Carolina Tropini

Human health is intimately connected with the tens of trillions of bacteria, fungi and viruses that live symbiotically in and on our bodies. This complex community, our microbiota, is as unique as fingerprints, continually adapting and evolving. Within our gut, these microbes generate compounds that nourish us, profoundly influencing functions from digestion and immunity, to brain health. The gut microbiota is also malleable, making this ecosystem an enticing target for precision medicine. Yet, despite its potential, direct clinical applications of microbiota therapies have been sparse, primarily due to our limited grasp of how these microbial communities truly impact human health. 

In the Tropini lab, we are investigating how we can use the microbiota to sense disease locally in the gut. We are also how the introduction of specific microbiota members lost through industrialization can lead to how a disrupted physical environment in diseases such as inflammatory bowel disease (IBD) 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. 

1. Osmotic diarrhea is a prevalent condition, caused by food intolerance, celiac disease, and widespread use of laxatives. Previous work has shown that, during osmotic diarrhea, there is increased susceptibility to infection by pathogens, indicating that disrupted abiotic conditions may have detrimental effects on key microbiota functions, including colonization resistance. In previous work we have shown that osmotic diarrhea disrupts the colonic environment, leads to extinction of key bacterial families, and decreases microbial diversity. We seek to discover the mechanisms involved in microbiota resilience to osmotic perturbation due to osmotic diarrhea by determining the behavior of key microbial families in clinical samples and then testing specific mechanisms in the laboratory.
2. One of the ways that bacterial community dynamics are affected during abiotic perturbations is through changes in the infective and reproductive abilities of viruses that infect bacteria, known as bacteriophages or phages. Although phages are the most abundant organisms on Earth, we know very little about the complexities of the relationship between them and their bacterial hosts, particularly in the context of abiotic perturbations. Understanding the molecular mechanisms underlying this interaction is essential to understanding microbial communities associated with various hosts and environments. Our lab aims to unravel the bacterial as well as phage-dependent mechanisms by which phage infection is resilient to environmental perturbations.
3. The varying abiotic intestinal microenvironment (pH, osmolality, mucus availability) in inflammatory bowel disease (IBD) restricts the ability of certain bacteria to grow in the gut, thereby limiting fecal microbiota transplant (FMT) efficacy. We know very little about the mechanisms of interplay between the gut microbiota and abiotic environmental conditions in IBD. Our objectives are therefore to 1) determine how the IBD microbiota changes the abiotic gut environment and 2) predict and engineer the ability of microbial members from healthy subjects to colonize an altered IBD gut environment and ameliorate it. By characterizing the luminal environment (pH, osmolality, mucus and bacterial components) from IBD models and human biopsies and using in vitro and bioengineering approaches combined with computational analysis we aim to create a predictive model of the interplay between gut environment and microbial communities in IBD. This understanding is necessary to improve treatment efficacy and to develop novel personalized IBD therapies.