina McMahon, a UW–Madison professor of bacteriology and civil and environmental engineering, is cautiously optimistic about the national microbiome push, if for no other reason than it puts a spotlight on a corner of biology that is only now wending its way into public consciousness.

“The buzz is awesome,” she says. “Bringing the spotlight to the microbiome generally lets people know it’s not just about the gut microbiome,” an area that has received notoriety due mostly to its implications for human health.

McMahon studies microbial ecology in freshwater systems such as Lake Mendota and in the sludge processed at wastewater treatment plants. Her group is particularly interested in organisms that store phosphorus, a chemical nutrient and pollutant that helps spur the lake’s epic algae blooms.

Federico_Rey

Federico Rey

At UW–Madison, exploration of the microbiome is occurring in many different labs and contexts, ranging from surveys of the microbiomes of the bat wing, copepods and Lake Michigan algae to the gut microbiomes of the Wisconsin high school class of 1957 as part of the Wisconsin Longitudinal Study (WLS).

Bacteriologist Federico Rey, who helps lead the WLS microbiome effort, is excited about the national push, but is naturally concerned about the competition. “I think it is really exciting to see how much interest there is in this field. Funding for this kind of research is going up, but it is nerve-wracking to see how much money other universities are putting into it. How is the University of Wisconsin going to compete?”

Wisconsin’s strengths, he says, reside in breadth of expertise, “a collaborative spirit and fantastic students.” But to be successful in a big way will require bringing all of those things and associated technologies — rapid gene sequencing, bioinformatics, computational resources and biologists — together to solve big problems.

Melissa-Christopherson

Melissa Christopherson

The microbiome can also be a powerful teaching opportunity. Melissa Christopherson, a faculty associate in the Department of Bacteriology, took her microbiology capstone students on a tour of the microbiome of the human mouth this past semester, comparing the oral microbiomes of student athletes to see if there were differences in the microbial communities in elite athletes compared to others and if diet had an influence on the microbial cast of characters. The project’s findings are now being prepared for publication.

“One of the aims of this initiative is education,” says Christopherson, who was on hand for the May 13 White House summit where the initiative was announced by Jo Handelsman, a former UW–Madison professor of bacteriology and now associate director for science in the White House Office of Science and Technology Policy.

“There are only one or two examples of a course like this around the country,” Christopherson notes. “The students in this course got their money’s worth. They worked their butts off. A project like this is a way to summarize a lot of the things they’ve learned.”

The initiative rests on the growing array of technologies that make the sequencing and analysis of genetic material cheap and easy, says civil and environmental engineering Professor Dan Noguera. Most microorganisms can’t be cultured in the lab, but they can be cracked open and their genetic material can be plumbed with growing speed and accuracy.

U.W. Madison College of Engineering Dept of Civil & Environmental Engineering Portraits of faculty & staff

Dan Noguera

“We’re able to do things we weren’t able to do 10 or 12 years ago,” says Noguera, who uses a Madison sewage treatment plant as a laboratory. “There are some very sophisticated tools and models, but only a few people are good at using them and interpreting them, so the hope is there will be some synergy.”

One potential upshot of the initiative, he observes, is the opportunity for the development of centers on the scale of the Department of Energy’s Great Lakes Bioenergy Research Center, a collaboration of UW–Madison and Michigan State University whose mission is to develop the next generation of biofuels.

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

Chemistry lessons from bacteria may improve biofuel production

Thursday, June 9th, 2016

If you’re made of carbon, precious few things are as important to life as death.

A dead tree may represent a literal windfall of the building blocks necessary for making new plants and animals and the energy to sustain them.

“The recycling of plant carbon is fundamental to the function of our ecosystems,” says Cameron Currie, professor of bacteriology at the University of Wisconsin–Madison. “We get food, water, air, energy — almost everything — through those ecosystem services. It’s how our planet operates.”

But the component parts of a dead tree were carefully assembled in the first place, and don’t just fall apart for easy recycling.

