Addressing the Emerging Issue of Antibiotic Resistance: Antimicrobial resistance (AMR) is projected to be a major healthcare challenge in the next 50 years. While resistance mechanisms in single species are well-understood, microbial community responses to antibiotics are less predictable. Bacteria in biofilms are protected from antibiotics and engage in multispecies interactions that promote survival, while horizontal gene transfer spreads resistance.

A key research focus of our group is understanding antibiotic resistance dynamics in microbial communities. Using microfluidic devices, we control stressors and predict microbial responses. Our goal is to develop targeted antimicrobial strategies, including formulations that selectively target harmful organisms. For cases requiring complete eradication, such as implant-associated infections, we employ nanotextured surfaces to induce mechanical microbial rupture. By integrating chemical and physical approaches, we aim to enhance antimicrobial effectiveness.

Development of Microbial Formulations for Environmental Applications and Bioprocesses: Advances in sequencing technologies are revolutionizing microbial applications, enabling new approaches to environmental and bioprocess development. As the circular economy grows, bioprocessing and waste management efforts are critical. However, microbial identification alone is not enough; we must also understand their interactions within communities and ecosystems.

Microbial communities thrive on cooperation, which can be leveraged to improve processes like bioremediation. Traditional bioremediation design methods often rely on trial and error, leading to inefficiencies due to microbial task redundancy and competition. Many industrial bioprocesses use single-species formulations, which require extensive strain modifications.

In our lab we aim to enhance bioprocesses by engineering microbial communities. By pairing strains with complementary functions and understanding their metabolic interactions, we can optimize efficiency and predict outcomes. We  design scalable, efficient processes, considering factors like microbial interactions, timing, and process design. This approach enables the development of advanced bioprocesses and bioremediation systems

Engineering Microbial Communities for Gut Microbiome Therapies: The gut microbiome is a highly diverse ecosystem that varies significantly between individuals. A loss of diversity and integrity in the microbiome is a key factor in microbiome-related diseases, but the underlying mechanisms are not fully understood. My research group applies chemical and biological engineering principles to better understand this complex system and develop microbial therapies poised to play a major role in the pharmaceutical and biomedical industries.

To study microbial effects, we recapitulate the gut microenvironment using gut microbiome-on-a-chip systems. These microfluidic devices simulate fluid flow, oxygenation, peristalsis, and host-microbe interactions at the microbial scale. Integrated with advanced microscopy and analytics, these systems allow us to investigate microbial community composition, structural properties, and the effects of perturbations.

Our approach provides a foundation for linking an individual’s microbiome to their health through precision medicine. We explore microbial therapies, including prebiotics, probiotics, and microbial transplants, to develop preventive and therapeutic strategies for diseases like cancer, inflammatory bowel disease, and non-alcoholic fatty liver disease, all of which are strongly linked to microbiome imbalances.