Gibbons Lab Overview

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“We are moving islands, inoculated at birth with a unique set of microbes that are integral to the functioning of our bodies. When the ecology of these microbial communities breaks down, so does our health.”

–Sean Gibbons, PhD, Associate Professor
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Research Overview

The Gibbons Lab employs empirical and computational approaches to study how and why complex adaptive systems reorder themselves in response to environmental change. In particular, the mammalian gut microbiome is a superb system for exploring how rapid eco-evolutionary dynamics can reshape ecosystem function (i.e. human health). We tackle basic science questions at the boundary between ecology and evolution and leverage insights gained from this research to develop ecologically aware therapeutics to treat complex diseases.

Research Foci

Microbial Ecology and Evolution: Microbial communities form the foundation of our planetary life support system. We study how bacterial populations coalesce to form complex ecological communities in dynamic environments. We are particularly interested in how these evolving communities maintain stability and functional resilience in the face of environmental fluctuations. We focus on microbial communities residing in the mammalian gut. These gut microbes provide crucial services to their hosts. Loss of key bacterial diversity, changes in community structure, and undesirable evolutionary trajectories can result in disease states.

Bioinformatic Tools and Methods: Microbial communities cannot be observed directly. We use molecular techniques to measure DNA, RNA, protein, lipids, and small molecules, which allow us to infer the form and function of microbial systems. In particular, we employ high-throughput DNA sequencing to quantify the taxonomic and functional content of a microbial community. These data are highly complex, containing many zeros (i.e. sparse), in addition to several forms of technical, sampling, and biological biases/noise that are difficult to disentangle. In order to form an accurate picture of these communities, novel bioinformatic and statistical techniques are required. We develop tools and techniques for dealing with batch effects, compositionality, sparsity, and other issues that can hamper analyses. Furthermore, we try to integrate our tools into open source software packages, like QIIME2, so that they are accessible to the rest of the research community. Please visit the lab github page for more details.

Gut Microbiome and Health: The gut microbiome is an integral component of the human body – almost like an organ. Dozens of inflammatory conditions (e.g. inflammatory bowel disease, obesity, and rheumatoid arthritis) have been associated with the microbiome, in addition to several cancers and cognitive disorders. We mine large databases, like the Wellness 100K Project, to identify promising associations (directed and undirected) between microbial communities and human health. These associations serve as hypotheses for in vivo, ex vivo, and in silico testing. We use these data, along with existing knowledge bases, to build mechanistic models that map ecological structure to community phenotypes. Our goal is to establish causality for a subset of microbe-host associations and to build tools for designing ecosystem interventions, which will allow for the translation of these insights into novel treatments for complex diseases. Ultimately, we want to develop ‘ecological therapeutics’ to treat complex conditions that emerge from many interacting factors and often require a personalized intervention (i.e. there will never be a single ‘pill’ that can be deployed to treat the disease). The microbiome is quickly becoming a new branch of medical science. Just as we all have our own unique genomes, we also have unique microbiomes. Understanding the composition and function of our unique gut communities will be crucial in the development of personalized, preventative, and predictive medicine.