The group studies the organization and dynamics of microbial communities as they relate to human health and industrial biotechnology.
We develop and apply novel technologies within the fields of systems biology, functional metagenomics, synthetic biology, lab evolution, microfluidics and microbiomics to study:
- Antibiotic resistance in human pathogens and microbial communities
- Interactions between the human microbiome and its host
- Bacterial evolution and evolutionary constraints
- Synthetic microbial communities
Our work is broadly aimed towards understanding how biological systems establish, organize and evolve. We use cutting edge technology and aim to translate our basic research findings into entities, policies and education that provide long term benefits to society.
Antibiotic resistance reservoirs
Bacterial evolution is rendering our medicines against many infections useless threatening to bring us back to the pre-antibiotic era. In many cases resistance to a particular antibiotic did not evolve within the resistant human pathogen, but rather was acquired by lateral gene transfer from other resistant bacteria. These resistant donor bacteria need not be pathogenic, yet they contribute to the evolution of antibiotic resistance in human pathogens by serving as an accessible reservoir of resistance genes. We are using a variety of culture-dependent and culture-independent methods to characterize how these reservoirs are interacting, with the ultimate goal of creating quantitative models for how antibiotic resistance genes arise in human pathogens.
Structure and evolution of synthetic and natural microbial communities
An overwhelming number of important processes ranging from dietary processing in humans to global carbon cycling are driven by microbial communities. The community structure is complex and the underlying principles governing the establishment and evolution of these communities are poorly understood. We are studying a combination of synthetic engineered communities and natural communities to further our understanding of these fundamental principles.