From diet blogs to health influencers to the probiotic sodas on the shelves of your local retail store, chances are you’ve heard about the latest wellness craze: Fix your gut, and you’ll be golden!
But is it really that simple?
While there’s growing evidence that the gut microbiome plays a critical role in overall health, the science behind altering it—for better or for worse—is far more complex than a daily dose of yogurt, a change in diet or an over-the-counter probiotic gummy.
Georg Gerber, MD, PhD, and his research team at Mass General Brigham are diving deeper into that complexity.
Their work goes beyond consumer trends to dig into the scientific details, using advanced computational models and experimental biology to understand how trillions of microbes interact within the gut and throughout our body—and how we can better understand those interactions to treat diseases such as food allergies and C. difficile infections.
We sat down with Dr. Gerber to learn more about his lab’s approach, the role of computational biology and artificial intelligence (AI) in microbiome research, and what’s next in the journey toward personalized, gut microbiome-based medicine.
Q: How did you get started at Brigham and Women's Hospital and begin your lab?
I’ve been at Brigham and Women’s Hospital (BWH) since 2008. My journey started as a medical student at Harvard, where I did my first clinical rotations at the Brigham.
I also did a student rotation in pathology, which really resonated with me and led me to pursue it as a career. After finishing my residency in pathology at BWH, I stayed on as a faculty member.
Over time, I developed my own research lab focusing on computational biology and the microbiome, which has become a central theme in my work.
Q: What led you to the gut microbiome, and what makes it so compelling?
Early in my career, I focused on gene regulation and human genetics, but my interests shifted significantly after meeting Lynn Bry, MD, PhD, at BWH, who introduced me to the world of the microbiome about 15 years ago.
Since then, I’ve become deeply fascinated by the trillions of microbes that live in and on our bodies, and how they interact with us—impacting everything from immunity and metabolism to mental health.
What makes the microbiome particularly compelling is that it represents a dynamic, ever-changing ecosystem within us, made up of countless microbial species that interact with each other and with our own biology.
Unlike our genetic code, which is essentially fixed from birth, the microbiome is modifiable.
People can influence their microbiome through diet, lifestyle, and other interventions, giving them a degree of control over their health that isn’t possible with genetics alone.
My lab is dedicated to exploring these complex relationships and understanding how we can harness these changes to the microbiome to improve health outcomes for a wide range of conditions.
Q: How does computational biology contribute to your gut microbiome research?
These tools and algorithms help us uncover patterns and relationships in complex biological systems, like a super-powered microscope that reveals not just individual cells, but the intricate networks and interactions that drive health and disease.
This approach is crucial in microbiome research, where we’re dealing with hundreds to thousands of microbial species and massive datasets. Computational biology helps us to make sense of this complexity and identify meaningful connections.
In my lab, we apply these methods to a variety of clinical conditions. Two conditions we’ve investigated in depth are food allergies and infections.
For food allergies, we’ve investigated how the microbiome influences immune responses to foods, leading to new ideas for the prevention and treatment of allergies.
One of these strategies involves live bacterial therapies, which means giving patients specific strains of microbes that occur in the healthy gut to treat or prevent a disease.
In the realm of infections, it’s well established that a disrupted microbiome can make people more susceptible to attack by certain microorganisms.
Our research has identified specific microbes that can increase or lessen susceptibility to certain infections.
Some of our findings are now pointing toward therapeutic strategies that could be used in clinical practice, demonstrating the power of computational biology to translate big data into real-world health solutions.
Q: What is MDSINE2, and what did your recent study in Nature Microbiology find?
MDSINE2 (pronounced “M Design Two”) is a computational tool we developed to help design live bacterial therapeutics, or living treatments made of beneficial bacteria.
The “design” aspect refers to our goal of rationally selecting and combining microbial species that can be introduced into a patient’s microbiome to achieve a desired effect, such as fighting an infection or preventing an allergy.
MDSINE2 analyzes how the microbiome changes over time and predicts interactions between different microbes.
This is crucial because, unlike traditional drugs that target a single molecule or pathway, live bacterial therapeutics must function within a complex, pre-existing ecosystem.
Our recent Nature Microbiology paper demonstrates how MDSINE2 can be used to predict which microbes will thrive or decline when introduced into a community, helping us design more effective interventions.
We’ve already applied this tool to conditions such as C. difficile infection and are expanding its use to other diseases.
Q: What are the next steps for your research?
The next major step is integrating microbiome data with host data—such as immune system activity—to build more comprehensive models.
This will help us predict how interventions affect both microbes and patients, advancing us toward personalized therapies and real-world clinical applications.
We’re also exploring how AI can accelerate this work. We recently received a grant from the Massachusetts Life Sciences Center to establish the Lab for Deep Learning and AI for Microbiome at BWH.
The lab uses advanced AI tools to analyze how the microbiome changes over time and how it interacts with us.
What’s fascinating is that our microbiomes contain about 150 times as many genes as our own genomes, and the functions of most of these microbial genes remain unknown.
So, one very exciting application of AI is figuring out what these genes do and how they can impact human health.
Q: What advice would you give to aspiring scientists?
My biggest piece of advice is to find a good mentor and surround yourself with supportive colleagues. It’s of course important to pursue what you’re passionate about, but science is a very social pursuit.
I think popular media often gives the impression that scientists are loners, but that’s not the reality. Your mentors and colleagues in the lab will play a crucial role in your research.
In fact, I believe that who you work with is one of the biggest determinants of success and whether projects ultimately succeed.
Fun Facts File: Georg Gerber, MD, PhD
What is your favorite movie?
I'm a big fan of Stanley Kubrick, who directed several of my favorite films, "2001: A Space Odyssey" being one of them.
What would you be doing if you were not working in medicine and science?
Before pursuing a career in medicine and science, I actually had a career in Hollywood, working in film production and 3D graphics.
I ran a production company and was involved in creating visual effects.
While I enjoyed that work, I ultimately decided to return to academia and pursue an MD/PhD, applying my technical and creative skills to medical research.
I still enjoy art and creative projects when I have the time, but my main focus is now on science and medicine.
(Editor's note: The image above, while representative of the general aesthetic of 2001: A Space Odyssey, is a stock photo and not from the movie itself. Apologies in advance to any Kubrick purists out there, but we did not want to risk any copyright issues. )
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