The Burn Microbiome

UNC’s Dana Walsh creates a new research method to better understand how to battle airway bacteria common in smoke inhalation victims.

Dana Walsh, a fifth-year graduate student in the toxicology curriculum, never intended to come to the UNC School of Medicine. She’s from Detroit Lakes, Minnesota, a lovely town among the rolling hills and lakes of the Upper Midwest. But while working as a lab technician at North Dakota State University in Fargo – not far from her hometown – she decided to pursue a PhD, probably in microbiology.  One day, a friend at NDSU told Walsh, “You know, you should check out UNC.”

Walsh had never considered moving so far away, but she did check it out and she did apply. To her surprise she was invited for an interview.

Five years later, she’s on the verge of becoming the first person in her family to attain a doctorate degree. During her time here, Walsh was encouraged to pursue a unique research project, which earned her an invitation to speak at the Southern Region Burn Conference in Tampa, Florida, where she won first place for her student oral presentation.

We met with Dana for a Student Profile to discuss her path to research and her work on the microbiome as it relates to smoke inhalation after burn injury.

Name: Dana Walsh

Birthdate: February 24, 1987

Hometown: Detroit Lakes, Minnesota

Education: BA in biology, Concordia College; PhD candidate, UNC Curriculum in Toxicology

Mentors: David Diaz-Sanchez, PhD; Ilona Jaspers, PhD

Goal: To use next-generation genetic sequencing methods to study the microbiota in smoke inhalation victims to inform better treatment strategies.

Extracurriculars: DNA Day, science outreach for middle school students, Graduate Professional Student Federation Senator, Research Day, toxicology speaker’s series planning committee, translational medicine program planning committee, NC Museum of Natural Sciences volunteer

Hobbies: mountain biking, ferret keeping, hiking

History

“I’ve always been curious; as a kid, I always wanted to know how things worked. And I was creative; you have to be creative to be a scientist. When I was a kid I wanted to be a veterinarian, but when I got older I didn’t really see many job prospects. In high school, I briefly thought about computer science and English. But then I discovered biology during my post-secondary enrollment – when I took college courses while still in high school.

“I liked learning about how life works, and the environment fascinated me. I took a microbiology course as an undergraduate and really liked learning about bacteria that can infect us. That’s how my interest in the microbiome developed. We usually think of bacteria as causing disease, but so many bacteria are commensal organisms; they can benefit us. So my viewpoint flipped and I was fascinated.

Why Research?

“I thought of going to medical school and interviewed once to get into an MD/PhD program but didn’t get in. The next year, I was applying just to medical schools and realized I wasn’t as interested in becoming a medical doctor. I was more interested in doing research.

“Concordia College was small and at the time didn’t have much research going on, but I did take a semester-long research course, during which I worked on a project to infect mice with bacteria to see how that changed the RNA expression in their brain.

“I also had two summer research experiences – one at Notre Dame, where I studied a method to extract and quantify organic carbon from soil. And the second was an internship at the Cincinnati Children’s Hospital, where I looked at fatty acid oxidation in the heart. Some kids have a mutation in that oxidation process, and they wind up with heart issues.

“The best part of these experiences was the chance to investigate things and learn something new. And doing more translational research that applied to patients was a great experience.”

Why UNC?

“A friend at North Dakota State, where I worked as a lab technician for a year after college, recommended that I apply here. She was a master’s student while I was there, and she was applying to PhD programs. We discussed schools and she recommended UNC because of its reputation. I thought it couldn’t hurt to apply, but I didn’t think I’d go because it’s so far from Minnesota. But I came here and was really impressed with the program.

“When you first begin, the  Biological and Biomedical Sciences  Program gives you such a broad opportunity if you’re not entirely sure what kind of research you want to do. You rotate through different labs and get experience before deciding what you want to get into.  If I had gone to any of the other schools I applied to, I would’ve ended up in microbiology and not toxicology because I wouldn’t have had the chance to experience toxicology.”

Why the Diaz-Sanchez and Jaspers labs?

“I really liked how toxicology allowed me to combine my interest in the environment with human health. David and Ilona, my co-mentors, were very willing to let me pursue a project of my choosing even though no one in their labs had experience with what interested me most.

“Also, toxicology itself has a lot of industry and government positions available, and getting a tenure-track position is not as likely these days.”

What’s your project?

“I study the microbiome – the bacterial DNA within us – in burn patients. This came about because Ilona Jaspers collaborates with the North Carolina Jaycee Burn Center at UNC.

“When patients have inhalation injuries, they get bronchial washings to get soot out of their airways. In the past, the washings were thrown out. Due to Ilona’s collaboration, the washings are saved in a repository so we have access to all these washings from patients throughout their stays. And we’re using them to look at bacterial DNA.

“These patients are more prone to bacterial infections. Pneumonia, for instance, can increase mortality rate. So it should be helpful to identify early on what organism is causing an infection. In a clinic, they traditionally do this through culturing bacteria or sometimes through PCR – [polymerase chain reaction, a common technique used to multiply DNA.]

“Next-generation [genetic] sequencing lets you look at a range of bacteria and figure out their relative abundance. So we can say that this bacterium is dominating and this bacterial population is shrinking. Potentially you could use that information to see what patient variables might affect the composition of bacteria and how these bacterial populations change over time. We might be able to use specific treatments to target specific bacteria and lower their prevalence. Maybe this approach would encourage more beneficial bacteria to flourish.

“There are studies now looking at airway microbiomes specifically in disease states, such as chronic obstructive pulmonary disease, cystic fibrosis, and asthma.

“In healthy people, there’s debate about whether there is any bacteria in our airways. But we know that after injury, bacteria can colonize.

“I developed a method to extract DNA from bronchial washings. No one had done that before. There are methods for extracting it from fecal matter. But those methods didn’t give me high yields of DNA or good enough quality. So I combined portions of other methods to make a new one that works really well. It gives us more accuracy in sequencing because we can trace where that original molecule came from.

“Another student, Scott Yourstone in Jeff Dangl’s lab, developed a pipeline to analyze our data so we can identify what bacteria are in our samples and their relative abundance.

“Because of this project, I’ve had to learn various programs, computer languages, and statistical packages to determine which bacteria are significantly enriched in patients and which bacteria aren’t. We can add patient variables to our analyses, which is what I’m working on now.

“We’ve found that anaerobic bacteria – which don’t need oxygen to colonize – are enriched in patients with acute lung injury after smoke inhalation.  These patients are not oxygenating as well, and part of the problem is probably these bacteria.

“The advantage to this method is that we could identify earlier the main infecting organisms and treat patients earlier and more effectively to potentially prevent poor outcomes later during recovery.”

What are your future goals?

“I’m in my fifth year now. I plan to finish in the next six to 12 months. We should have some papers published soon, which would help.

“Then I’d like to do a postdoctoral fellowship related to the microbiome. My husband and I want to move back to the Midwest where our families are. There’s a lot of good research up there, too. Eventually, I see myself going into industry or government, especially to look at environmental exposures and their effects on the human microbiome and how this interaction might influence health outcomes.

“If there’s an opportunity to go into academics, I’d of course be open to it, but it seems like there’s not as much funding for that these days. Yet, the microbiome is a hot area right now, so who knows. We’ll see.”

Share This: