From mice, clues to microbiome’s influence on metabolic disease

Friday, February 17th, 2017
germ-free mice

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

The community of microorganisms that resides in the gut, known as the microbiome, has been shown to work in tandem with the genes of a host organism to regulate insulin secretion, a key variable in the onset of the metabolic disease diabetes.

That is the primary finding of a study published Feb. 14 in the journal Cell Reports by a team led by University of Wisconsin–Madison researchers Alan Attie and Federico Rey. The new report describes experiments in mice showing how genetic variation in a host animal shapes the microbiome — a rich ecosystem of mostly beneficial microorganisms that resides in the gut — and sets the table for the onset of metabolic disease.

“We’re trying to use genetics to find out how bugs affect diabetes and metabolism,” explains Attie, a UW–Madison professor of biochemistry and a corresponding author of the study.

Peeling back the complex interplay of genes, diet and the trillions of microorganisms that live in the guts of humans and other animals, Rey, Attie and their colleagues are beginning to work out the subtleties of how host genes shape the composition of the microbiome and contribute to an animal’s phenotype and, ultimately, diet-induced metabolic disease.

“We’re trying to use genetics to find out how bugs affect diabetes and metabolism,” explains Alan Attie, a UW–Madison professor of biochemistry. Photo: College of Agricultural and Life Sciences/UW-Madison

Metabolic diseases such as diabetes have long been known to be influenced by both genes and diet. Understanding the role of the microbes that live in the gut and help process nutrients not only promises a fuller understanding of the link between genes, diet and disease, but may also be a pathway to pinpointing the genes responsible for conditions like diabetes.

“We’re asking whether or not there is a chain of causality between gut microbiota and (disease) phenotype,” says Attie. “Genetics is the anchor. If something is associated with a gene, it is truly a causal relationship, not just a correlation.”

To leverage that approach, the new Wisconsin study employed a cohort of eight strains of mice whose genetics collectively mirror the genetic diversity of the human population.

“These mice show tremendous phenotypic diversity,” says Attie. “Some are lean. Some are susceptible to obesity. Some are resistant to obesity. Some of these phenotypes can be partially transmitted by gut microbiota.”

Clues to the influence of genes on the composition of the microbiome emerged from experiments where mice were raised in a germ-free environment and challenged by a diet high in fat and sugar. Through fecal transplants, microbiomes could be effectively traded bewteen strains, helping researchers home in on the interplay between genes and the microbiome.

“Our study suggests that a lot of the genetic variation we see among these eight strains of mice is reflected in their microbiomes,” notes Rey, a UW–Madison professor of bacteriology and a corresponding author of the study. “And we have evidence that the composition of the gut microbiota is controlled by the genomes of the mice. We’re trying to find the genes that control the composition of the gut microbiota and (dictate) host phenotype.”

Federico Rey

“Our study suggests that a lot of the genetic variation we see among these eight strains of mice is reflected in their microbiomes,” notes Federico Rey, a UW–Madison professor of bacteriology. Photo: College of Agricultural and Life Sciences/UW-Madison

In response to diet, the Wisconsin group observed a “remarkable variation” in mice whose genetics make them prone to diabetes. They also noticed an accompanying change in the makeup of the animals’ gut microbiomes. Some of the bacteria, according to Rey and Attie, could be linked to metabolic traits such as body weight, and glucose and insulin levels.

The microbiome plays a crucial role in processing nutrients. Food not metabolized directly by a host like a mouse or a human is subsequently processed in the gut by the bacteria of the microbiome. As the microbes metabolize food, they produce an astonishing number of small molecules, chemicals and hormones that circulate in a host and can influence health in an animal.

Among those metabolites, perhaps as many as 20,000 in all, are what are called short-chain fatty acids, which serve as signaling molecules in the intestine and associated organs like the liver and pancreas. In particular, they are key regulators of energy and glucose.

Gut microbes also influence the physiology of the host by modifying bile acids produced by the liver, which are also processed by the microbiome to produce secondary metabolites that can exert an influence on disease and health.

Mice in the study that were put on a rich diet and received microbiome transplants helped the Wisconsin team expose functional differences attributable to two different transplanted microbiomes, including a link between the gut microbiome and insulin secretion.

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

The inner world of athletes: Using technology to explore a microbial medical mystery

Tuesday, February 14th, 2017

So many things typically distinguish accomplished athletes from the rest of us—greater strength and endurance, better balance, faster reactions—but one of the more surprising differences is that, according to dental studies, they also tend to get more cavities.

