The Fight for Safer Food

The Fight for Safer Food

To confront the threat of persistent foodborne pathogens, Steve Bowden turns to novel techniques to understand and take down those threats.

By Kyle Wong

Nearly one in six Americans suffer from foodborne illnesses each year, according to the Centers for Disease Control and Prevention (CDC). Scientists like the University of Minnesota’s Steve Bowden are working to change that.

Standard food-safety processes like pasteurization, freezing, and fermentation kill foodborne pathogenic bacteria, but these pathogens evolve to survive. Through mutation and the acquisition of new genes, pathogens can cause outbreaks from unfamiliar sources such as fresh produce, spices, and peanut butter. Bowden, an assistant professor in the Department of Food Science and Nutrition and a member of the BioTechnology Institute, is developing strategies to eliminate new and persistent pathogens.

One common offender is Salmonella, a bacterial species that infects millions of Americans each year, leading to thousands of hospitalizations and hundreds of deaths. Bowden studies how Salmonella responds to stresses in the food environments where it thrives. He seeks to identify common genetic traits that enable Salmonella to survive and grow under varied conditions. Ultimately, he hopes to develop procedures that eliminate harmful bacteria from the food system. “We want to understand why certain outbreaks occur in specific types of food and if there is a correlation with the genes found in those specific types of bacteria,” says Bowden.

To target specific foodborne pathogens, Bowden’s lab engineers a type of virus called a bacteriophage that infects and then kills bacteria. But identifying phages that work is only half the battle. Because pathogens are so diverse, effective treatment requires the right combination of phages to remove all of the pathogen targets and ensure food safety. To make things more complicated, the food matrix can also affect the phage’s efficacy. One cocktail of phages might succeed on one food but fail to remove the same pathogen in another.

Nonetheless, the Food and Drug Administration (FDA) has approved some phage cocktails. They are entirely harmless to humans and assist in the control of foodborne pathogenic bacteria during food processing. Their potential use as a safe, natural method to improve food safety is garnering interest in the food industry. Still, further research is required to enhance their efficacy and improve manufacturing methods.

Despite these challenges, Bowden’s longstanding fascination with molecular biology and microbiology keeps him motivated: “I was surprised by how many foodborne illnesses there are. I want to make use of genome sequencing to try and control these pathogens. What’s interesting about molecular biology is how we can apply it to make the world safer.”

Bowden’s drive to understand foodborne pathogens couldn’t have come at a better time. Addressing global threats to food safety, such as climate change and antibiotic resistance, requires broad thinking and a flexible approach. Bowden brings a global perspective to his work. After earning his Ph.D. in biochemistry at the University of Cambridge, he worked as a postdoc in the United Kingdom and Japan. “I feel lucky to have been in so many labs and learn different perspectives,” he says. “It’s helped broaden my appreciation for different ways to do research.”

The experience helped prepare Bowden for his research at the University of Minnesota. “The drive to understand a problem and develop techniques to study that problem has kept me in academia,” he says. “I’m excited to see what direction it takes.”

Kyle Wong is a writing intern in the University of Minnesota Science Communications Lab, majoring in Microbiology. He can be reached at

Advancing Biotech Byte by Byte

Advancing Biotech Byte by Byte

How computational biology is solving the big data dilemma, one question at a time.

Plus Q&A’s with Dan Knights and Chad Myers

When you log onto Facebook, your profile provides the company with a truckload of data about you — where you hang out, what you “Like”, and who your friends are. What’s more, the computational algorithms used by social media sites are getting better and better at identifying whom you should befriend, or what you should “Like.” Surprisingly, Computational Biologists in the University of Minnesota’s Biotechnology Institute (BTI) are using some of these same algorithmic techniques to power new paradigms in data acquisition and analysis for biology.

