The human gut microbiome is a dense ecosystem that collectively yields functions including diverse chemical transformations distributed among constituent community members and colonization resistance to intestinal pathogens that influences human physiology. A detailed and mechanistic understanding of the ecological and molecular forces that shape the assembly, activity and stability of the gut microbiota are largely unknown. Central to this problem is systematically mapping unknown inter-species interactions that realize emergent community-level properties and developing predictive computational models to describe ecosystem behaviors. We are developing a general framework to dissect the organization principles of the gut microbiota to pinpoint molecular mechanisms that shape community assembly and stability in response to environmental perturbations. Our general framework aims to decipher interactions among constituent members of a human gut microbiome synthetic ecology that mirrors the diversity of the natural system using measurements of lower- order assemblages to predict multi-species community behaviors. We will map ecological behaviors to molecules and genetic factors by elucidating gene expression profiles, single-cell phenotypes, genetic determinants of community structure and function and interrogating metabolic activities using genome-scale modeling. Leveraging these multifaceted approaches, we will investigate the principles of colonization resistance to C. difficile, ecological interactions that influence the stability and activity of butyrate-producing bacteria and molecular mechanisms that enable probiotics to realize stable ecological functions. Our work will ultimately lead to mathematical and biological principles that describe the complex behaviors of microbial communities to environmental pressures and will have profound impact across all areas of biology and medicine.
A detailed and mechanistic understanding of the molecular and ecological basis of assembly and stability of the gut microbiome in response to environmental pressures would have profound implications on our ability to remodel the microbiome to improve human health. Elucidating the organizational principles of the gut microbiota would enable design of stable and functionally active consortia to restore homeostasis following an environmental perturbation and guide strategies for precision manipulation of the structure and activity of the gut microbiota. The goal of this proposal is to develop a general framework to understand the ecological and molecular processes that underlie the structure, activity and stability of the gut microbiota in response to nutrient shifts, antibiotic exposure and invasion by pathogens.