Katrine WhiteSon: BioChemist

"I’m interested in understanding how microbes that live in our bodies affect our health. In one study I did, we took saliva samples from 5 different people at 3 different times and found that oral microbial communities are persistent. Once you have a stable microbial community, it sticks with you. If you get your teeth cleaned, three days later, they’ll be back. If you share food with other people, some microbes might invade and become persistent members of your community, but probably not. They grow in biofilms. It's like they have roots. The microbial community you have in your mouth and in your gut is part of you."


"My husband is a particle physicist. We met in a Danish class at Berkeley, a small class of only 4 people. Most classes at Berkeley have hundreds of kids."

"So you guys made up 50% of the class!"

"We had good odds. When I finished grad school, my first child was born, about 3 weeks after I defended my PhD. I had a big audience at my defense and I was very pregnant. Then, my husband and I moved to Irvine, CA where I was a lecturer for a year, and then to Geneva, Switzerland where he worked on the particle collider at CERN. There, I got involved in a genomic research lab and gained access to high throughput DNA sequencing data, which was new at the time. I took samples from healthy people and extracted the microbial DNA and amplified particular genes to determine which microbes were present. In the last 100 years of microbiology, most scientists have studied one bacteria at a time, and only the ones that are easy to grow. However, the recent revolution in the speed and cost of DNA sequencing has allowed microbiologists to study microbial communities without even having to grow them, opening the door to the thousands of microbes that live on the human body and in other environments."


"People will cystic fibrosis (CF) inherit a mutation that prevents them from forming mucus properly, which leads to problems in their mucus-lined membranes, including their lungs. Microbes get into your lungs all the time, and if you’re healthy, you eject them through mucociliary clearance. But people with CF have really thick mucus that interferes with this mechanism. As a result, they have dense microbial communities living in their lungs and, once or twice a year, their symptoms exacerbate. Unfortunately, there’s no way to diagnose when an exacerbation is about to occur. There’s no molecular test, so when doctors choose which antibiotic to use, they just guess.

I’m doing parallel studies: taking breath samples from patients at San Diego’s CF clinic and extracting microbial DNA. I read a paper by Don Blake’s lab; they found that some metabolites, or molecular biomarkers, were more abundant in the breath samples of CF patients, but they couldn’t tell whether the metabolites were coming from the microbes or the humans. Because each piece of DNA encodes a certain function, sequencing microbial DNA allows me to figure out which microbes are present and determine if they’re producing the metabolites in the breath samples. The ultimate goal of my research is to use this data to diagnose which microbes are abundant before an exacerbation occurs so they can be targeted."


"10 years ago, there was a famous experiment by Jeff Gordon. He took gut bacteria from an obese person and put them into germ-free mice, and the mice became obese. Similarly, we use antibiotics to fatten up farm animals. If you give low doses of antibiotics to pigs or cows or chickens, they gain weight more quickly. That’s something we’re doing on purpose in agriculture, but we’re actually performing the same experiment on our population. We all take antibiotics, especially in our childhoods. In the popular book, 'Missing Microbes,' Marty Blaser describes how the average American child gets 18 doses of antibiotics before the age of 18. He’s done experiments demonstrating that giving antibiotics to baby mice -- whether in pulses the way humans take them or in continuous small doses the way farm animals take them -- leads to increased adiposity in the adult mice"