In the case of cellulose — a key structural component in plant cell walls and the most abundant organic compound in life on land — a world of specialized microbes handles this careful deconstruction. Much of that work is done by fungi growing on decaying plants, but bacteria in the soil, in the guts of animals like cows and working alongside insects, get the job done, too.

cellulosetesttubes

Researchers tried to grow different strains of Streptomyces bacteria on dead plant material (filter paper). Successful cellulose processing strains tapped special genes to produce enzymes that break down cellulose. Photo: Currie Lab/UW-Madison.

A new analysis of a group of bacteria called Streptomyces reveals the way some strains of the microbe developed advanced abilities to tear up cellulose, and points out more efficient ways we might mimic those abilities to make fuel from otherwise unusable plant material.

Streptomyces were long thought to be prominent contributors at work in breaking down cellulose, and to be equally active in the cause across hundreds or thousands of strains of the bacteria.

“That assumption — which is based on a very good, old study of one type of Streptomyces — is not right on the mark,” says Brian Fox, a UW–Madison biochemistry professor and co-author of the study published today in the journal PLOS Biology. “What we see now is that there’s a relatively small group of types of Streptomyces that is far more effective at breaking down cellulose, and a much larger group that is far less effective.”

The UW–Madison researchers measured the relative abilities of more than 200 types of Streptomyces bacteria by growing them on simple sugar and on a good source of cellulose: filter paper (which is made of dead trees).

They were able to collect the genomes of more than 120 of those strains, and identify the genes — and the ways key genes were expressed — that set strong cellulose degraders apart from poor ones.

“The strains that aren’t good at degrading cellulose mostly express the same genes whether we grow them on glucose or on plant material,” says Gina Lewin, a bacteriology graduate student and study co-author. “The strains that are really good at degrading cellulose totally change their gene expression when we grow them on plant material.”

The successful Streptomyces strains — which were typically those found living in communities with insects — ramp up production of certain enzymes, the proteins that do the cleaving and dissolving and picking apart of cellulose.

celluloseStreptomyces

Counter to long-held belief about the bacteria Streptomyces, seen growing here in a petri dish, the ability to break down a stubborn molecule in plant cell walls called cellulose may be limited to just a few gifted strains. Photo: Adam Book/UW-Madison

“There are families — six or eight or maybe 10 of these enzymes — that all of the active Streptomyces have,” Fox says. “And this paper shows that the most abundant one of them has to be there or the whole thing collapses.”

It’s the particular combinations of enzymes that makes the research useful to scientists working on biofuels.

Biofuels are typically made from the sugars easily extracted from the same parts of plants we eat.

“We eat the kernels off the corn cob,” Currie says. “But most of the energy in that corn plant is in the part which is not digestible to us. It’s not in the cob. It’s in the green parts, like the stalk and the leaves.”

Evolving microbes like Streptomyces have been sharpening the way they make use of those parts of plants almost as long as the plants themselves have been growing on land. That’s hundreds of millions of years. On the other hand, the Department of Energy’s UW–Madison-based Great Lakes Bioenergy Research Center, which funded the Streptomyces study, was established in 2007.

“The natural world is responding to the same kind of things that humans are,” Fox says. “We need to get food. We need to get energy. And different types of organisms are achieving their needs in different ways. It’s worth looking at how they do it.”

The new study identifies important enzymes, and new groups of enzymes, produced when Streptomyces flex particular genes. If they represent an improvement over current industrial processes, the microbes’ tricks could make for a great boon to bioenergy production.

“For a cellulosic biofuel plant, enzymes are one of the most expensive parts of making biofuels,” Lewin says. “So, if you can identify enzymes that work even just slightly better, that could mean a difference of millions of dollars in costs and cheaper energy.”

Banner photo: The ability to break down the cellulose in plant material is rare in Streptomyces bacteria, except in strains that live alongside insects — honeybees, leaf-cutter ants (above), some beetles —that eat or make use of the woody parts of plants. Photo: Don Parsons/UW-Madison.

