Fellowship Program Builds Bridges in Microbiome Sciences

Microbes quietly shape our world, influencing everything from the air we breathe to the food we eat. Despite their vast impact, research into microbial systems has long been fragmented—split across academic disciplines and institutional silos.

A fellowship program at the University of Maryland is underway to bridge those gaps.

Now in its second year, the Microbiome Center Fellowship brings together eight graduate students from across campus to collaborate on research spanning human, environmental and agricultural microbiomes.

The seven-month program fosters interdisciplinary connections and prepares students to tackle global challenges with a systems-level approach to microbiome science. Fellows receive an $8,000 stipend and gain access to shared computational and sequencing resources, including those at the University of Maryland Institute for Advanced Computer Studies.

The program is coordinated by the UMD Center of Excellence in Microbiome Sciences, which began operations in 2023 with startup funding from the UMD Grand Challenges Grant program.

“Microbes are everywhere, from human and animal health to agriculture and the environment,” says Gabi Steinbach, associate research scientist and program coordinator of the center. “Different habitats host diverse microbes that make up complex microbiomes, and microbes move between these environments, linking them together.”

Steinbach notes a unique aspect to the fellowship: students’ advisers joining in on the networking and community-building activities, creating additional opportunities for cross-disciplinary connections among both faculty and students.

“We’re building a community where students not only gain technical skills, but also learn to work across cultural and disciplinary divides,” Steinbach says.“They get to connect with faculty and peers from diverse fields, which is essential for advancing microbiome science.”

For example, at a recent launch meeting, fellows, their advisers, and program leaders took part in activities designed to spark collaboration—including a research and resource-sharing speed chatting session that participants found both productive and fun.

This year’s Fellows include Raunak Dey and Nakia Fallen from the College of Computer, Mathematical, and Natural Sciences; Claire Barlow from the School of Public Health; Darby Steinman, Ingrid Roselyne Dukundane and Yuzhu Mao from the A. James Clark School of Engineering; and Erin Harrelson and Yue Jiang from the College of Agriculture and Natural Resources.

Throughout the program, these students will participate in team science training, cross-disciplinary workshops, and seminars aimed at preparing them to collaborate across disciplines and translate scientific principles into transformative action. The Fellows will also organize and host an invited panel in December, choosing a topic themselves based on what they have explored together throughout the fellowship. The capstone event will be open to the campus community and will showcase the collaborative outcomes of the program.

“We’re excited to see how these students take what they’ve learned and shape the future of microbiome science,” Steinbach says. “Their panel in December will showcase the kind of innovative, cross-disciplinary thinking we need to solve complex challenges.”

—Story by Melissa Brachfeld, UMIACS communications group

Zierden Receives NSF CAREER Award To Address Women’s Health Disparities

A University of Maryland (UMD) chemical engineer developing specialized therapies for women’s health was named a recipient of the National Science Foundation’s Faculty Early Career Development Program (CAREER) Award—making a step forward in addressing gaps in gynecological care. 

Hannah Zierden, an assistant professor of chemical and biomolecular engineering at UMD, will lead a new initiative that integrates research and education to advance knowledge of the female reproductive tract. The NSF CAREER award is her latest recognition for this ongoing work. 

“I am incredibly honored to receive the NSF funding support for our work, and excited to begin diving into our hypotheses in hopes of uncovering mechanisms that drive female reproductive health,” said Zierden.

The assistant professor will investigate the vaginal microbiome—a home for living bacteria in the female reproductive system—which is responsible for promoting the overall health in this tract, hoping to understand how new treatments could evolve from biological systems. 

She will focus on studying bacterial extracellular vesicles (bEVs), which are biological nanoparticles released by bacteria that enable cell communication between bacteria and host cells, with potential implications for female reproductive diseases. How bEVs come to form is unknown, and there is generally limited knowledge surrounding their fate and function within the female reproductive tract. These limitations slow progress towards treatments for infertility, preterm birth, and sexually transmitted infections. Zierden’s goal is to understand how bEVs impact women’s health throughout the lifespan.