In the case of Facebook data, an “edge”is defined by connections to Friends or
actions that a user takes, such as a “Like” or status update. The company stores
all of this information and uses it to personalize your experience on the site. Consider Friend recommendations, for example. “The concept is simple,” says Chad Myers, a BTI member with appointments in both the College of Biological Science (CBS) and the College of Science and Engineering (CSE). “Facebook looks at your set of edges, and someone else’s set of edges, and it says, you share this many edges in common, so you are probably Friends, too. That approach can be really accurate in biological data, as well.”

An “edge” in biological data could fall into a multitude of categories, but the core concept is the same. Biological molecules that perform similar functions often exhibit similar
patterns in large genome-scale datasets. Computational algorithms can then identify and analyze these patterns in the data.

“We can measure similarity in data, but we don’t necessarily have to understand every aspect of it,” says Myers. “Based on how closely associated certain unknown genes or proteins are to more thoroughly annotated genes or proteins, we can guess what functions the unknown molecules might serve.”

With the advent of genomics and other next-generation technologies, the biotech sector is collecting unprecedented quantities of high-dimensional biological data. The increasing complexity and volume of these data could provide significant insights in biology, yet they also introduce unprecedented computational challenges.

For example, think of a simple organism like yeast. One researcher might study a cellular process by using a high-powered microscope to generate video with thousands of frames, each containing of millions of pixels. Another researcher might use state-of-the-art spectrometry to catalogue hundreds or thousands of protein interactions. Yet another might apply genome sequencing to measure quantitative gene expression levels across the genome for hundreds or thousands of samples. Each of these data collection endeavors is a hard problem to solve individually, yet perhaps the ultimate challenge is to understand how these data sets, taken together, tell an integrated story about biology.

Simply put, the human brain cannot process such vast collections of data points. Furthermore, Excel spreadsheets no longer suffice to make sense of these interrelated pools of information. “Computational biologists develop new methods, and define new paradigms to look at data with computational techniques,” says Myers, whose research maps out millions of genetic interactions in organisms all the way from yeast to human cells.

One of the techniques Myers has developed relies — like Facebook — on similarities between clusters of genes. If certain genes display similar expression patterns under a variety of controlled circumstances, it can be inferred that their functions might be similar.

Dan Knights, a member of BTI and the Department of Computer Science and Engineering works in a different sector of Computational Biology. Knights’ research investigates the rapidly evolving microbiomes of human and non-human primates. Both Myers and Knights use primarily genomic sequencing information and advanced computational techniques to pave the way from raw data to an integrated understanding of biology.

“We’re interested in how you can define a healthy gut microbiome,” says Knights, who looks at not just one genome, but at all the genomes present within a subject’s gastrointestinal tract at a given time. “This turns out to be quite challenging because a diverse gut microbiome with hundreds or thousands of different species living in it is actually more healthy than one with only 100 species or 50 species.”

Computational biologists fall along a spectrum. “Some researchers focus more on the biology, others focus entirely on developing new algorithms,” says Knights. Both Myers’ and Knights’ labs do a bit of both. Some of their work involves designing and executing wet lab experiments; the rest involves building tools to process data from those experiments, and other experiments by collaborators across the world.

“Researchers developing computational approaches often have an abstract perspective of biological systems,” says Myers. “While specific biological questions motivate our work, when we develop a method, we rarely only develop it for a specific biological system or even species. The problems that are most exciting are the ones where, if we solve it here, it will also solve someone’s problem out there.”

By deriving solutions that cut across disciplines, faculty in BTI work on a broad range of problems. The same technologies enabling the genomics revolution are also being applied to precision agriculture, sensors in manufacturing, bioremediation, and other environmental concerns like climate change.

Ultimately, researchers in the biology sphere aim to construct models with strong
predictive power. For instance, Myers hopes to understand how genetic interactions influence phenotypes, either in normal or disease states. Likewise, Knights hopes to create diagnostic tests that can predict health consequences based on the community of microbes living within a person’s gastrointestinal tract.

