Modeling microbial complexity

Modeling microbial complexity

Modeling microbial complexity

Will Harcombe combines experimental and computational models to decode complex microbial interactions.

By Bernard Cook III

The role of E. coli in causing food-borne illness is well known. Less well known, however, is the way microbes interact with each other. Like humans, they exchange resources and live in communities. Understanding these complex interactions could help scientists predict and even control the properties of a microbial community—yielding new tools for treating infections, promoting human and animal health, and improving soil productivity. 

Will Harcombe, an associate professor of Ecology, Evolution and Behavior and a member of the BioTechnology Institute, studies microbial interaction by looking at the exchange of chemicals among microbial species. “One of the fundamental ways [microbes] can influence each other is just by taking up and releasing chemicals into the environment,” he says. “Will they compete by trying to eat the same resource? Or will they facilitate each other by one secreting a product that helps another?”

Model Behavior

To make sense of microbial interactions, Harcombe starts with a model of how he expects microbes to interact. At its core, a model is a tool that describes how the output of a system depends on its inputs. Harcombe’s models consist of equations that relate the abundance of two microbial species, the output, to defined inputs like available nutrients and spatial distribution. Using the model, he can test what happens to the abundance of two microbial species when placed in an environment with defined nutrients. Importantly, this allows him to observe what the microbes do when they interact in the ways he suspects.

After generating computer-based results, Harcombe replicates this experiment in the lab.  Harcombe places two or more species of microbes together and tracks the resources they exchange. At the same time, he observes population-level characteristics such as growth rates, colony shape and species abundance. By simultaneously monitoring resources and community traits, he can answer questions about the spatial organization, the ratio between species and how available nutrients impact the exchange of resources. 

Sometimes experiments align with the results generated by his model. In other cases, they differ from — or even contradict — the model.

Two-Species Surprise

In one study, Harcombe and his colleagues wanted to investigate the dynamics between two microbial species, each of which depends on the other for survival. One (E. coli) was modified to require a nutrient—methionine—produced by the other (S. enterica). S. enterica, for its part, needs acetate excreted by E. coli.

One might expect these microbial colonies would thrive when cultured together — and when cultured alone, neither would make it. Per his computer model, that’s precisely what happened. When cultured in the lab, he saw the same results.

 Then came a surprise. In the lab, Harcombe introduced a virus that infects one species but not the other. Because each species’ survival depends on the other, Harcombe expected that infection would impact both. 

When he introduced a virus that only infected S. enterica, his prediction was spot on. When he introduced a virus that only infected E. coli, he ended with fewer E. coli as predicted, but surprisingly, he also found more S. enterica relative to pre-infection numbers. What was he missing?

Answering that question experimentally would have required painstaking tests, altering one variable at a time until he understood what was happening. While that approach might eventually provide an answer, it would be costly. Without knowing which explanations were plausible, Harcombe could spend years testing possible mechanisms responsible for the odd result. 

Productive Insights

Enter modeling. If the microbes weren’t behaving the way he expected, there must be something else; different metabolites or different types of interactions to explain the observations. So rather than running experiments to identify the mechanisms at play, Harcombe put those possibilities into the model. Once he found a model approximating his observation, he could confirm his conjecture with additional experimentation.

Harcombe suspected some E. coli developed resistance to the virus, protecting them from extinction. He further postulated that others would burst and release a wealth of nutrients. Together, they might provide an abundance of the acetate S. enterica need to thrive. Incorporating these mechanisms into his model yielded results that closely mirrored the experimental model.

“The biggest surprise to me in this study is that bacteria could get the elements they needed from other species by eating the dead,” says Harcombe.

Back in the lab, Harcombe ran additional experiments to test the model. For the most part, they supported his hypothesis. The only thing missing was a second consequence of E. coli developing a resistance to the virus. Virus-resistant E. coli produced more acetate than their nonresistant counterparts.

Harcombe is pleased with the way the experiment-plus-model approach has boosted his ability to solve microbial mysteries, and how the solutions stand to benefit humanity. Harcombe and colleagues use these models to predict how microbes respond to antibiotics and engineer interactions into microbial communities in soils to render crops more resilient to a changing climate. “Going forward, I’m really optimistic that we will be able to continue to develop our understanding of fundamental processes and apply it in these different areas.”

Mapping uncertainty

Mapping uncertainty

Mapping Uncertainty

Can gene regulatory networks help scientists predict cell behavior and improve therapeutics for cancer and other diseases?

