How Our Microbiomes affect Nutrition & Pharmacology with Peter Turnbaugh

Peter Turnbaugh is a professor at UCSF studying the human microbiome’s effect on pharmacology and nutrition. In our conversation, we discuss his journey to become a scientist and help pioneer the microbiome field starting in graduate school. We talk about his research as a fellow at Harvard then professor at UCSF, and his lab’s current work. A key theme across the conversation is learning by doing.
Peter’s work has been anchored around predicting and controlling the metabolism of complex microbial communities. Going to a liberal arts college, Whitman College, Peter gravitated more to science because the grades seemed more objective. An experience in a stem cell lab helped Peter learn that science is not just a series of facts and helped spark him to apply to a PhD program. He applied to a bunch of schools, getting rejected by many of them like UCSF, and got into 2 programs. Peter ultimately chose to attend WUSTL. This might have been one of the best, and luckiest, decisions Peter made.

Washington University in St. Louis was an epicenter for the Human Genome Project and is a hotbed of genomics/bioinformatics talent. Going in his rotations, Peter was excited about genomics and wanted to work on more computational problems. He ended up joining Jeffrey Gordon’s lab, a legend in genomics. Jeff gave Peter the nickname, “Professor,” almost foretelling his future. Ruth Ley had also just joined the lab as a postdoctoral fellow after working with Norman Pace and wanted to study microbes across mammals. She had gone to the St. Louis Zoo to collect samples. On Peter’s first day in the lab, the fridge was full of wild animal poop to study. At the time metagenomics was not widely accepted - many genome scientists thought microbial communities would be impossible to understand.

This is around 2004 and there wasn’t a checklist to follow. Peter, Ruth, and the lab had to not be shy to ask for help in order to pioneer a new field of the human microbiome. This ultimately led to 2 papers in 2006 that established gut microbes associated with obesity.
After writing up his thesis, Peter wanted to “keep going as far as he can go” with science. He became a Bauer Fellow at Harvard, rejected by UCSF again during this process, and was excited to start his own lab. Similar to his grad school research, Peter learned by doing to build a lab. The lab’s initial idea was to switch from studying host-associated microbes' role in diet to pharmacology. Xenobiotics seemed “really weird” and an open field to study. A 2013 paper showed how diet can alter the human microbiome, where the lab had to run the trial themselves - feeding participants a veggie or meat-only diet over 5 days. This type of work helped Peter finally get into UCSF and become a professor.
The next skill he had to learn while doing was grant writing. Up until then, Peter had only written grad school applications and a 3-page proposal to Harvard that gave him 5 years of guaranteed funding. At UCSF, he’s built a highly successful group leading the way on the study of the human microbiome and how it intersects with diet & pharmacology. He’s expanded to work on CRISPR/phage research now, and excited to see how that thread grows over the next few years. Looking back, Peter has gained a greater appreciation for the community, something his grad school mentor, Jeffrey Gordon had emphasized. Just as much as multiple genes affect something like height or a disease, it’s important to go beyond a single microbe causing a phenotype.