Computational biology is an excellent tool for organizing, identifying and analyzing trends in data sets. Computers won’t, however, eliminate the need for deeply experienced experts. “You can never automate human intuition, especially that of biologists,” says Myers. “There might be thousands of hypotheses that are consistent with the data you’ve measured, but a good geneticist or molecular biologist can really narrow that hypothesis space quickly based on intuition.”

Rather than computers replacing people, computers are changing how humans interact with data. Computational processes are becoming increasingly iterative, meaning that data analysis is not a simple one-off affair. Instead, one set of computations could
reveal a pattern that a human would need to detect and/or interpret. Then the next set of computations would be designed to further investigate  this particular pattern, in a cycle that repeats indefinitely.

It’s no longer  just that one human detects such patterns. “Projects are getting bigger and more multi-disciplinary,” says Knights, who leans heavily on both local and global collaborators. “Disciplines are converging. Everyone’s trying to put the pieces together right now, because it’s all one giant system.”

At the intersection of computer science and biology lie exquisite opportunities to build new technologies and solve major problems. Visit to read more about the exciting work being completed by BTI faculty.

Insights from our Insides, a Q&A with Dan Knights

Insights from our Insides, a Q&A with Dan Knights

Microbiomes are rapidly evolving, and this computational biologist is out to debug the mystery of why.

Colleen Smith

We are what we eat but there’s also a host of microbes living in our guts that help us make the most of all that food. Computational Biologist, Dan Knights investigates the dynamic and rapidly evolving relationship between humans and the bugs living within.

Just like macro-organisms, bacteria have specific environmental needs — and in the case of gut bugs, that environment is the gastrointestinal tract. Central to the concept of the ‘microbiome’ is that a symbiotic relationship exists between this community of microbes and their human hosts. Yet when conditions change, so do microbiomes, and a lot is changing in our world right now.

Knights’ work focuses on understanding what makes a microbiome healthy, and what drives it towards illness. Read more about how he melds biology with bytes in the Q&A below.

Since microbiomes can contain so many different species at once, how do you collect meaningful information about them?

“The main way that we study microbiomes is to grind up their DNA and sequence it. If you try to grow the bugs, you get an enormous bias towards bugs that grow easily in the lab. For a long time, people thought one of the main gut bugs was E. coli. It turns out E. coli just grows really well in a petri dish. E. coli is in most people, but in a healthy individual, it only takes up about one tenth of a percent. We’ve found that instead, if you grind up the DNA and sequence it, you can capture all of the diversity that’s there.”

As a computational biologist, how does computer science affect your work?

“We spend about half of our time designing experiments, carrying out experiments, and analyzing the data. The other half of the time is spent developing new algorithms. The most exciting parts are when we’re developing new tools to support the experiments we’re running, so we really get synergy between the two disciplines of Biology and Computer Science.”

How do computer algorithms aid your research?

“The first way in which we use algorithms is to go from the raw DNA to understanding which bugs they come from, what they might be doing, or which types of genes they are. After we’ve done that raw interpretation, there’s another set of algorithms that we use to interpret the biological significance of the bugs we find. We want to know which are the good bugs and which are the bad ones, and we want to build a new test that will tell you how healthy your microbiome is, based on the species present within it.”

What does a healthy microbiome look like?

“A healthy gut microbiome has hundreds or thousands of different species living in it, and that’s actually more healthy than one that has 50 or 100 species. The diversity makes our data sets high dimensional, but there’s also high variation in bugs between healthy people, in a certain person over time, or between people with a given disease.

It’s not something like blood pressure, where you have a simple ratio. Instead, there are hundreds of numbers, so it presents a very interesting computational problem. What we’re doing primarily is trying to enable precision medicine with the microbiome. This means being able to tell as precisely as possible which species and which strains are in a person, and then to be able to classify them as being healthy or unhealthy. If a person’s microbiome is unhealthy, we say that it is in a state of dysbiosis.”

Does dysbiosis happen on a case-by-case basis, or is something broader occurring?

