Carolina Tropini

Integrating biophysics and the gut microbiota.

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Carolina Tropini

Carolina Tropini

I am a JSMF postdoctoral fellow in Dr. Sonnenburg’s lab at Stanford University. In my PhD I developed a deep understanding of the molecular biophysics of bacteria; in my postdoctoral work I am translating this approach to studying complex communities of microbes.
My goal is to determine the interplay between the gut environment, microbial colonization and disease, and to apply the principles that I elucidate to effectively reprogram diseased host habitats.


Born in Italy, Provincia di Cuneo, I moved to Canada in 2001 and graduated from UBC Biophysics in May 2008; I attended Stanford University as a PhD student in the School of Medicine's Biophysics program and graduated in 2014.

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Current research

My mission is to unravel how the physical and mechanical interactions between microbiota and host impact community dynamics and evolution in health and disease.

Physical perturbations on the microbiota

Two to five billion cases of diarrhea occur each year in humans, primarily due to infections; however, little is known about the long-term effects of diarrhea on the health of our intestinal flora. Using computational tools, high-throughput sequencing, transcriptomics and metabolomics combined with imaging of the gut, we seek to understand how the intestinal microbiota responds to periods of osmotic stress, and importantly, how the recovery progresses after a large portion of the microbiome has been depleted.

Microfluidic model of the microbiota

I am developing a microfluidic system to test how chemical and osmotic perturbations affect gut microbe species in the absence of host interactions. The ability to monitor the real-time dynamics of a complex microbial community during physical perturbations will allow us to characterize relevant members and key metabolic pathways involved during disruption of the normal equilibrium. To achieve fine-scale microfluidic control we use an Elveflow controller.

Mucus mechanics

Mechanical properties of the mucosal layer can apply selective growth pressures to gut microbes involving entire macromolecular complexes such as the cell wall and membrane. Therefore, I am interested in studying how the host creates a primary line of defense by establishing and shedding mechanical barriers such as the intestinal mucus, whose physical and chemical characteristics select for a specific and stable set of commensal microbes. We are performing microrheology on mucus and assaying the effects of changes in mechanical properties to microbes in collaboration with the Spakowitz lab at Stanford.

Teaching and outreach

I am committed to sharing research and quantitative methods beyond the lab.


Phylosophy and Examples.

3D Animations

Adding visuals to presentations.

Women in physics

UBC event to welcome high school women to physics and astronomy (WOW).

Molecular Cloning Manual and Tutorial

A short introduction.

Adventures in science

Seminar series for science undergraduates.


Fairchild Science Building,
299 Campus Drive,
Stanford, CA

Tel: (+1) 650-721-2961