Mapping the Urobiome for Better Bladder Health

For more than a century, it was thought that urine was sterile. Then, in 2014, scientists upended that assumption by confirming that even the healthiest person’s urine contains bacteria. Now, more than 10 years after this discovery, the universe of the urobiome remains largely uncharted. Unlocking its secrets could lead to a better understanding of bladder health and spark new treatments for the millions of people worldwide who suffer from frequent urinary tract infections (UTIs) and overactive bladder (OAB).

A key research question for Jean-Philippe “JP” Gourdine, assistant professor of chemistry, is: How do bladder bacteria survive in the harsh environment of the urinary tract? He thinks the answer may be found in the sugar chains found on uromodulin, the most abundant protein in urine. Uromodulin helps clear the body of uropathogenic E. coli, the primary bacteria responsible for UTIs. Bacteria attach to uromodulin’s sugars and are then carried out of the body through urine.

“Since these sugars can remove ‘bad’ bacteria, I wondered if another possible role for uromodulin might be serving as a kind of sugar reservoir—something maybe ‘good’ bacteria could feed on, much like what happens in the gut,” says Gourdine.

Gourdine first became interested in the urobiome several years ago when he was a senior research associate working with the Karstens Lab at Oregon Health & Science University (OHSU). The lab, led by Lisa Karstens, an associate professor at OHSU, focuses on the human microbiome and its relationship to health and disease using bioinformatics, or the use of computer science and mathematics to understand biological phenomena. During his time at OHSU, Gourdine applied his knowledge of glycobiology—the study of glycans or sugars found on the surface of most cells—to identify the genes bacteria use to metabolize sugars.

When he joined Lewis & Clark in 2021, Gourdine began to establish a lab where he could conduct in vitro experiments to confirm what he identified using bioinformatics techniques—specifically, to characterize the enzymes in bladder bacteria that can help break down sugars.

“We are looking at a number of questions,” says Gourdine. “How does the bacteria get there? Because some of the bacteria found in the urinary tract resemble what is present in the gut or vagina, but some are really unique. What do these bacteria live on? And what conditions are present that help bacteria persist?”

Gourdine’s research has recently received a boost from the National Science Foundation (NSF) through its Launching Early-Career Academic Pathways in Mathematical and Physical Sciences program. In addition to supporting the purchase of new lab equipment, the funds are enabling paid research experiences for six Lewis & Clark undergraduate students over the next two years.

 

Photo Essay

The Uncharted Universe of the Urobiome

Assistant Professor of Chemistry JP Gourdine’s Biochemistry Lab (CHEM 336) class.

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A Research-Focused Curriculum

The undergraduate student researchers working with Gourdine are laying the groundwork for in vitro experiments.

“We can sequence the genome of different bacteria using bioinformatics, and predict that this or that gene might be involved in one particular pathway,” says Gourdine. “But, until we do the work in vitro, we can only suggest, not confirm, the findings.”

One of the students working with Gourdine to confirm his findings is Elie Al Khoury BA ’26.

“I didn’t expect to be working in a lab like this because I thought, ‘It’s a small liberal arts college,’” says Al Khoury, a biochemistry and molecular biology major, who has already coauthored a published paper with Gourdine. He also recently presented with him at the 2025 Society of Glycobiology’s annual meeting. “When I saw that working in this lab was related to the medical world, I jumped at the opportunity to be involved.”

Al Khoury is currently the only student trained to work with the lab’s frozen urine samples. He currently spends most of his lab time optimizing the process of purifying uromodulin for use in experiments.

“I would like to give a shoutout to JP,” says Al Khoury. “I feel like I have been given so many opportunities—doing research, going to conferences, and getting his support for everything I do. I did not expect to come out of college with, like, a publication, maybe more, under my name.”

AJ Schroeder BA ’26 and Jules Tri BA ’26 are both biochemistry and molecular biology majors working on purifying GH 38, a protein that bladder bacteria may utilize to “feed” on uromoduline’s sugars. Both Schroeder and Tri have found working in Gourdine’s lab to be among the most enriching experiences of their Lewis & Clark education.

“I always liked taking things apart and putting them back together as a kid,” says Schroeder. But, she knew early on that a field like engineering was not for her. “I am interested in seeing how the pieces come together and what pieces you can change in a system that’s already kind of predetermined, which is what lab work is.”

Tri, who is interested in medicine but not in being a doctor, finds the challenges of lab work among the most rewarding.

“What’s so fun about this lab,” says Tri, “is when we’re not able to get results easily. Because then we can test out all these different ways that would help produce the protein we are working on. It really builds our knowledge of how all the different steps work.”

Next year, Gourdine will continue this work while on sabbatical in Grenoble, France. He will be collaborating with the Center for Research on Plant Macromolecules, a leading glycosciences lab. Gourdine hopes to build future opportunities for his students, whether in Portland or Grenoble, and he will continue to seek grant funds to help him pay student researchers.

“I want to make sure that our students can get actual lab experience and really see ‘This is what the life of a scientist can be.’”

Chemistry