“Something broader is happening with modernization. We have cross-sectional data where we can see that people who are in a developing country tend to have significantly more diverse microbiota than, say, people living in the USA. If you can find very rural peoples living in developing countries, their guts are even more diverse. We don’t know what benefits those missing bugs are conferring, but we do have epidemic levels of obesity, diabetes, Crohn’s disease, colitis, asthma, and allergies — all of which are linked to a shift in your gut bugs, and all of which are also linked to increased exposure to antibiotics in kids.

It’s likely that we’re missing some of the bugs that we evolved to have. Which exact ones are crucial, we don’t know, but that’s one of the things that we’re studying in our primate microbiome project.”

What patterns have you found through these projects?

“We found that when we have samples from wild monkeys, two different species of monkey will have completely different gut microbiota. But as soon as they move into captivity, they lose most of their native bugs and acquire modern human bugs.

It seems as though there is an axis of dysbiosis. If you start with wild monkeys and continue along to captive monkeys, the next group you get to is non-westernized humans, and then all the way at the end, the farthest ones from the wild, are Americans. And that’s not where you want to be. Our studies of recent immigrants in Minnesota have confirmed this pattern.”

How could biotechnology help those suffering from dysbiosis?

“One way is to give someone new bugs — i.e. a probiotic — although what people typically think of as probiotics is a very limited set of bugs. You can find thousands of probiotics on Amazon, but if you look at the ingredients, it’s the same small set of strains over and over. We’re talking about a much broader set, so that would include bugs like Faecalibacterium prausnitzii. That’s a good bug. Everybody who’s healthy has it. Every time we study a disease, it’s depleted in people who have the disease or are at risk, and yet you can’t buy it.
It’s not a probiotic yet, but that’s an example of a bug we could potentially use as a therapeutic.

Another way is to give someone prebiotics, which are food specifically for your bugs rather than the bugs themselves. You could supplement with a particular chemical that you know encourages certain types of bugs to grow.

Or, there could be targeted antibiotics that would protect certain members of the microbiome without being as comprehensive or broadly destructive.”

Why is this dysbiosis happening, and how can computational biologists contribute to solutions?

“Everyone’s trying to put the pieces together right now, because it’s all one giant system. You can’t really study human endocrinology without considering the bugs, and you can’t study how the bugs are affecting the human without endocrinology and immunology, so research teams are converging, and projects are getting bigger, more multidisciplinary, and more reliant on computation.

It took decades to build a functioning model of a complete cell, in a very simple organism. To do that for multicellular organisms and bacterial communities is still quite far beyond reach. The golden apple would be to have a full computational model of everything in the human body. Everything you have to do in between where we are now and that point of
the comprehensive model is fair game for computational biology.

Some people are modeling low level physical processes between interacting molecules. Others are a level up from that, measuring the activity of enzymes and how different expression levels change in response to environmental conditions. Then there are people studying communities of cells and cell-cell heterogeneity, and so on up the line. All of those problems  require computational biology.”

Q&A with Michael Freeman

Q&A with Michael Freeman

New BTI faculty member translates unknown microbial languages into novel possibilities for biotech.

By Colleen Smith

Michael Freeman joins the Biotechnology Institute this Spring as a new faculty in the College of Biological Sciences. Hired in the Synthetic Biology Cluster, Freeman specializes in the biosynthetic pathways that produce small molecules called natural products.

Natural products are molecules often manufactured by microbes, and they come in many different shapes and sizes. In human health, these biomolecules are of interest for their potential uses as new antibiotics or anticancer drugs. In microbial ecosystems, they also serve many other functions — most of which are presently undefined.

At the University of Minnesota, Freeman will target intriguing bacteria that have not previously been cultured or easily manipulated in the laboratory setting. By studying unknown — and often remarkable — microorganisms, Freeman’s work could lead down new avenues in biotech.

What fundamental question motivates your research?

“Microbes are vitally linked to human health. They live in the soil, affecting how our food grows. They live in our guts, affecting how we digest our food. Yet despite their importance, we still don’t know much about which bacteria are present in these different environments, what they are doing, or how they communicate. My main motivation is to learn how bacteria communicate with each other and the outside world.

With all the genomic sequencing data that is coming out now, my research builds on the idea that we now have a new window into microbial metabolisms. In particular, I’m interested in how microbes communicate with each other through the language of natural products. I focus on the way bacteria construct that language.”

When you say language, what do you mean?

“Well, I’m trying to convey a simple definition of language as a series of words that are built by a sequence of letters. One type of bacterial language is constructed of ‘words’ called peptides, a class of natural products. Peptides are made with amino acid ‘letters’ — each of which must be synthesized by the microbe in a very specific way. Understanding this language, and how to manipulate it, is really the holy grail.”

Do all microbes or bacteria use the same type of communication?

“Bacteria speak many different languages. Some are constructed with novel ‘letters,’ which imply new functions and new chemistry as a product of evolution. Others share common letters or words, even if they’re from completely different environments. However, we don’t always know which bacteria is speaking which language — and even if we do, we don’t know anything about how they are doing it. That’s the puzzle we’re trying to solve.”

Enzymes are specialized proteins that catalyze chemical reactions within living organisms. Why does it matter that uncultured bacteria can use strange enzymes to produce new letters?

“Most organisms use 20 letters for speaking the language of peptides. New enzyme functions essentially expand this number to create drastically more complex words and thus, a richer language. Functionally, these enzyme modifications affect the shape and behavior of peptides, and in turn the microorganisms, in unique and important ways.

How do you detect and decipher the products of novel enzymes?

“Mass spectrometry has played a vital role in my research. I use this extremely sensitive technique because the quantities of the molecules available to me are very, very low sometimes, and the modifications are very, very subtle. If you think of amino acids as letters, then mass spectrometry describes each letter present in a peptide, and in which order, so that you can accurately read the word. ”

Synthetic biology is an emergent and multidisciplinary field that involves the engineering of biological molecules. How does your research fit into this discipline?

“I define myself as a Natural Product Biochemist who uses Synthetic Biology to aid my research. It’s my tool rather than my primary research focus.

Synthetic biology has come a long way for DNA or RNA, but for natural products, it’s still in its infancy. You cannot yet easily piece together letters to make any word you would like to have. The biggest problem is being able to systematically build on the information that you do receive, and have it feed back into your understanding, so that you can actually build more and more complex molecules.”

What new information do you want to feed back into the field?

“If you want to study and produce new compounds, and figure out the different languages microbes use, you need to know not only how to manipulate and work with bacteria, but also how to pair particular natural products with particular bacterial models.

I’m interested in developing expression hosts from different genera, orders, and possibly even phyla in order to standardize how we approach bacterial model systems, under a very limited set of conditions, and using specific vectors. With the backdrop of symbiosis, the coup d’état would be to grow a macro-organism essentially as an incubator for other bacteria.”

How could a greater understanding of microbes and the languages they use contribute to new biotechnologies?

“Oh, in many, many ways. For instance, if we learn how microbes talk to each other, then we give ourselves the opportunity to make them listen, so to speak. This could be in the context of our own gut bacteria to improve health or in bioremediation processes, to become more responsible stewards of the planet. Finding new molecules may lead to new pharmaceutical drugs, and new enzymes can always lead to new opportunities in modifying those drugs or other materials. It is an incredibly exciting time for my field of science and I feel very lucky to be a part of it.”

Fungal Pests Reassessed

Fungal Pests Reassessed

BTI researcher maps the gene expression of a fungus to better understand how the microorganism eats.

By Allison Kronberg

Some fungi have developed a bad reputation as pests eating wood from the buildings where people live and work. But BTI researcher Jonathan Schilling is challenging old assumptions and finding new reasons to study the ubiquitous microorganisms.

Research in Schilling’s fungal biology lab suggests that plant- or wood-degrading fungi may find their way into a variety of new technologies, from insulation and indoor air filtration, to biofuel production.