By Bernard Cook III

It’s one of the big mysteries of biology. Why do genetically identical cells often differ in the way they move, which proteins they produce and how they respond to their surroundings? Casim Sarkar, a professor in Biomedical Engineering and a member of the BioTechnology Institute, is working to solve this enigma by studying gene regulatory networks — the interaction between genes and the proteins they produce.  

Sarkar likens these gene regulatory networks to computer code that governs which genes are turned on, what proteins they produce and in what quantity. As it turns out, a cell’s behavior (for example, how it moves) and the decisions it makes (whether to move) are largely determined by gene regulatory networks and how they interact with the cell’s environment. 

To begin unraveling the link between gene regulatory networks and cell behavior, Sarkar’s lab borrowed the concept of the “epigenetic landscape” from developmental biologists. Initially, the epigenetic landscape was developed as a visual metaphor to demonstrate how a stem cell (a cell that has not yet developed a specific function) becomes one of many cells with a defined function, like a neuron or a muscle cell. According to Sarkar, “The landscape looks like a ski slope where you can take different paths all starting from the same point.” 

Like a ski slope, the epigenetic landscape has defined features like height, steepness and surrounding hills and valleys, which collectively inform what a cell — in this case, the skier — will do next. Picture placing a marble on a Pringle: in some directions, it may move downward and in others it can only go up. Let go, and the marble will most likely move downward. Like this, a cell on or near a crest is likely to move downhill and perform actions that are more likely, while a cell in a valley is met with resistance and likely won’t change its behavior at all (unless, like a skier, it has accumulated sufficient prior momentum to move upwards).

Instead of simply using the landscape to conceptualize cell behavior, Sarkar’s lab is developing a computer-based epigenetic landscape to predict what a cell in a given state might do next — and the likelihood of that outcome. This approach is particularly useful because it allows him to incorporate elements like cell-to-cell variability and DNA modifications, two features of gene regulatory networks that may push two otherwise identical cells to do different things in the same circumstances. In his model, these elements play a role in determining the shape of the landscape, which allows Sarkar and his team to make predictions about cellular behavior by accounting for these confounding elements. Importantly, this approach also allows him to pinpoint facets of the gene regulatory network that drive two identical cells to behave differently. 

Understanding why identical cells take different paths may help improve therapies for cancer and other conditions. In cancer, for example, tumors consist primarily of cells that proliferate rapidly. But some cancers also contain dormant cells that evade standard chemotherapy and often cause relapse. Sarkar’s approach could identify aspects of the gene regulatory network that push some cells to choose dormancy, which in turn, may help researchers keep these cells dormant or identify an intervention that awakens dormant cells and renders them vulnerable to standard chemotherapy. 

Sarkar’s long-term goal is to make concrete predictions about what a cell might do in specific environmental conditions as a result of the underlying gene regulatory network. Solving this mystery could help engineers working with stem cells create tissues with the desired structure and function and improve therapeutic strategies to combat antibiotic resistance.

Enzyme advances promise to boost the bioeconomy

Enzyme advances promise to boost the bioeconomy

Enzyme advances promise to boost the bioeconomy

Enzyme technology symposium brings together researchers from North America and Japan working on cutting-edge applications.

By Stephanie Xenos

Around 85 researchers and industry partners involved in developing new enzyme-based applications recently came together at the University of Minnesota for the 1st North America-Japan Enzyme Technology Symposium. The symposium, organized by the BioTechnology Institute and Amano Enzyme Japan, focused on enzyme technology relating to biocatalysis and food, two key areas of the growing bioeconomy. 

“This symposium provided opportunities for new collaborations and learning about new enzyme applications that are particularly relevant for advancing the bioeconomy in Minnesota given the abundant agricultural and forest resources in our state,” says Claudia Schmidt-Dannert, director of the BioTechnology Institute.

Speakers covered a range of topics including modifications in the rate at which plants absorb light, in wood xylan to make polymers for food packaging, and in polyunsaturated fatty acids to make therapeutics.

“Enzyme applications make our lives better and our environment cleaner but most people are unaware of their importance since they work for us out of sight,” says Romas Kazlauskas, a professor in Biochemistry, Molecular Biology and Biophysics, and one of the organizers of the symposium. “Enzymes make our laundry detergents more effective, are used to make the COVID-19 drug Paxlovid, and improve the texture and taste of our foods. This symposium provided examples of current and future applications of enzymes.”

The symposium provided students and postdocs to engage with experts from industry and academia, and learn about the breadth of enzyme applications.

