Katherine Pollard: “Decoding the Human Microbiome”

Katherine Pollard, PhD, visited Stanford Medical School to deliver the Computational Immunology Seminar. She discusses how her lab at the Gladstone Institutes uses big data and high-performance computing to study the human microbiome and learn how it influences health and disease.

The human microbiome plays a role in processes as diverse as metabolism, immune function, and mental health. Yet despite the importance of this system, scientists are just beginning to uncover which microorganisms reside in and on our bodies and determine what functions they perform. The development of innovative technology and analytical methods has enabled researchers like Dr. Pollard to decode the complex interactions between our human cells and microbial brethren, and infer meaning from the staggering amounts of data 10 trillion organisms create.

Dr. Pollard is a senior investigator at the Gladstone Institutes, director of the Gladstone Convergence Zone, and a professor of epidemiology and biostatistics at UCSF.

Table of Contents
0:00 Katherine Pollard "Decoding the Human Microbiome"
5:24 Estimating microbe or gene abundance
6:18 How to compare across genes or microbes
7:41 How to compare across samples
8:32 No association between Firmicutes and obesity
11:39 Housekeeping genes associated with disease?
11:42 Is functional variation underestimated?
15:40 Challenges that prevent accurate comparative metagenomics
21:09 Genome size varies and leads to systematic bias in abundance estimates
25:09 Estimating gene copy number from metagenomes
28:27 Average genome size: a gut microbiome biomarker
30:08 Microbiome data mining
37:13 Different strains in different places
40:07 Microbiome dynamics in colitis disease process
43:02 Infant gut microbiome dynamics
46:24 What have we learned?
47:58 Career advice and Katherine's career path
53:30 Acknowledgements
54:20 Q&A