“Since I’ve been at the University of Minnesota, I’ve branched out from looking at these organisms as pests to looking at their potential in biotechnology, as well as their importance in nature,” Schilling says.

The United States Department of Energy has funded Schilling to study specific mechanisms that control how fungi eat. “The research could help biofuel companies understand the steps a fungus takes when it degrades plants,” Schilling says.

According to Schilling, the companies have an interest in finding alternative ways to make fuel from biomass, because current processes are costly and require multiple biochemical steps. Some fungi are able to consolidate those steps, and if companies are able to tap into that ability, it could make biofuels cheaper for consumers.

A recent DOE grant, is called Connectomics — a term borrowed from neurology. The term is derived from a method of study usually used to map the real-time expression of the nerves in the human brain. Schilling has applied this method to the gene expression of fungal systems.

To produce the maps, Schilling and his lab grow a fungus named Postia placenta on wood wafers. The team then cuts the wafers into slices, like a loaf of bread, and analyzes each slice. When they put the data back together, it produces a connectome map, which shows how the fungus expresses genes and operates differently at various growth regions.

But the fungus works very slowly, so commercial use may not be likely just yet.

Instead, Schilling hopes future researchers will take advantage of the maps, using the information on fungal genome and gene expression to create new technologies or improve existing ones.

“On the science side, we’re providing a service,” Schilling says. “I offer tools. Other researchers need to go out and solve practical problems.” Schilling is hopeful that a PNAS paper, which he anticipates will be published in early fall, will be a jumping off point for others to engage with and find applications for his research.

Schilling and his students work with biomaterial companies throughout the country on research ranging from the study and application of fungi as an adhesive for window and door companies, to illuminating the characteristics of Scoby — the fungus used to produce the unconventional tea remedy, kombucha. This fall he will be teaching a new course in applied mycology. foster a new generation of scientists interested in fungi. The variety of application shows that fungal “pests” have the potential to create biotech solutions, too.

Mushrooms in the Marketplace

When they aren’t researching biotech applications of fungi, students in the Mycology Club engage with local communities by selling edible mushrooms at the University of Minnesota Farmers Market.

Standing in the pouring rain might not make a lot of people happy, but as graduate student Gerald Presley turned a small umbrella-like wine cap mushroom upside down to explain how its gill margin would expand as it matured, he had a smile on his face. More rain means more fungi — and that’s good for a fungal garden.

Presley is a graduate student in lab of BTI member Jonathan Schilling (BTI/Plant Pathology). He is also president of the UMN Mycology Club. The student group hosts workshops, lectures, and activities related to fungi. They also tend the fungal garden.

The garden has hundreds of logs blooming with fungi, so the group has also been able to raise money and interact with the local community by selling mushrooms not used    for research at the Farmers Market.

“It’s always good to find a practical application outside of the laboratory,” Presley says. “It’s been great for us.”

The club first starting selling mushrooms at the farmers market in 2013, two years after it was founded. It sells a variety of edible fungi, including shitake, wine cap, and oyster mushrooms. The Mycology Club has since teamed up with the certified organic student farm Cornercopia, which sells the mushrooms at its stand, as well.

“People like the mushrooms,” Presley said. “So they’ll come to the stand… and then they might buy some of [Cornercopia’s] stuff, too.”

Cornercopia locations — outside the Andrew Boss Meat Lab in St. Paul and in  Gateway Plaza on the East Bank — are ideal because they attract customers beyond the student body. Local chefs have even begun purchasing student-grown mushrooms for their restaurants.

The stand has shoppers talking about mushrooms. “We hear people say things like, ‘Oh, what I do with mushrooms is…’ or ‘I found a bunch of morels’ or ‘I’ve got this spot with a bunch of chanterelles this year,” Presley says. “People who come up and actually talk to us, they’ve always got their story, and it’s a chance for us to teach.”

The Mycology Club sells the mushrooms for about $10 per pound, earning about $200 over the past two seasons. The small profit, along with grant money and proceeds from selling mushroom spawn, are more than enough to support the low-cost group. “It’s kept the club alive,” Presley explains.

