Evolutionary Dynamics in Microbial Communities: Lessons from the Lab, the Whiteboard, and the Microbiome


Microbial communities drive important biochemical cycles, from the ocean to the soil to the human gut. Their composition is shaped by ecological forces, but also by the rapid pace of microbial evolution, which can fix genetic changes over years, months, and even days. However, we currently know little about the evolutionary forces that operate within microbial communities, or how we could infer them from modern genomic data. In this talk, I will describe two related approaches we are using to address this question. The first part will focus on the quasi-stable communities that we observed in a long-term evolution experiment in E. coli. I will describe a new theoretical approach for modeling the population genetics of this process, generalizing traditional models of resource competition from ecology. The second part will focus on more complex communities, using the gut microbiome as a model system. I will describe a new approach we have developed for extracting evolutionary signals from a large panel of human gut metagenomes, and for interpreting these signals using simple models of population genetics. We find that gut bacteria can evolve within their hosts on human-relevant timescales, while the quantitative patterns of variation reveal interesting departures from traditional population genetic assumptions. Together, our work suggests that ongoing evolution may play an important role in shaping the structure of microbial communities, and that quantitative models will be crucial for unraveling these effects. 

Tuesday, February 12, 2019 - 14:00

704 Thackeray Hall

Speaker Information
Dr. Benjamin Good
University of California, Berkeley