A selection of symposium talks are available to view.

Undercover Operative: Environmental Microbiologist Infiltrates the World of Human Microbiome Research 

Undercover Operative: Environmental Microbiologist Infiltrates the World of Human Microbiome Research 

Undercover Operative: Environmental Microbiologist Infiltrates the World of Human Microbiome Research 

BTI Researcher Christopher Staley uses an ecology framework to tackle the human microbiome and its intricate secrets. 

By Emerson Mehring

Can your poop cure disease? Sounds ridiculous until you hear stories from patients helped by a fecal microbiota transplant (FMT). BTI Researcher Christopher Staley left the banks of the Mississippi River and dove head first into the diverse ecosystem living inside our digestive tract: the microbiome. But how did he get there?

During his undergraduate and graduate studies, Staley met Michael Sadowsky, a distinguished microbiologist and then director of the University of Minnesota BioTechnology Institute. After mingling at several research conferences, Sadowsky offered Staley a job studying water quality at pollution sites along the Mississippi River. Staley’s role was to isolate and analyze DNA sequences from microorganisms living in the water and sediment.

With no expertise in mathematical modeling for biological systems or computational biology, Staley was concerned about his new position, but Sadowsky reassured him he was a good fit. Staley offered a new perspective to the team of bioinformatic scientists that would process the data. He understood the connections to the larger ecosystem.

“I learned how to speak both languages,” recounts Staley. “And we found eight stories hidden in their data which were all eventually published.”

Much like the waters of the Mississippi, the digestive tract harbors countless microbial communities. When Sadowsky introduced Staley to fellow BTI researcher Alexander Khoruts’ work on the microbiome, a natural partnership emerged. 

Khoruts and Sadowsky were instrumental in developing the modern use of microbiota transplant therapeutics (MTT), though the practice dates to fourth-century China when people suffering from severe diarrhea were treated using a soup of dried fecal matter (yes, you read that correctly) to restore the balance of bacteria in the gut. Khoruts and Sadowsky sought a modern approach to help patients suffering from stubborn Clostridium difficile infections that cause severe stomach cramping, diarrhea, and abdominal pain. But faced with the complexity of the microbiome, Khoruts and his team had many unanswered questions.

After analyzing their dataset, Staley recognized that environmental science offered some solutions. “The tools and techniques we used studying the river are the same for fecal samples. They thought their questions were hard, but I saw them through a different lens.” He recalls the collaboration as a success because they respected each other’s expertise, which presented complementary analytical perspectives. 

After dabbling in clinical research, Staley’s curiosity was piqued, so he pursued a position in the Department of Surgery at the University of Minnesota. 

Navigating the transition from environmental to clinical research was challenging. Staley built on his background in ecology to explore links between the microbiome and human disease while working with University of Minnesota physician Armin Rashidi, who studies the effects of leukemia treatment on the microbiome. 

Knowing that antibiotics can wreak havoc on the microbial balance in the body, Rashidi sought to understand the potential impact on his patients. Working together, Rashidi and Staley determined that antibiotics—while effective in treating harmful infections—also destroyed the helpful bacteria that keep our bodies healthy. This paradox proved fundamental to understanding the connection between the microbiome and disease and how microbial communities interact to support and undermine human health.

The microbiome has been linked to obesity, colorectal cancer, and almost every illness researchers could find. And while microbiome research has blossomed over the last decade, Staley estimates about 15 percent of studies pay adequate attention to microbial community function, and even fewer explore a critical component of bacterial communication: quorum sensing. Staley’s new focus is on disrupting the signaling molecules bacteria use to communicate with quorum quenching techniques, in collaboration with BTI investigator Mikael Elias, which prevent synchronized behavior in microbial communities.

“Of course, they’re talking in there,” says Staley. “Did you think the bacteria were just sitting there, ignoring each other? There are trillions of them!”

In preliminary testing in mice, Staley found evidence that quorum sensing could play a significant role in the gut-body connection. When fed a Western diet, quorum-quenching mice were more resistant to diet-induced obesity than mice in the control group. While only a preliminary trial, Staley is enthusiastic about digging into the mechanics of bacterial communication and its impact on the human body. 

Does he miss the Mississippi and his work in environmental science? Staley’s lab is a short walk from the mighty river, and as he points out: “First, I was looking for the effects of pollutants on a body of water, and now I’m analyzing fecal matter for how bacteria impact the body … it’s almost the same!”