This intriguing phenomenon was the subject of a capstone course in microbiology this past spring, offering undergrads a chance to be part of a burgeoning worldwide scientific effort while using cutting-edge technology.

athletes microbe Grow story

Students compared the oral microbiomes of athletes to figure out why athletes get more cavities. Photo: Sevie Kenyon

There are trillions of microbes in the human body; the community of microbes that lives in each of us is our microbiome. As more and more research focuses on microbiomes, it’s becoming clear they play a significant role in human health and wellness. Microbiology 551 students worked to add to that body of research using a next-generation DNA sequencer manufactured by the California-based company Illumina.

“It’s only our department and maybe one or two in California that are doing hands-on work with undergraduates in teaching this technique,” says co-instructor Melissa Christopherson. Christopherson teaches the course with Tim Paustian, both faculty associates in the Department of Bacteriology. “Having students conduct meaningful research with these modern techniques makes them more competitive in the job market and better able to navigate the field of microbiology.”

Students were tasked with comparing the oral microbiomes of athletes and nonathletes, using saliva samples. They sampled a range of students, from UW athletes to occasional exercisers to students who hadn’t exercised for at least five weeks. Once students collected and prepared the samples—including their own oral microbiomes—they sequenced the DNA and determined which microbes were present in each sample.

With so many samples, the students were able to look beyond the question of exercise to test other hypotheses they developed themselves.

“We wound up taking the same data set and asking other questions,” explains Samantha Gieger, who graduated in May with a BS in microbiology and genetics. “In groups of four or five, we looked at the effects of dairy, caffeine or using an electric toothbrush.”

Students presented their projects at a poster session last semester, and their work is currently being analyzed for publication. Their findings will become part of the growing research into microbiomes. Student Sophie Carr BS’16 and Christopherson were invited to the White House last spring for a summit announcing the launch of the National Microbiome Initiative.

As a capstone class, the course offered a research experience requiring students to integrate diverse bodies of knowledge to solve a problem. And it quickly proved invaluable as students considered next steps in their careers.

“I’ve learned so much—how to go about research, what to do when encountering a problem. Troubleshooting is such an important technique,” says Isaiah Rozich BS’16, then a senior majoring in microbiology and Spanish. “Figuring out which solution is best takes a lot of time, and it opened my eyes to what life as a researcher will be like. While it’s overwhelming, I think the end result is gratifying.”

This story was originally published in the Fall 2016 issue of Grow magazine.

UW-Madison launches Microbiome Initiative

Wednesday, January 11th, 2017

We are not alone. Each of us carries a wide array of microbial species that outnumber our cells tenfold. Recent studies have shown that the complement of microorganisms, the microbiome, is an important determinant of human health and disease. The microbiomes of other animals, plants, soil, bodies of water, and the atmosphere play similarly important roles.

Petri dish cultures of soil bacteria for Plant Pathology research

Cell cultures in a petri dish. A new $1 million initiative to seed new lines of Wisconsin microbiome research will support interdisciplinary research and infrastructure. Photo: Jeff Miller

Our understanding of the diversity and roles of these microbiomes is limited, a fact that led the White House Office of Science and Technology Policy to launch the National Microbiome Initiative last year. Stakeholders, including UW–Madison, have responded with new commitments to develop a comprehensive understanding of microbiomes across all ecosystems.

A new UW–Madison Microbiome Initiative comes with $1 million in grant funding administered by the vice chancellor for research and graduate education to support interdisciplinary research, infrastructure, and research community enhancements related to the microbiome.

“Microbiome science has the potential to revolutionize areas such as health care, agriculture, biomanufacturing, environmental management, and more,” says Marsha Mailick, UW–Madison’s vice chancellor for research and graduate education. “The potential of microbiome research is enormous — it could create revolutionary technologies. By providing seed funding for microbiome projects at UW–Madison, we hope to position our faculty to be more competitive when applying for federal funding for their research in this area.”

“Microbes influence our everyday existence in immeasurable ways. They are master chemists who have provided us with the air that we breathe. Their signatures are present in the geological record, and they are essential for many things that we take for granted from the food that we eat to the water that we drink and our health,” says Tim Donohue, UW–Madison professor of bacteriology and past president of the American Society for Microbiology.

Microbiomes maintain healthy function of these diverse ecosystems, influencing human health, climate change, food security and other factors. Dysfunctional microbiomes are associated with issues including human chronic diseases such as obesity, diabetes and asthma; global impacts such as climate change; and reductions in agricultural productivity. Many industrial processes such as biofuel production and food processing depend on healthy microbial communities.

Tim Donohue, professor of bacteriology

Tim Donohue

Although new technologies have enabled exciting discoveries about the importance of microbiomes, scientists still lack the knowledge and tools to manage microbiomes in a manner that prevents dysfunction or restores healthy function.

“Advances in genomics and analytical, imaging and computational methods can be combined to understand the hidden activities of our microbial partners and how we might harness them for future environmental, agricultural, health and economic benefits,” Donohue says. “UW-Madison has the domain expertise in the biological, physical and social sciences and a rich history of collaboration. I predict this investment will build new connections from all corners of the campus and help position us as a global leader in this emerging field.”

