Gut Predictions: Building a Predictive Model of the Gut Microbiome

There are trillions of individual microbes living in the human gut, representing hundreds of species. This community of microbes (collectively the "microbiome") is a dynamic, complex, and mysterious entity and one that has an enormous impact on human health. Some bacteria are good for us, helping us, for example, to digest our food, while other bacteria make us sick. How these bacteria live and interact as a community is largely a mystery. While traditional microbiological techniques help us to understand the individuals in the community, we need more comprehensive methods to study how the community as a whole interacts.

Our project brings together two distinct fields: network science and microbiology. Network science is a tool that can be used to effectively analyze large systems, looking at the big picture of how a system such as the microbiome is connected, and how changing connections will influence the system as a whole. We aim to determine which bacteria promote stability in the healthy microbiome and which are responsible for disrupting the microbiome in disease.  Given the complexity of the microbiome, the tools of network science will allow us to systematically design and propose treatment strategies for numerous human diseases.

Matt Biggs Research Bio

Matthew Biggs is a PhD student in the Biomedical Engineering department, studying in the Computational Systems Biology Lab. As an engineer, he has a special interest in not only understanding microbes, but in improving them, and the way they interact with humans. This collaborative project affords him the opportunity to work together with an accomplished network scientist to use math to understand the "broken" microbial communities in patients with Inflammatory Bowel Disease. He hopes to make progress in our understanding of these microbial communities, but also to gain novel insight into how we can fix them to the benefit of patients.

Advisor: Jason Papin, PhD, Biomedical Engineering

Steven Steinway Research Bio

Steven Steinway began his training as an MD/PhD student because of his interests in helping patients through clinical care and translational research. His research goal is to use network science to make fundamental insights into human disease through advances in diagnosis and treatment. This led him to join the laboratory of the Cancer Center Director for his PhD training, where he has focused on understanding a liver cancer metastasis network and a network that causes a rare leukemia. This project provides a novel context for him to apply networks science to a critical and emerging disease model, the human gut microbiome.  

Advisor: Thomas P. Loughran, MD, Cancer Center Director