Given what researchers understand about bEVs, these organisms are a growing area of interest as a therapeutic technology given their physical properties. In other words, bEVs could someday be used to deliver treatments within the female reproductive tract.  

“The human body sends a wide variety of signals to coordinate biological functions. Some of those signals are sent by bacterial cells–including bacteria in the female reproductive tract. While bEVs have gotten a lot of attention in recent years, bEVs from vaginal bacteria have been largely neglected,” explained Zierden, who is also a member of the UMD Center of Excellence in Microbiome Sciences. “If we can understand the interactions between bEVs and female reproductive tract cells, we will build a foundation for using bEVs as a potential therapeutic for women’s health,” she said.  

The educational portion of the initiative aims to spark interest in the microbiome sciences within pre-college student populations. In collaboration with the Baltimore Underground Science Space, Zierden will establish an internship program for students from local community colleges. She will also recruit high school students to her lab to provide them with experiential learning opportunities while working towards her research goal. 

“Zierden’s innovative approach to investigating drug delivery in the vaginal microbiome is a testament to her dedication and to our department’s commitment to advancing women’s health,” said Peter Kofinas, Chair of the Department of Chemical and Biomolecular Engineering. “We look forward to seeing the impact of her work, which has tremendous potential to reshape how we think about gynecological care and inspire the next generation of engineers.”

Story by A. James Clark School of Engineering

Congressional Leaders Visit Ghodssi’s MATRIX Lab

MATRIX Lab Director of Remote Sensing and Microsystems Justin Stine (left) explains the work on ingestible capsules going on in the building’s new Advanced Manufacturing Lab.

The Maryland Autonomous Technologies Research Innovation and eXploration (MATRIX) Lab hosted part of a Congressional visit to Southern Maryland by U.S. Senator Chris Van Hollen and U.S. Representatives Steny Hoyer and Sarah Elfreth. On May 19, the members of Congress, plus U.S. Senator Angela Alsobrooks, toured the Naval Air Station Patuxent River, the USMSM SMART Building, and the MATRIX Lab at the University of Maryland (UMD) to learn about how different sectors collaborate to teach students in-demand skills, strengthening the region’s workforce and its economy.

“I am proud of our outstanding federal and state representatives for all they do to provide access and opportunities for our students across the state of Maryland,” said Reza Ghodssi, Distinguished University Professor of Engineering at UMD, a member of the UMD Center of Excellence in Microbiome Sciences, and the Executive Director of Research and Innovation at the MATRIX Lab. “Education and research are always the backbones of what makes the U.S. the world’s leader in science and technology. Thank you to Senator Van Hollen, Representative Steny Hoyer, and Representative Sarah Elfreth for touring the MATRIX Lab during their visit to Southern Maryland and meeting our students and researchers.”

At the MATRIX Lab, representatives from organizations presented examples of how academia, military, government, industry, and nonprofit organizations collaborate to create opportunities in Southern Maryland.

Speakers represented USMSM, the Southern Maryland Navy Alliance (SMNA), St. Mary’s County Economic Development, the Patuxent Partnership, UMD, and the College of Southern Maryland (CSM).

These organizations and many more work together to promote STEM education through field trips, camps, and other activities and give students the hands-on experience they need to succeed through apprenticeships and internships. The organizations also strengthen the technical workforce through promoting educational and professional pathways and creating lifelong learning and development opportunities. When all of these sectors are in constant communication, they empower the community with in-demand skills that real-world employers are looking for.

After the briefings, the members of Congress toured the lab spaces and were able to meet and speak with the researchers and students using the building’s state-of-the-art facilities and cutting-edge equipment.

“The UMD MATRIX Lab is a national leader in research and innovation and an important driver of economic growth and workforce development across Southern Maryland,” said Senator Van Hollen from Maryland’s 8th District. “Seeing their work firsthand and hearing from students and researchers about its impact is not only inspiring, but also highlights the power of partnership in the region between academic institutions, the military, and across the public and private sectors. I’ll continue working to support the critical work being done by UMD and its partners.”

Representative Hoyer of Maryland’s 5th District appreciated the collaboration across sectors that he witnessed on the tour.

“Ensuring Maryland and America stay competitive in the 21st-century global economy requires encouraging academia, government, and the private sector to collaborate together more closely than ever before. I was pleased to see that cooperation at work in Southern Maryland,” he said. “The researchers and innovators at the UMD MATRIX Lab and its partner institutions are helping our state and country get ahead, which is why I will continue to do everything I can to support their vital work.”

Representative Elfreth of Maryland’s 3rd District was impressed at the innovative research coming out of Ghodssi’s lab.

“The innovation at the UMD MATRIX Lab is second to none,” she said. “Senator Van Hollen, Congressman Hoyer, and I had the opportunity to meet with their scientists and learn more about their groundbreaking research on ingestible capsules, autonomous aerial refueling, underwater systems, and more. In Congress, Team Maryland will continue to advocate for university research funding to keep our state at the forefront of research and innovation.”

Story by A. James Clark School of Engineering

Mealtime ‘Swap’ Helps Researchers Understand Heart Health

An alarm bell dinged, and Fernanda Sato dashed to the oven to remove a steaming tray of eggs. The University of Maryland master’s student was preparing breakfast in a campus kitchen for a half-dozen people dropping off samples from previous meals—in a manner of speaking.

Nutrition and food science students with UMD’s College of Agriculture and Natural Sciences are conducting an experiment on 24 participants, anchored by a typical American diet: egg and cheese croissant sandwiches, flour tortillas and crackers, for example. Because the menu largely eschews fruits, fiber and whole grain, it’s not the gold standard of nutrition, and that’s the point.

The meals lack catechins, a natural antioxidant chemical found in certain foods and beverages like apples, fava beans, sweet potatoes, blackberries, dark chocolate, green tea and red wine and thought to support heart health. The researchers want to confirm that premise, but they also suspect that only some eaters reap the biggest nutritional rewards of catechins, and they want to know why.

During a testing period that ended last week, participants hewed to low-catechin diets for three days, but half consumed catechin-rich cranberry-apple juice throughout the period while a control group drank a placebo drink made with sugars and artificial flavors and coloring.

Before and after the regimen, each participant submitted stool and urine samples. In the coming months the UMD team will probe the now-frozen specimens, looking for biomarkers of catechin digestion—a good sign—and compare it to participants’ blood pressure and body composition.

“Some people’s gut bacteria can metabolize the catechins to a greater extent so that they’re absorbed into the bloodstream, as opposed to, forgive me, just pooping it out,” explained Associate Professor Margaret Slavin, who is leading the UMD study, funded by the U.S. Department of Agriculture.

After eating their on-campus breakfasts, participants left with freezer bags packed with low-catechin lunches, dinners and snacks prepared by UMD students in Slavin’s lab. The menu included turkey and cheese wraps, soybean nuts and meatloaf, mashed potatoes and glazed carrots. (Each participant spent one week in the intervention group and one week in the control group.)

Recruited through campus flyers offering cash compensation, most participants appeared to be students, though Slavin didn’t ask. After gathering data about their typical diets, her team devised a menu with similar foods.

Last Monday, Sato arrived at the industrial-size kitchen lab in Marie Mount Hall at 6 a.m., donned an apron and hairnet and began prepping breakfast. After graduation she plans to launch a career as a clinical dietitian for hospital patients with diabetes, cardiovascular disease and other health issues, assessing their nutrition status and recommending diets.

After the eggs had been scrambled and baked twice, Sato removed them from the oven and took their temperature—“185 degrees, we’re good,” she said—and passed the tray to another student who measured 120-gram portions into serving cups.