The club uses the money to fund biannual barbeques, teaching workshops, and guest speakers. When Presley and other student officers graduate, they will tap the 300 students on the Mycology Club’s email list so the club can continue to sell fungi grown by a new crop of mycologists.

Science, It’s What’s for Dinner

Science, It’s What’s for Dinner

New BTI member David Baumler aims to develop novel biotech for protecting local and global food supplies.

By Estelle Smith

If it’s on the shelf at the grocery store, it must be safe to eat… right? Hopefully, that answer is yes. Yet a dazzling array of microorganisms — not all of them friendly — enjoy human grub in our gastrointestinal tracts as much as we do. How can science help to guarantee the safety of our foods and bodies against an army of opportunist bugs?

David Baumler, a faculty member in the Department of Food Science and Nutrition and new member of the BioTechnology Institute, develops technologies that could improve the safety and nutritional value of the food supply chain, both locally in the Midwest and across the world. “I go where the problems facing people are,” says Baumler, who hopes to engineer solutions for major health and economic problems.

Baumler’s background includes biochemical investigation of everything from pathogenic foodborne bugs and biofuel-producing bacteria to ancient microbes that thrive in the most extreme conditions on the planet. “I cross paths with BTI faculty who work on topics like bioremediation and fermentation,” says Baumler. His wide-ranging experience allows him to ask questions that cut across academic disciplines, often with promising results.

For instance, Baumler was the first to build a computational model of the metabolism of a pathogenic E. coli strain based on approximately 20 bacterial genomes — a small number compared to those available today, but an important technological leap at the time. “We tied together all the genes that produce reactions within the organism,” says Baumler. “We could then simulate almost an entire cell on a computer.” He continues to build computational models in an ever-expanding variety of contexts and organisms.

Such models provide insights that lead directly to important applications. “We look at all the information in the genome to figure out what an organism really needs to grow better,” says Baumler. If you know what an organism needs to survive, you can provide it with an optimized environment when you want it to flourish. Alternatively, you can remove what it needs if you want to kill it.

Some of Baumler’s current projects tackle the challenge of warding off prevalent food-borne pathogens like Listeria and Salmonella. One recent project even revisited a malicious
microbe from the middle ages. European collaborators dug  up corpses of bubonic plague victims and sequenced bacterial genomes trapped in their teeth. Based on these
genomes, Baumler built a model that helped reveal fatal secrets buried in the past.

Another of Baumler’s projects aims to cultivate new probiotics that could keep livestock healthier. Minnesota’s beloved turkey flocks, for example, haven’t been plumping up properly — to the tune of 30 million dollars per year in lost revenue. Baumler hopes to fatten the birds by replenishing an important bug that appears to have flown the coop of their microbiomes.

Dairy, another economic boon for the Midwest, has its own set of microbial mishaps. Milk quality and flavor can be compromised by germs, but when and where do they enter the product chain? In parallel with a massive initiative launched by IBM and the Mars candy company, Baumler will spearhead an effort to record comprehensive genetic data on dairy products at every stage of their journey from the cow to your fridge. This information could enable food makers to detect problems as they arise rather than after the fact.

To address epidemic malnutrition, Baumler also mines his personal collection of over 400 varieties of chili peppers in search of vitamin-rich (but not too spicy) varieties. “Chilies are a culturally accepted food in every country in the world,” he says, noting that 30% of all children suffer from insufficient vitamin A. “We could breed new strains and share seeds with everybody around the world to alleviate vitamin deficiencies.”

Baumler —  who has even been known to dress in a chili pepper outfit and sing the praises of his favorite plant — is a big picture thinker with an animated approach to teaching and research. “For me and my students, BTI is opening doors for networking, new information, new funding opportunities, and new collaborations,” he says. “As a BTI member with a background in food science and nutrition, I hope to bring new types of research questions to other BTI members, as well.”