CMIT Alumni Profile: Sean Gibbons, PhD

Shelby Doyle, PhD | Center for Microbiome Informatics and Therapeutics

Photo: Sean Gibbons

Dr. Sean Gibbons has leveraged his CMIT postdoctoral training into an Assistant Professorship at the Institute for Systems Biology in Seattle, Washington. After witnessing the tangible impact human gut microbiome research had for patients and families, Gibbons has focused his own laboratory on understanding how the unique composition of an individual’s gut microbiome impacts health and well-being.

Awakening to academics

Gibbons academic career started in the public school system in Montana, where he grew up surrounded by nature on the Flathead Reservation, home to the Bitterroot Salish, Kootenai, and Pend d’Oreilles tribes (along with many non-tribal residents, like Gibbons and his family). He describes himself as having been curious and interested in school, but without strong academic ambitions until his undergraduate studies at the University of Montana made him suddenly “wake up.”

Exposed to new topics—French literature, history, art, molecular biology, physics–by professors that saw his potential, Gibbons discovered a new academic ambition that resulted in three bachelor’s degrees: molecular biology, French language and literature, and microbiology with a minor in chemistry.

After graduation, Gibbons’ microbial physiology professor offered him a position as his laboratory manager, triggering a domino effect for Gibbons’ research career. His first peer-reviewed publication from that experience inspired his Fulbright Graduate Fellowship application, which sponsored his master’s studies at Uppsala University in Sweden in microbiology and synthetic biology. 

From there, Gibbons returned to the U.S. to work on several projects, mainly in microbial ecology: surveying natural microbial ecology in Montana, studying the impact of fungi on plant roots and studying how microbes shape the physical properties of soil. His microbial ecology work continued as a member of the Earth Microbiome Project team at the University of Chicago, where he ultimately completed a Ph.D. in biophysical sciences.

When looking for what to do next, it was published works from CMIT Co-Director Eric Alm linking clinical antibiotic resistance to agricultural microbes from the foods we eat that inspired Gibbons to bring his talents to MIT.

The noble act of translation

When newly minted Dr. Gibbons arrived at MIT, the Center for Microbiome Informatics and Therapeutics was in its infancy, and he was able to try his hand at many projects that are now part and parcel to the CMIT approach.

“The clinical piece was totally new to me,” he says, recalling the steep learning curve to navigate the operational and regulatory complexities of human subject research—more complex than sampling soils and plants. But in his tenure at CMIT, he learned these skills and amassed a proven track record in human microbiome science: bioinformatics approaches to human microbiome research, such as methods for time series analysis or batch correction; contributions to the cataloging of human gut microbes for the BIO-ML and GMbC biobanks; and contributions to several clinical studies, including a diet supplement study supported by our CMIT-HST Clinical Award.

Reflecting on his experience, Dr. Gibbons recalls how CMIT shifted his view of an academic research career. Prior to CMIT, Gibbons says, “I hadn’t thought as much about translating [research] into the real world,” citing tacit messages in academia about how “pure science” should be siloed away from clinical trials and commercialization. But seeing the thank you notes coming to OpenBiome from patients cured of life-threatening C. difficile infections through FMT (fecal microbiota transplants) changed his mind about what a noble scientific career looks like.

Further, the speed at which microbiome research on FMT treatments was rapidly translated into the clinic changed his thinking about the immediacy of clinical impact, even in this emerging field. Seeing translation of FMT treatments happen in just a handful of years inspired him to ask of his own work: how can you quickly pivot [this] to something that’s usable in the real world?

The next chapter in clinical impact

It seems this question has at least in part guided him to take the next step in his academic career to the Institute for Systems Biology (ISB) in Seattle, WA, where Gibbons says it was their specific approach to interdisciplinary science and human cohort design that convinced him he could make an impact there.

In clinical studies, Gibbons says there are two choices: emphasize the number of enrolled participants, taking only a few measurements or emphasize the number of patient measurements you make, enrolling smaller numbers of patients. At the ISB, he brings his unique expertise to a team running smaller, data-rich trials so that “even if the trial fails” they can “discover what is going on biologically that led to this failure” to move the field forward and glean more detailed clinical insights.

He is excited about the clinical potential of this approach, citing that these types of studies have already powered microbiome insights from his group that will impact how microbiome science is incorporated into clinical care. Specifically, Gibbons and his ISB collaborators have shown that the microbiome diversity in gut can be predicted from a blood sample, that specific microbial fermentation byproducts in the gut are linked to longevity, and that microbiome functional profiles can be used to predict response to weight-loss interventions.

New hopes on the horizon

Looking ahead, Gibbons is excited to get his research group back to the bench after focusing on purely computational work since the onset of the COVID-19 pandemic. In his lab, he says it is important that everyone “can use a pipette and write a script in Python” and the reintegration of these activities will enable exciting new projects.

Gibbons says the next big question his group is tackling is one of precision medicine: how do you leverage the information about the microbiome to optimally target [drug, dietary, or probiotic] interventions to different people?

Though the time it will take to answer this question will vary for different applications, Gibbons is optimistic about the opportunity for short-term clinical impact if the field can find innovative ways to integrate complex information and make holistic, system-scale predictions.

Citing a “virtual gut” model called MICOM recently developed by his lab, which draws on a curated set of metabolic models of the gut microbiome, Gibbons says we are getting close to predicting metabolic outputs from a patient’s microbiome. While it still may be decades before we can simulate an individual’s gut community metabolism with the same accuracy achieved for industrial bioreactor systems, Gibbons suggests that tools for leveraging patient microbiome data to make clinical decisions—a recommendation for fiber consumption, suggestions for prescribing specific classes of drugs to increase efficacy and decrease side-effects—could be feasible within the next few years.

The Gibbons lab develops computational and experimental tools for investigating host-associated microbial communities to explore the interactions between ecology, evolution, and ecosystem function, applying these insights to develop personalized interventions for improving human health and well-being. His post-doctoral studies were supported by CMIT and the Neil and Anna Rasmussen Family Foundation. At the ISB, Dr. Sean Gibbons is supported by a Washington Research Foundation Distinguished Investigator Award.

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