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

Xylome’s quest to lower the cost of cellulosic ethanol

Monday, May 23rd, 2016

In their lab on a 20-acre prairie in Madison, Wisconsin, Xylome scientists are busy tinkering with the yeasts that live in the bellies of wood-boring beetles. A spin-off from the Great Lakes Bioenergy Research Center (GLBRC), Xylome is lowering the cost of making ethanol by creating new yeast strains that more efficiently convert cellulosic biomass to fuel.

While the early stages of biofuel manufacturing focused on fermenting corn grain to ethanol, corn is not the only available feedstock for making biofuel. Cellulosic biomass – i.e., wood, perennial grasses, and the non-food portion of plants – offers another, arguably more sustainable feedstock for fuels.

GLBRC-Tom-Jeffries

Tom Jeffries (L) and Tom Kelleher (R) conduct R&D and provide research services from Xylome’s labs at University Research Park, Madison, WI.

And yet developing an economically viable cellulosic biofuel pipeline remains a technically challenging endeavor. Compared to corn, the sugars in cellulosic biomass are much more difficult to access and convert to fuel. The sugar xylose, in particular, which accounts for up to 20 –30% of the dry weight of non-food plants, is notoriously difficult to ferment.

“In order to make ethanol out of cellulosic biomass economically,” says Tom Jeffries, Xylome founder and UW–Madison professor emeritus of microbiology and bacteriology, “the technical problem of how to ferment xylose needed to be solved. It’s a problem I’ve worked on for decades.”

It’s also a problem that got a lift in 2006, when Louisiana State University biologist Meredith Blackwell discovered xylose-fermenting yeasts in the guts of wood-boring beetles. Well-acquainted with Jeffries’ research, Blackwell sent him samples of a particularly interesting yeast species she named Spathaspora passalidarum, and it has been the focus of his work ever since.

“These yeasts inhabit the mid-gut,” says Jeffries, “where they consume the sugars the beetles chew on. They have a huge capacity for degrading not only xylose and other complex sugars, but also cellulose.”

Engineering S. passalidarum to even more effectively ferment xylose and other plant sugars is the work that defines Xylome.

Sequencing the S. passalidarum genome and deepening their understanding of the yeasts’ physiology and biochemistry has allowed Xylome scientists to increase the rate and efficiency of the yeast’s ability to ferment sugars, including xylose, to ethanol.

“We don’t introduce any extraneous genes in this process,” says Jeffries. “We take a native organism with a desirable capability, modify the organism’s genes in useful ways, and put them back into the cell. And it’s working! They’re hardy organisms – it’s not difficult to scale up the process.”

GLBRC-yeast

A microscopic image of one of Jeffries’ yeast strains.

Jeffries emphasizes that Xylome is not focused on establishing new biofuel facilities. Existing ethanol plants, he says, are already built just where they need to be – in the middle of fields, adjacent to railroad tracks, and on rivers.

“Ethanol plants have easy access to feedstocks, transport, and towns that can provide labor. They’ve obtained air and water permits and have community acceptance and support – all very important things!” Jeffries says. “And none of these things has to change when a plant shifts from processing grain to processing cellulosic feedstocks if you have the right fermentation capability.”

Xylome’s first-generation product, a cellulose- and xylose-fermenting yeast strain developed with GLBRC support, will debut at the International Fuel Ethanol Workshop & Expo in June 2016. And Jeffries is confident that Xylome’s product will go a long way in helping grain ethanol producers enter the market for second-generation, cellulosic fuels and chemicals.

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 GLBRC, visit www.glbrc.org or visit us on twitter @glbioenergy.

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

Panda poop study provides insights into microbiome, reproductive troubles

Wednesday, May 18th, 2016

A stomachache can put a real damper on your love life — especially if you’re a giant panda.

