The buzz of the air conditioner is the first thing I notice as I open the door to the office of Travis Gibson, PhD. Outside, rain taps aggressively against the window overlooking a gray Longwood Medical Area.
I walked in feeling a bit nervous—after all, I was about to dive into the work of someone whose world revolves around extremely complex science and engineering, far outside my comfort zone.
A child’s drawings sit on his desk. A whiteboard is packed with research plans and formulas I can’t begin to understand.
Two pieces of art hint at a creative side beneath the science and engineering knowledge. It’s a small detail, but it puts me at ease. Maybe we’ll have more in common than I initially expected.
Gibson welcomes me into the room and shows me a chair. Right away, I sense his passion for his work and just as clearly, I see his kindness.
As we talk, he weaves in bits about his hobbies and life outside the lab.
I really enjoy those moments—they help me see the person behind the science and make it easier to connect with him.
An enthusiastic postdoctoral fellow walks in with a smile. I glance at his badge, and it reads ‘Younhun Kim, PhD.’ He’s the first author on their most recent peer-reviewed paper and, as Gibson puts it, “has been my ‘ride or die’ since he was a PhD student at MIT.”
Gibson and Kim sit across from each other discuss upcoming grant deadlines and the progress of their current projects.
They’re studying how bacteria change and evolve by looking closely at bacterial DNA, efforts that have led to the development of a new tool called ChronoStrain.
By understanding how the population levels of individual bacteria strains change over time, ChronoStrain could improve how physicians treat infections, prevent disease outbreaks, and even develop new medical treatments for patients.
But how exactly do you track the DNA of something as small and fast-changing as bacteria?
From Control Theory Engineering to Gut Microbiome Research
Gibson’s scientific journey didn’t begin in biology. He earned his PhD in control theory, a field at the intersection of mathematics and engineering that focuses on guiding the behavior of complex systems, at the Massachusetts Institute of Technology (MIT).
During his doctoral studies, he interned at NASA and Boeing, applying his expertise in control theory and engineering to real-world challenges.
Working in a hospital was never part of his plan. But life, as it often does, had other ideas.
“I had been offered a position as a postdoctoral research fellow at Caltech in California,” Gibson says. “But my girlfriend [at the time] was a nurse at Beth Israel Deaconess Medical Center. A long-distance relationship really wasn’t in the cards and I knew that a move to the West Coast would likely be the end of the of the relationship.”
So, he pivoted. He scrambled to find a fellowship closer to home and landed at Brigham and Women’s Hospital (BWH) studying the gut microbiome—the community of microorganisms that live in the digestive tract and play a crucial role in digestion, immune function and overall health.
The shift was dramatic. “I changed research directions 180 degrees. I didn’t know anything about the microbiome,” he says. “It was completely insane.”
But Gibson brought something valuable to the field from his engineering background. He knew how to make sense of complicated systems and find patterns in messy and complicated data.
“During my training, I picked up new skills in things such as inference and statistical modeling,” he explains. “Now, those are a big part of how my lab works.”
Gibson completed two postdoctoral fellowships, both at Brigham and Women’s Hospital (BWH). “The first one was in the Channing Division of Network Medicine, Department of Medicine. The second was in the pathology department.”
In both roles, his research focused on the microbiome, though the nature of the work evolved significantly. “The first fellowship was more about looking at the microbiome from a high-level, systems biology perspective,” he says. “I wasn’t connected to the clinical or experimental side of things.”
That changed during his second fellowship. “I switched to the Pathology Department and trained under Georg Gerber, an MD-PhD who also co-directs the Massachusetts Host-Microbiome Center,” he says. “This is where I really cut my teeth and rounded out my background. I designed animal experiments and got to better understand how a real clinical and experimental microbiology lab works.”
While computational work remained a constant throughout both fellowships, the second postdoc marked a turning point that introduced Gibson to the world of clinical and experimental biology.”
Close to the end of his second fellowship, Gibson began applying for faculty positions in the Boston area to continue his scientific career.
But his unique background made him stand out to the leadership at BWH.
“They asked me not to leave,” he says with a smile. “So, I stayed. Moved a few doors down. And started doing the work I continue doing today.”
ChronoStrain: Connecting the Dots Over Time
Studying the human microbiome is expensive. Scientists often spend millions collecting samples and sequencing DNA.
But after all that effort, the data is often analyzed using generic, off-the-shelf software tools that can miss crucial and extremely important information.
“Researchers will conduct a study and spend $25 million to recruit the patient cohort and conduct all the sequencing,” Gibson says. “And then when it comes to the computational side, they’ll just use an off-the-shelf thing. You’re really leaving a lot on the table.”
That’s where Gibson and his research team come in. Instead of relying on standard tools, they build their own tools that are designed to answer specific scientific questions.
One of their newest tools is called ChronoStrain.
How ChronoStrain Works
Imagine trying to put together a puzzle, but instead of having all the pieces at once, you get a few pieces each week.
If you look at each batch of pieces on its own, it’s hard to see the what the finished puzzle will look like.
But if you keep each set of pieces and compare them to each other, you start to notice how they fit together.
ChronoStrain works in a similar way. It looks at DNA from bacteria collected at different times. Because DNA sequencing isn’t perfect, small errors or changes can occur.
Instead of treating each sample as something completely new, ChronoStrain compares them to other samples and asks, “Could these pieces belong to the same puzzle?”
By connecting the pieces over time, ChronoStrain builds a clearer picture of how bacteria grow and change.
This could help scientists and doctors better understand infections and long-term health problems and make smarter decisions about how to treat them.
How ChronoStrain Could Help Patients
ChronoStrain has the potential to make a significant impact on patient care.
For people who suffer from recurring infections such as urinary tract infections (UTIs), it could help detect exactly which bacteria are causing the infection and how those bacterial populations are changing over time.
With that information, doctors can choose more effective treatments, avoid unnecessary antibiotics, and help patients recover more quickly.
In hospitals, ChronoStrain could also be used to track how infections spread between patients or rooms, especially for hard-to-detect bacteria such as C. difficile.
ChronoStrain has also been used to track bacterial strains in infants, helping researchers understand how early-life microbes colonize the gut and whether different strains persist or have turnover.
While the tool is still being applied in ongoing studies, the early insights it has provided are promising.
For Gibson, ChronoStrain is more than just a tool. It represents years of persistence, collaboration, and a commitment to following curiosity across disciplines, even when that meant starting over from the beginning in an unknown field of study.
“That’s the whole story of the paper—it started out as the first thing that I started working on when I was an instructor a long, long time ago, and then has taken a long time, but eventually paid off.” Gibson says.
Sometimes, scientific innovations don’t begin with certainty, but with a question and the motivation to follow it.
In Travis Gibson’s case, it also began with the decision to stay in Boston for love, which, as it turns out, was the right call in more ways than one.
His girlfriend—the nurse from Beth Israel—is now his wife. The children’s drawings on the wall that helped to put me at ease when I arrived? They were made by their first child.
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