Q&A with BTI Director Claudia Schmidt-Dannert

Q&A with BTI Director Claudia Schmidt-Dannert

Q&A with BTI Director Claudia Schmidt-Dannert

As the BioTechnology Institute’s new director, longtime faculty member Claudia Schmidt-Dannert aims to plant the institute firmly on the front lines of emerging needs and opportunities.

By Mary Hoff

Two decades ago, Claudia Schmidt-Dannert knew exactly where she wanted to be: at the frontlines of the intersection of biology and technology. And that meant joining the faculty of the University of Minnesota’s BioTechnology Institute. “BTI is actually one of the reasons I came to the University of Minnesota, because of this interaction between life sciences and engineering,” she says. “That’s very unique here.”

Named BTI director in January of this year, Schmidt-Dannert is working not only to strengthen interdisciplinary ties within the community as it recovers from disruptions due to the Covid pandemic, but also to firmly establish BTI’s position at the frontlines of biotechnology research and application during what could be the field’s most exciting times yet.

What do you hope to accomplish as director?

My focus is on keeping pace with biotechnology, really thinking about, “What are the next big things?” For example, biomanufacturing, biofabrication, new types of functional biomaterials for a range of applications—this is the future. We really must position ourselves very well in this space, make sure we are at the forefront of these types of efforts in biotechnology research, applied science, and development. We need to make sure we have the right people, resources and get people to collaborate across disciplines on these topics. We want to be spearheading new developments in biotechnology, looking at what biology can do to improve our future.

What strengths do you bring to the role?

I have a broad research background. I’m working both in fundamental areas of biotechnology but also in the engineering space, and my research spans from molecules to systems. I’m also very applied-minded. And I maybe bring a little bit more of a fresh perspective. We have a strong focus in bioremediation and environmental aspects of biotechnology. There are other and emerging focus areas in biootechnology that we should pay attention too and emphasize more. Also, I like collaboration and community-building. This is very important with a variety of stakeholders.

How important will BTI’s role in workforce training and strengthening Minnesota’s biotechnology be under your administration?

Most of our undergraduate and graduate students as well as postdocs will not follow an academic or medical career and instead many will seek out other employment in industry. There is high demand for skilled individuals from the biotechnology and biomanufacturing sector. We need to make sure that our students and postdocs are well prepared for these good-paying jobs. Over the past few years, BTI has collaborated with industrial partners on workforce development. I see this as an area that should be expanded. In addition, I feel strongly that meaningful biotechnology training should be incorporated at the undergraduate levels—where BTI can contribute. BTI also administers a small masters-level graduate program in microbial engineering that is aimed at students that want to go into industry. The student and postdoc-level workshop series as well as workshops offered through our NIH Biotechnology training program provide additional career relevant, professional skill sets.

Where do you see the big opportunities in the years ahead?

Biotechnology is very broad field, so there are many opportunities for different types of research. For example, synthetic biology is experiencing an influx of many new ideas in areas like materials sciences, sustainable biomanufacturing, artificial intelligence and computing. Addressing climate change, developing a circular bioeconomy, biomanufacturing and biofabrication—that’s where I see a lot of opportunities.

We also have very unique resources in Minnesota that go beyond our strong medical and agricultural industries. Northern Minnesota is rich in forests, water and minerals. My goal is to look at these resources as well as associated societal and environmental challenges associated with accessing these resources from a biotechnology perspective. I believe that there are many unique Minnesota-specific opportunities for biotechnology and bioeconomy development in our state.

What do you see as growth areas for the Institute?

I would like to continue building momentum and strength in synthetic biology. We have a research cluster in this area, but we have to further ramp up our expertise in this area. We are also lacking in certain cell-based manufacturing systems, especially for pharmaceuticals and biologics – we are not particularly strong in this area. Right now. we’re focused mostly on microbial systems with the new BRC [Biotechnology Resource Center] Microbial Cell Production Facility. But I also think mammalian cell cultures offer new opportunities for research. We need to bring in more young faculty with expertise in these areas.

Another goal is to build community, facilitate social interactions and provide more opportunities to exchange ideas among biotechnology research labs—crossing disciplines but also campuses. That was all put aside during Covid times, but it is very important. Without community, BTI is nothing but a collection of people. We’re going to have seminars followed by networking happy hours in both St. Paul and Minneapolis, not just by bringing in external speakers but having BTI labs give short talk to present their current research and where there research is headed. We are also reviving the graduate student and postdoc-led workshop series.