One minute it’s breeding season and you’re happily dining on fresh bamboo leaves, the next you’re left clutching your stomach while your gastrointestinal lining passes through your system. It exits your body as a thick, gooey, gelatinous mass.

Le Le stalk

Le Le, a male giant panda at the Memphis Zoo, feeds on a bamboo stalk. Researchers analyzed the percentage of feeding time Le Le and his female zoo mate, Ya Ya, spent feeding on bamboo leaves relative to stalks. Photo: Candace Williams

This is exactly what seems to happen to captive giant pandas, and the researchers behind a new study published in Frontiers in Microbiology are beginning to suspect it may play a role in their struggles to reproduce.

“We think they are sloughing off the internal mucous membrane of their gastrointestinal tract and because of this, they get really sick, which coincides with gestation,” says Garret Suen, a University of Wisconsin–Madison professor of bacteriology and co-author of the panda poop and feeding behavior study. “The pandas stop eating and they produce these painful, membranous fecal pellets.”

No one quite understands why these gelatinous masses, called mucoids, happen but Suen and his co-authors believe bamboo may be a factor. Evolutionarily speaking, giant pandas are not built to eat a sole diet of bamboo. As bears, their digestive systems are designed to break down meat and small amounts of plant material, yet in the wild and in captivity these bears are exclusively herbivorous. The study suggests this may lead to digestive troubles that could negatively affect panda pregnancy. It motivated the researchers to take a closer look at the gut bacteria involved.

“Gastrointestinal diseases are a major cause of mortality in wild and captive pandas but scientists understand very little about their digestive process,” says co-author Ashli Brown Johnson, state chemist and Mississippi State University associate professor of biochemistry, molecular biology, entomology and plant pathology. “By studying the microbial community in the panda’s gastrointestinal tract, we gain a better understanding of panda nutrition, which could help improve the health and reproduction of the endangered species.”

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Garret Suen

Suen, an Alfred Toepfer Faculty Fellow, also has other motivations. A renaissance man of the microbiome, his lab studies the gut bacteria of everything from cows to sloths to pandas. His interests are both fundamental and applied. For example, understanding how animals and their microbes break down fibrous plant materials could aid in more efficient production of biofuels. It could also lend insights into human digestive diseases.

For the study, Suen, Brown Johnson and co-first authors Candace Williams and Kim Dill-McFarland enlisted help from the Memphis Zoo, which has collected feeding behavior on its two giant pandas — Le Le (male) and Ya Ya (female) — since 2003. Williams, who conducted the work as a Ph.D. student in Brown Johnson’s lab, had also performed her master’s degree work at the zoo, watching the pandas feed for 12 hours a day.

Using data recorded by trained zoo docents, the research team analyzed how much time Ya Ya and Le Le spent feeding on both bamboo stalks and leaves. They saw dramatic shifts in eating behavior: The pandas ate leaves less than one percent of the time in winter and spring, but by August — when mucoids became more prevalent — nearly 60 percent of their feeding time was spent eating leaves.

Every summer, in captivity and in the wild, pandas switch from eating primarily the woody stalks of bamboo to the leaves. It is at this transition — which also coincides with when most female pandas become pregnant — that their digestion appears to go awry. In July and August, pandas pass more mucoids, cease eating, become lethargic, and express their discomfort and pain.

“If it’s happening every three to four days, and the pandas stop eating for half to a whole day — when they normally spend their whole day eating — that’s a lot,” says Dill-McFarland, a Ph.D. student in Suen’s lab.

leaf and culm

A fecal sample from a giant panda, showing a mix of bamboo stalk and leaves. Pandas eat up to a third of their body weight in bamboo every day. Photo: Candace Williams

The researchers studied bowel movements the pandas made in February 2013, during the season when pandas don’t normally have mucosal poop, and between June 29 and Aug. 22, 2014, when they more frequently pass mucoids. During this time, zookeepers collected the mucoids as well as the regular feces the bears produced immediately prior to and immediately after these events.

