Research

microbiome_streamplot

Human epithelial surfaces are colonized by hundreds of trillions of commensal microbes representing thousands of unique bacterial species (the human microbiota). Our lab seeks to understand, predict, and manipulate how human microbiota behave over time. We are particularly interested in how these human-associated microbial communities resist and respond to perturbation. Below are several research projects we are pursuing.

Predicting microbiome susceptibility to infection

We are actively collaborating with Regina LaRocque (Massachusetts General Hospital) and Firdausi Qadri (the International Center for Diarrheal Disease and Research, Bangladesh) to longitudinally study cholera infections among the residents of Dhaka, ...

Post-infection microbial successions

Through our work on cholera transmission , we have observed that waves of distinct bacterial species colonize human guts in the weeks following diarrheal infection. We are now using a combination of next-generation sequencing and microbial culturing techniques...

Microbiome dynamical network inference

We have collected some of the world's densest time-series of human behavior and commensal microbiota, having tracked these variables on daily time scales for weeks and even months. Now, we are using computational techniques to build dynamical models of...