In an adjacent kitchen Nora Baustian, a second-year doctoral student, filled each participant’s take-home freezer bag, including instructions on when to drink the beverages. (For the intervention group, spreading catechin consumption throughout the day increases potential absorption.)

Shortly after 8 a.m., Baustian carried a platter of eggs, roasted peppers and buttered toast into a classroom doubling as a dining room and served it to Tereza Varejkova, a UMD economics doctoral student who joined the study in part because of her interest in nutrition. There was also a personal benefit, she said: “It’s nice not to think about cooking.”

On the first day and day after the diet, participants dropped off their stool and urine samples, which will eventually be shipped out for lab analysis. Slavin’s team will break down the data in hopes of publishing its findings next year.

The study grew out of an earlier data collection phase starting in 2023, when 180 people consumed a soy-based snack that distinguished them as either “producers” and “nonproducers” of catechin-related metabolites. A mix of 24 participants moved on to the current study.

The results could help dietitians personalize diets based on microbial makeup. If someone knows their gut can metabolize catechins, they could consume foods and beverages with higher levels. For other people, scientists might find ways to change their microbial composition or develop metabolite supplements, Slavin said.

“Right now, nutritionists give blanket advice to consume certain food groups, like getting plenty of vegetables and fruits—this is valid based on what current evidence says,” said Slavin, who is a member of the UMD Center of Excellence in Microbiome Sciences. “But in the future, if we know that some people get more health benefits from certain foods, we could better target our recommendations to meet their individual needs.”

Story by John Tucker for Maryland Today

UMD Microbiome Center Co-Hosts Mid-Atlantic Microbiome Meetup

More than 140 participants representing industry, government and academia recently met in Baltimore to explore topics related to innovation and translation in microbiome research.

The 7th annual Mid-Atlantic Microbiome Meet-up, held on March 21 at the University of Maryland, Baltimore, highlighted ongoing microbiome research tied to human and animal health, agriculture, bioengineering, the environmental sciences, and more.

Co-hosted by the Center for Advanced Microbiome Research and Innovation (CAMRI) at the University of Maryland School of Medicine and the Center of Excellence in Microbiome Sciences at the University of Maryland, the one-day symposium featured two keynote talks, nine oral presentations and 42 poster presentations.

Just as important, say the event organizers, was the opportunity for participants from diverse scientific backgrounds—federal scientists, academic researchers and industry leaders involved in the biotech sector—to network and discuss possible collaborations.

“I was blown away by the breadth of the research presented at the meet-up and the level of participation by researchers exploring these topics,” says Mihai Pop, a professor of computer science at UMD who is helping lead microbiome research efforts on the UMD campus. “This demonstrates the important role microbial communities play in virtually all aspects of our lives.”

Pop noted that this year’s meetup drew participants from 10 higher education institutions, two research institutes, four federal institutions, and the American Society for Microbiology.

In the opening keynote, Susan Lynch, a professor of medicine from the University of California, San Francisco, spoke about the role of microbiome in allergic disease in infants. Lynch showed that early-life microbial exposures may drive the onset of asthma and eczema in infants, and proposed potential microbial-related therapies to address these important childhood conditions. 

The meet-up concluded with a presentation by Benjamin Wolfe, an associate professor from Tufts University, who spoke about the microbiome of fermented foods. Wolfe described the role microbes play in the fermentation processes used to produce many commonly-used foods (such as sourdough, cheese, kombucha, and more), and highlighted evolutionary and community design principles discovered in his laboratory that can be leveraged to manage microbial communities used in food production. 

The meeting was organized by CAMRI and was co-sponsored by Maryland Genomics, QIAGEN, AmpSeq and Symcel.

—Story by UMIACS communications group

Unlocking the Secret Carbon Storage in Soil

Farm soil is more than just dirt—it’s a carbon storage powerhouse. 

To prevent erosion and build nutrients in the soil, farmers often plant cover-crops to shield their main crop. These cover crops can help the soil store more carbon, thereby reducing the amount of greenhouse gases in the atmosphere.