The team studied five normal fecal samples from Ya Ya and one mucoid, and 13 regular bowel movements from Le Le and five mucoids. The samples arrived from the zoo like “chicken breasts wrapped in foil,” says Dill-McFarland.

Williams traveled to Madison to learn from Suen and Dill-McFarland how to analyze the microbial composition of panda poop. Regular panda poop resembles shredded bamboo stalks and was a challenge for the researchers to process. The mucoids were gooey, smelled “ghastly” (says Williams) and presented their own challenges.

The team found the panda poop had unusually low bacterial diversity relative to other herbivores, though the mix of bacteria changed day to day. The diversity dropped even lower right before mucoids, but then spiked in the mucoids themselves, which contained a different population of microbes than regular poop. In particular, they were made up of bacteria typically found in the gut lining.

They also found bacteria in the mucoids associated with dysfunctional digestion in humans, called Actinobacteria.

“What we think might be happening is that their diet is causing a strong internal reaction, leading to an inflammatory response,” says Suen. “Pandas are basically shedding their gastrointestinal lining to allow for the replacement of those microbes. It’s kind of like resetting the microbiome.”

While researchers can’t be certain why pandas experience this resetting, it is clear their diet is rough on the animals. At 220 to 275 pounds, pandas eat up to a third of their body weight in bamboo every day. It passes quickly through their digestive systems, which does not give the microbes in their guts much time to break things down. This is entirely different from other animals adapted to consuming plant matter, like cows, whose rumen microbes take up to 24 hours digesting the complex carbohydrates found in plants.

“I’m very interested in animals that eat way more than should be necessary to maintain their body size, and on the flip side, in animals that eat way less than should be required to maintain their body size,” says Suen.

tubes

tubes of feces from badgers, porcupines, lemurs and more sit on top of a lab freezer. Photo: Kelly Tyrrell, UW-Madison

The study does not provide solutions to prevent the gastrointestinal distress pandas experience, which Williams says is very hard to watch. Whether pandas feed on stalks or leaves appears related to chemical changes in the bamboo leaves themselves, a strategy some plants use to prevent herbivores from munching on them. And meat is out of the question.

“It’s gotten to the point where if you try to feed them meat, they get violently ill,” says Suen.

But the study does give scientists a place to start.

“Until recently, the gut microbiome hasn’t really played a role in the management of animals,” says Williams. “Having a balanced gut is important, and it’s also important that we know these things, especially about such unique animals. I strive to let people know how important the gut microbiome really is and the impact it has on reproduction, health and even immune function.”

That Ya Ya produced just a single mucoid is one limitation of the analysis, as is her unusual breeding cycle. However, pandas are incredibly difficult to study, the researchers say, and data of this kind are rare.

Additional researchers from Mississippi State University and the Memphis Zoological Society contributed to the study, which was funded by the United States Forest Service’s International Programs, the Memphis Zoological Society, the United States Department of Agriculture’s National Institute of Food and Agriculture, the Mississippi Agricultural and Forestry Experiment Station, and the Leo Seal Family Foundation.

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

UW expert at White House summit

Thursday, May 12th, 2016

On Friday, May 13, the White House Office of Science and Technology Policy will host an event on microbiomes – communities of microorganisms that live on and in people, plants, soil, oceans and the atmosphere. Microbiomes maintain healthy function of these ecosystems, influencing diverse features of the planet – human health, climate change and food security.

During the event, the administration will announce steps to advance the understanding of microbiome behavior and enable protection and restoration of healthy microbiome function, including by investigating fundamental principles that govern microbiomes across diverse ecosystems, and developing new tools to study microbiomes.

Lending expertise to the summit will be UW-Madison bacteriology Professor Timothy Donohue. Donohue directs the Department of Energy-supported Great Lakes Bioenergy Research Center and is an expert on biofuels and bio-based renewable energy technologies. Donohue can talk about microbiome research in general and, more specifically, how it might inform strategies for devising alternative fuel technologies. He can be reached at (608) 770-1283.