The microbiome transmission (motion) laboratory studies the human microbiome to better understand how bacteria move between human hosts, how microbial communities that reside in the human body work to permit or prevent bacterial transmission, and how resident microbial communities can be engineered to alter the transmission process. We focus specifically on the transmission of antibiotic-resistant bacterial pathogens. With our work, we seek (1) to better understand how endogenous microbial communities can protect against bacterial pathogen colonization and infection (i.e., the mechanisms of colonization resistance), and (2) to develop novel microbiome-based therapeutics (MBTs), which alter the composition of mucosal microbial communities to prevent and treat antibiotic-resistant bacterial infections.
We train students in molecular epidemiology and microbial ecology methods, including metagenomic sequencing, culturomics, whole-genome sequencing, and Bayesian modeling. These methods enable novel insights into bacterial transmission, how endogenous microbial communities affect transmission, and MBT pharmaco-dynamics/kinetics. Our laboratory has developed microbiome-based therapeutics and led phase-2 clinical trials to evaluate their effectiveness in combatting multidrug-resistant infections. We have also contributed methodologic advances to the field, including methods to quantify microbiome disruption and loss of colonization resistance that predict risk of infection, as well as Bayesian modeling approaches to trace microbes as they move between human hosts, the environment, and even other host species.
We serve as the core laboratory for the University of Pennsylvania’s Center for the Study of Antibiotic Resistance (C-STAR). During the COVID-19 pandemic, we applied our expertise in molecular epidemiology of infectious diseases to lead regional SARS-CoV-2 genomic surveillance, and we developed modeling approaches to understand SARS-CoV-2 transmission dynamics and the population impact of vaccination across the Philadelphia metropolitan region.