Jason Manzon, an environmental science and technology master’s student at the University of Maryland (UMD), is studying the growth of cover crops in a greenhouse to trace the movement of a special carbon isotope that shows where carbon goes when it enters the soil.

He’s experimenting with different moisture levels to understand the organic matter structure and long-term stability of soil carbon. 

Manzon is collaborating on this project with Stephanie Yarwood, an associate professor of environmental science and technology and a member of the UMD Center of Excellence in Microbiome Sciences.

Their work has the potential to help mitigate climate change and improve farming practices by keeping carbon in the soil.

This video was produced by UMD’s College of Agriculture and National Resources.

Designing A Drug to Prevent Preterm Birth

More than one in 10 babies in the United States are born at least three weeks before their due date. For these families, what should be a time of joy can instead lead to deep anxiety and a sense of helplessness. The economic consequences are enormous, too: the annual medical and associated costs of these preterm births add up to a staggering $25 billion in the United States alone. 

Even worse, progress on the problem has stalled: Accelerated FDA approval for a progesterone-based injection used to prevent preterm birth was withdrawn in late 2023 because it was not shown to be effective. Today, there is not a single FDA-approved treatment available.

Hannah Zierden, an assistant professor of chemical and biomolecular engineering at the University of Maryland (UMD) and member of the UMD Center of Excellence in Microbiome Sciences, hopes to create one. 

Zierden is currently testing the use of tiny particles known as bacterial extracellular vesicles (bEVs), which are produced by vaginal microbes, as a drug delivery mechanism. These particles, which are released by bacteria, function something like biological “mail” by delivering biological materials and communications from the cell to other parts of the body. Zierden says they could also be loaded with drugs or other materials and targeted to specific cells or tissues.

These bEVs hold particular promise not only because they can move drugs through vaginal mucus, a biological barrier that has proven to be a formidable challenge for scientists in the past, but because they can deliver drugs more precisely than injections, which can get diluted in circulation.

Currently, she is teaming up with fellow chemical and biomolecular engineering assistant professor Po-Yen Chen on a machine learning and AI project to help her identify bEV formulations that can be manufactured at scale and have the greatest potential for success.

Zierden says that advances in bEV drug delivery could re-open the door to the use of progesterone to prevent preterm birth. “When you can deliver drugs directly to the female reproductive tract, you can increase the payload to target tissues while decreasing off-target side effects,” she says.

Story by Erin Peterson, Engineering at Maryland magazine

Photograph by Maximilian Franz

Building Systems to Support More Powerful Real-Time Health Monitoring

Living systems transfer information through molecules and ions. The internet transfers information through electrons and photons. While each communication system is elegant and effective, the two have typically remained worlds apart: Scientists have struggled to find ways to connect the systems effectively—or even translate between them.

Still, the possibilities of the so-called “Internet of Life” are tantalizing, says William “Bill” Bentley, the Robert E. Fischell Distinguished Chair of Engineering and director of the Maryland Technology Enterprise Institute and Fischell Institute for Biomedical Devices.

“If we could transfer information from one system to another, you could imagine all sorts of new technologies and processes,” says Bentley, who is also a member of the UMD Center of Excellence in Microbiome Sciences.

One dream scenario? A device connected to the human body to sense disease progression and administer drugs as needed.

This future may be closer than ever. Work by Bentley and his colleagues, including longtime collaborator Greg Payne, a research professor and Fischell Institute Fellow in UMD’s Institute for Bioscience and Biotechnology Research, and recent alums Sally Wang Ph.D. ’23 and Chen-Yu Chen Ph.D. ’23, has uncovered a bridge in the communication gap between biological and electronic systems.

Bentley and his lab have created hydrogels developed from a substance known as chitin that can facilitate information transfer between microelectronics and biological systems. Then they developed a cutting-edge bioelectronic device, dubbed BioSpark, that receives and digitizes biological signals and returns electronic commands back. The team has even demonstrated how they could electronically control gene expression in bacteria.