How will the Biotechnology Resource Center expansion benefit the University and for the state?

The new Microbial Cell Manufacturing Facility will have six times the pace of the current BRC, which will bring much needed capacity in microbial biomanufacturing to the University. Currently, the BRC is operating at capacity and even must turn down biomanufacturing projects and clients because of this. There is a huge demand for the types of the service the BRC offers in the preclinical space. The expanded BRC will therefore be able to serve much better the needs of UM researchers, industry, and academic partners. The “old BRC” offers opportunities for the development of new workforce training programs in biomanufacturing.

What are the big emerging societal needs that biotechnology can address, and how is BTI positioning to address them?

It is clear that we need to find drastically new ways of mitigating climate change, by developing new bio-based technologies for sustainable manufacturing, energy conversion, combating greenhouse gas emission or converting and sequestering carbon dioxide and for addressing environmental concerns. I see BTI as a catalyst and facilitator of research in these areas by bringing people together to tackle ambitious problems as teams with diverse cross-disciplinary skill sets.

Synthetic Cells and Biofactories

Synthetic Cells and Biofactories

Synthetic Cells and Biofactories

Kate Adamala and the Build-a-Cell consortium look to synthetic biology for insight into the origins of life and a source for vital raw materials.

By Bernard Cook III

Your phone, your food, and the fuel that powers your car all depend on oil-derived petrochemicals. But experts anticipate oil reserves will run dry as early as 2070, forcing industries dependent on petrochemicals to look for alternatives that would fundamentally change the way they do business–and the way we live.

But scientists like Kate Adamala (BTI/Genetics, Cell Biology and Development) see another path forward. They envision a world where oil reserves disappear but one where we’ll still be able to meet our need for petrochemicals. Their solution? Create more life.

Adamala, a chemical engineer by training, is working to build living organisms from nonliving chemical components. These “synthetic cells” can help scientists explore the origin of life, accelerate drug discovery, or provide a renewable source of resources, like petrochemicals.

At its core, a synthetic cell is an organism that exhibits lifelike qualities. Much like a car, which is a collection of metal parts until arranged in the right way, cells are chemical bundles organized in a particular manner. Adamala constructs synthetic cells in her lab by encapsulating nucleic acids, amino acids, and ribosomes (the building blocks of cellular life) within a protective lipid coating. This method, known as the “bottom-up” approach, offers a key advantage: complete control over the cell’s components.

Natural cells can also be engineered to perform specific functions, but they’re resistant to change, and coaxing them into producing large quantities of desirable chemicals comes at a cost. When scientists engineer cells to create petrochemicals, for example, the build-up of those chemicals can damage the cell. “No self-respecting cell will make those chemicals because it’s toxic to them.”

Synthetic cells, however, are a blank slate. “Because we make them from scratch, they don’t have the baggage of 4 billion years of evolution,” Adamala remarks. They can be manufactured to do what scientists want them to do (like churning out petrochemicals). But, even with this level of control, there are still compromises. Adamala likens this to canine domestication. “I want my dog to sit on my lap and keep me warm in the winter. And he does that, but he cannot go out and hunt … so that’s the trade-off we made.”

Before synthetic cells can support a robust biomanufacturing economy, scientists like Adamala also need to resolve the physics of how cells self-replicate. To date, researchers have yet to determine how to make synthetic cells reproduce on their own–a crucial step toward using these organisms as in mini, living biofactories.

Like many scientists, Adamala grew up watching science fiction films and was fascinated by the search for life beyond earth. She earned her Ph.D. in astrobiology, but synthetic biology allowed her to explore her passion while producing tangible benefits for society. “The synthetic cell engineering field presented itself as everything I always wanted. It has connections to origins and astrobiology, so I can still say I’m looking for life on Mars! But it’s also incredibly applicable. It could solve some of the biggest problems our economy is facing now.”

Adamala isn’t the only scientist excited about this approach to cell engineering. The Build-a-Cell consortium, co-founded and led by Adamala, intends to construct a network of scientists sharing ideas, data, success stories, and failures–not unlike open-source software platforms that depend on shared knowledge to drive innovation. Adamala is hopeful that by uniting researchers via Build-a-Cell, they’ll get there sooner rather than later.

Once we unlock their potential, synthetic cells could produce fuel for our cars, fibers for clothing, and fertilizers to increase crop yields. They may also accelerate biomedical discovery or offer a glimpse into the life of our earliest ancestors. One day, they may even enable us to survive on Mars.