Our Research

Human health is intimately connected with the tens of trillions of bacteria, fungi and viruses that live symbiotically in and on our bodies. Our microbiota is a remarkable consortium of microbes, unique to each person, and is constantly evolving and adapting. Gut microbes produce compounds that are directly absorbed into our blood, both nourishing us and affecting human functions as diverse as digestion, immunity, and neurodegeneration. The gut microbiota is also malleable, making this ecosystem an enticing target for precision medicine. To date, there have been few direct applications of microbiota therapies in the clinic, due to the lack of understanding of the mechanisms connecting these microbial communities to human health. More than 20 million Canadians suffer every year from digestive disorders that implicate the gut microbiota: it is imperative that we translate what is learned in the lab, and apply it to the clinic.

In the Tropini lab, we are investigating how a disrupted physical environment in diseases such as inflammatory bowel disease (IBD) and chronic diarrhea affect the microbiota and host at a multi-scale level. We are a cross-disciplinary group that incorporates techniques from microbiology, bioengineering, biophysics and more to create highly parallel assays and study how bacteria and communities function, with the eventual goal of translating the knowledge we gain to improve human health.


Approaches

Multiscale dynamics

We aim to predict the dynamics during physical perturbations on multiple temporal and spatial scales, from the subcellular to the cellular, community and host scales.

Microbiota engineering

We want to engineer microbes and microbial communities to modify and ameliorate the gut environment during disease.

Computational analysis

We do bioinformatics and design simulations to connect our multi-scale data, create predictive models and stimulate new experiments.

Quantitative imaging

We go beyond sequencing, we want to observe microbiota dynamics and interactions in situ, and as much as we can, in real time.


Areas of Interest

Osmotic and Other Physical Perturbations

Osmolality (the concentration of solute particles in a solution) tightly limits the ability of bacteria to grow beyond an optimal range. Osmolality in the gut changes dramatically during malabsorption and osmotic diarrhea. Most laxatives cause an osmolality shift and lead to changes in microbiota composition. We want to understand how this happens and the long term effects of physical perturbations.

Phage dynamics

Bacteriophages (phages) are the most abundant organisms on Earth. They are an essential, yet neglected, driver of bacterial dynamics in environmental as well as host-associated microbial communities. We are investigating their interplay with physical perturbations and bacterial communities.

Inflammatory Bowel Diseases

The gut habitat is dramatically altered by inflammatory bowel disease (IBD) and applies a strong selective pressure on the microbiota. We are studying the connection between the gut microbiota, the gut microenvironment and IBD.

Microbial invasion dynamics

Some bacteria are able to colonize a seemingly saturated gut microbial community and persist without causing host inflammation. We want to understand the mechanisms of their colonization.