Their work could lead to biosensors that monitor, in real-time, our microbiome health or oxidative damage in blood serum linked to health conditions such as schizophrenia—or even take corrective action. “When you open up communication between biology and electronics, it’s a completely new way of getting information,” Bentley says.

Story by Erin Peterson, Engineering at Maryland magazine

Photograph by Maximilian Franz

Mihai Pop Is Named an MPower Professor

Mihai Pop, a professor of computer science and director of the University of Maryland Center of Excellence in Microbiome Sciences, was just named an MPower Professor, a prestigious honor that recognizes, incentivizes and fosters collaborations between faculty at the University of Maryland, College Park and the University of Maryland, Baltimore.  

Pop is part of a cohort of seven faculty named as MPower Professors this year. To be considered for the MPower Professorship, faculty must demonstrate collaboration on strategic research that would be unattainable or difficult to achieve acting independently of one another and must embrace the mission of MPower—to collectively strengthen and serve the state of Maryland and its citizens.  

Each MPower Professor receives $150,000, allocated over three years, to apply to their salary or to support supplemental research activities.

“I’m deeply inspired by this incredible group of MPower Professors, who are not only dedicating themselves to solving some of the most complex problems facing society, but also embracing the power of cross-disciplinary and cross-institutional collaboration,” said UMD President Darryll J. Pines. “By working together, we unlock new creative potential and develop innovative solutions that we couldn’t achieve alone.”

In addition to his leadership role in the microbiome center, Pop is the current director of University of Maryland Institute for Advanced Computer Studies and is a core faculty member in the Center for Bioinformatics and Computational Biology. His research focuses on the development of sequence assembly algorithms and analysis of genomic data sets. His lab developed widely used computational tools for the analysis of genomic and metagenomic data. Pop is globally recognized for his efforts to diversify the computer science and computational biology communities.

Detecting Troubling Gastrointestinal Conditions Earlier With Ingestible Capsules

As the prevalence of gastrointestinal (GI) diseases continues to skyrocket—the American Cancer Society predicts colorectal cancer will be the leading cause of cancer death for people under 50 by 2030, and both inflammatory bowel disease (IBD) and gastroesophageal reflux disease (GERD) are on the rise—finding new ways to monitor our GI health has become imperative. 

One area that holds particular promise: sensor-packed ingestible capsules that patients can swallow as easily as their morning vitamins.

Depending on the need, the capsules could be developed to gather valuable information—or even to precisely deliver drugs, says Reza Ghodssi, the Herbert Rabin Distinguished Chair in Engineering, executive director of research and innovation at UMD’s MATRIX Lab, and a member of the UMD Center of Excellence in Microbiome Sciences.

“PillCams can already take pictures as they travel through patients’ GI tracts, but similar technologies could have electrochemical sensing capabilities,” he says. “They could survey GI tissue for the harmful thinning of the mucosal layer, which can’t always be observed with a PillCam, or to identify the onset of a potentially cancerous tumor.”

Ghodssi, who has been building miniature devices, sensors, and actuators for more than three decades, has gathered researchers with diverse expertise from across the university—electrical engineers, mechanical engineers, bioengineers, chemists, computer scientists, and data scientists, for starters—to create tiny devices that contain electrochemical sensing electrodes, communications electronics, and batteries inside tiny 3D-printed shells; data collected from the device can be transmitted wirelessly to a cell phone.

His students are fueling further insights: Just this year, materials science and engineering Ph.D. student and Clark Doctoral Fellow Joshua Levy was recognized for award-winning work linked to microneedle drug deliveries in the context of ingestible capsules. 

The challenges of creating a device small enough to be swallowed that contains sensors to collect and share meaningful data are myriad, but Ghodssi sees a future where these devices won’t just find problems, but help us sidestep them entirely. “When you understand how your body is working,” he says, “you can prevent the diseases before they occur.”

Story by Erin Peterson, Engineering at Maryland magazine

Photograph by Maximilian Franz