UCL Division of Biosciences


GEE Seminar - Professor Katherine Pollard, University of California, San Francisco

27 April 2022, 4:00 pm–5:00 pm


Title: 'Tracking Evolutionary and Ecological Dynamics of the Human Microbiome with Genetic Variants'

Event Information

Open to

UCL staff | UCL students | UCL alumni




Amy Godfrey



Academic Host: Francois Balloux / Lucy van Dorp
Abstract: In this talk, I will describe our efforts to assemble diverse genomes, catalog genetic diversity, and develop computationally efficient tools for genotyping human gut microbes from shotgun metagenomic data. A key concept in our methods is the k-mer, a short DNA sequence that we use as a computational probe for rapidly assaying genetic variants. Using these tools, we tracked strain transmission in families and a fecal transplant clinical trial, revealing patterns that would be missed with species-level analysis. With longitudinal metagenomics data, we detected and quantified rates of strain replacement, mutation, and adaptive introgression within hosts. While evolution on the background of existing strains is a strong signature on time scales less than one year, strain replacement dominates over host lifetime. Finally, I will describe ongoing modeling work that aims to link strain-level variants to phenotypic differences of gut microbes and their hosts. These strategies can be extended to study microbes in other human body sites as well as microbiomes from animals, plants and other environments. 

About the Speaker

Professor Katherine Pollard

PI / Director of the Institute for Data Science and Biotechnology at University of California, San Francisco

I received my Ph.D. and M.A. from UC Berkeley Division of Biostatistics under the supervision of Mark van der Laan. My research at Berkeley included developing computationally intensive statistical methods for analysis of microarray data with applications in cancer biology. After graduating, I did a postdoc at UC Berkeley with Sandrine Dudoit. I developed Bioconductor open source software packages for clustering and multiple hypothesis testing. In 2003, I began a comparative genomics NIH Postdoctoral Fellowship in the labs of David Haussler and Todd Lowe in the Center for Biomolecular Science & Engineering at UC Santa Cruz. I was part of the Chimpanzee Sequencing and Analysis Consortium that published the sequence of the Chimp Genome, and I used this sequence to identify the fastest evolving regions in the human genome. In 2005, I joined the faculty at the UC Davis Genome Center and Department of Statistics. I moved to Gladstone/UCSF in Fall 2008, where I am Director of the Institute for Data Science and Biotechnology focused on emerging technologies and informatics. I am an advocate for women in science at UCSF and beyond. I was honored to receive the Gladstone Mentoring Award in 2019.

More about Professor Katherine Pollard