The federal government has been investing in microbiome research for several years. More than a dozen federal departments and agencies support microbiome research today, and the magnitude of investment has recently grown: A 2015 report released by the National Science and Technology Council noted that annual federal investment into microbiome research tripled over fiscal years 2012–2014, with more than $922 million invested during this three-year period.

The goal of the National Microbiome Initiative is to generate research that elucidates general principles of microbiome behavior by finding commonalities across different habitats. UW–Madison is perfectly positioned to respond to this call because of the campus’s breadth and depth of microbiome research, Mailick says.

Waisman Center 5/30/14 (Photo @ Andy Manis)

Marsha Mailick

A large, multidisciplinary group of UW researchers across five UW–Madison schools and colleges has been focusing on microbiome research. Over the last few years, 25 UW–Madison faculty have submitted 67 research proposals to federal agencies and other funders, resulting in 20 awards that currently generate approximately $8 million annually.

“Given recent and projected investments in this area by federal agencies and private foundations, there is an opportunity for substantial growth in extramural support,” Mailick says. “That’s why we have launched the UW–Madison Microbiome Initiative.”

Funding for the UW–Madison initiative comes equally from the Chancellor’s Office and the Office of the Vice Chancellor for Research and Graduate Education.

UW-Madison faculty researchers are invited to submit proposals for research programs, infrastructure or planning activities intended to increase the breadth and depth of microbiome research on campus.

A UW–Madison committee of subject matter experts will review the proposals to identify those that hold the most promise for sustained research programs or galvanizing the community of microbiome researchers. The committee will then make recommendations to the vice chancellor’s office. The OVCRGE will make final selections.

Research and infrastructure projects will be eligible for a maximum award of $250,000. Research community enhancement awards are up to $10,000. Funding is to be spent over two years. The deadline to apply is March 15.

More information and application

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

Antibiotics off the beaten path

Monday, January 9th, 2017

As more antibiotic-resistant “superbugs” emerge, it’s clear that we desperately need new antimicrobial drugs. Yet, over the past couple of decades, antibiotic discovery has largely been stagnant.

“The reality is there’s almost no new antibiotics that are developed. And that’s because pharmaceutical companies have decreased their investment—in part because of the rediscovery issue,” explains bacteriology professor Cameron Currie.

antibiotics Currie

Bar codes help the team keep track of the promising microbial strains they’re analyzing. Photo: Sevie Kenyon

The “rediscovery issue” refers to the fact that soil has historically been the prime source of new antibiotics—but it seems to be tapped out. When scientists screen soil microbes for new antibiotics, they keep finding the same compounds over and over again.

Currie is part of a team that is looking elsewhere.

Currie and his colleagues have been focusing their efforts on microbes that are associated with insects, plants and marine life from all around the United States, funded by a $16 million grant from the National Institutes of Health that was awarded in 2014.

“One of the major hurdles is finding new compounds, and that’s where we’re really excelling,” says Currie, a co-principal investigator on the grant. His partner is David Andes in the UW–Madison School of Medicine and Public Health.

At the front end, the work involves some good old-fashioned bioprospecting. Currie’s group, which is in charge of the terrestrial sphere, has gathered more than 2,000 flies, aphids, caterpillars, bees, ants and other insects, as well as mushrooms and plants, from locales near and far, including Alaska, Hawaii and Wisconsin’s Devil’s Lake.

Caitlin Carlson

Caitlin Carlson, an associate research specialist in Cameron Currie’s lab, on the search for new antibiotics. Photo: Sevie Kenyon

Back at the lab, things get high-tech pretty quickly. Microbes are isolated from the samples and tested for antimicrobial activity. Promising strains undergo genetic sequencing that allows Currie’s group to determine how likely they are to produce novel antibiotic compounds. From there, other scientists involved in the grant go on to test the most promising compounds in a mouse model of infection. This approach has already yielded some exciting drug candidates.

“We have 9,000 strains to screen, and we have already found some new compounds that are effective at combating infections in mice and have low toxicity,” says Currie.

With so many samples to process, Currie’s group adopted bar code technology to help them keep track. They have a bar code reader—like you’d find in a grocery store— connected to a lab computer that they use to scan petri dishes, look up samples and add new data. For each microbial strain they’ve isolated, the database has photos of the “host” insect or plant, GPS coordinates for the collection site, assay results, genetic sequence and much more.

At this point, Currie feels confident that the project will pay off, and he’s eager to see one of the group’s compounds go into human clinical trials.

“If you find one new antibiotic that gets used in treatment, it’s a major success. You’re saving people’s lives,” Currie says.

This story was originally published in the Fall 2016 issue of Grow magazine.

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.