Holly Arnold portrait on gray background

February 28, 2024
By Jens Odegaard. Photo courtesy of Dr. Holly Arnold. 

Dr. Holly Arnold is a brand-new assistant professor in the Department of Biomedical Sciences at Oregon State University’s Carlson College of Veterinary Medicine. But she’s not a new face in the college. 

Eleven years ago she was wrapping up a master’s in computer science and machine learning (focused on microbial ecology and bioinformatics) from the University of Oregon in Eugene. She was also volunteering at the Heartland Humane society in Corvallis, “as a fun thing to do. And then it hit me: I like animals and I like science, so maybe there is a career path as a clinician scientist. So, I decided to apply to veterinary school – which my mother likes to call my quarter-life crisis,” Arnold said with a laugh.  

Already familiar with Corvallis, Arnold was attracted to the Oregon State University Carlson College of Veterinary Medicine for its smaller class sizes and better student-to-teacher ratio compared to some of the bigger veterinary colleges across the country. “And I really liked the community feel of Corvallis,” she said. Arnold was accepted to the program and started classes for her veterinary degree in the fall of 2016. 

Her original goal was to complete her doctor of veterinary medicine at Oregon State and then “get a Ph.D. at some point.” Serendipitously, while starting her first year in vet school, the college launched a comparative health sciences graduate degree program, with one of the tracks designed for DVM students to earn a concurrent Ph.D. It’s a multidisciplinary program where students and faculty mentors design an individualized research plan built around a core of biomedical and clinical sciences courses. Faculty involved in the program have wide ranging expertise, including bioinformatics (applying computational tools and analysis to biological data) and the microbiome. This dovetailed with Arnold’s earlier education at the University of Oregon. 

Arnold seized the opportunity to combine both her clinical and research interests. “I've always been attracted to the clinician scientist side of things. I think clinics and research really go well with each other,” she said. “Clinical medicine informs research questions because the problems are walking in the door. And then on the other side of things, it's really exciting when you have a research question and then you're able to inform clinical practice.” 

In the comparative health sciences program, Arnold connected with Thomas Sharpton, an associate professor in the Oregon State University Departments of Statistics and Microbiology, and joined his research lab. The Sharpton Lab focuses on defining “how the gut microbiome impacts vertebrate health, behavior and evolution and ultimately aims to use this knowledge to design novel disease diagnostics and therapeutics,” according to the lab website. And the research “relies on microbiology, bioinformatic and systems biology techniques, and often involves developing novel computational and analytical methods to efficiently analyze massive data sets.”  

For Arnold, it was the perfect fit. “He’s been an amazing mentor, very supportive of a nontraditional career path, and I would not have been able to do the program without him,” she said.  

For her doctoral thesis, Arnold worked on building a bioinformatic tool that helps scientists like herself determine the effects of microbiomes on their host organisms at a level of specificity they haven’t had before. 

A microbiome is the whole community of microorganisms – think bacteria, viruses and fungi – that live on and in ecosystems including humans and animals, such as the gut microbiome. Current methods for associating microbiomes with their hosts are limited to classifying them with broad historically assigned taxonomic labels. 

“So, for example E. coli. If you look at all the organisms labeled as E. coli there’s a lot of different E. coli, and they do a lot of different things. Some of them are pathogenic [disease causing] and some of them are not pathogenic. Some of them associate with humans and animals. Some of them can’t colonize and persist within animal hosts,” Arnold said. “That means, that as scientists, when we're trying to communicate things, we do a bad job because our label for the organism doesn't always capture the ecological nature of that organism. The goal of my work is to enable us to associate microbial members to host health status without the need to rely on historic labels, which don’t always capture the microbial function of interest. That should give us a higher resolution at being able to distinguish how microbes associate with health and disease that we haven't had in the past. Only by pinpointing a microbe’s ecological functions (such as causing disease or enhancing health span) will we be able to impact strategies to stop disease transmission, or to cultivate microbes which associate with positive health benefits such as enhancing longevity, reducing inflammation or enhancing physical performance.” 

Arnold is now building on this research as she launches her own lab as a research faculty member. She graduated with her DVM in 2020 and her Ph.D. in 2021. Following that, she both interned as a critical care veterinary intern at the college’s veterinary teaching hospital and did postdoctoral research before being hired as an assistant professor of research in fall of 2023.

Her hope with the Arnold Lab is to continue to unlock the secrets of the microbiome by “organizing the world’s microbial information” to identify microbes with known effects on human physiology (both positive and negative), and to catalog them in a systematic and unbiased manner, leaving behind the use of historic labels which slow research progress.

Her current projects seek to link microbial members to enhanced cognitive performance in mice, cats and humans as well as establish microbial signatures that might associate with neurodegenerative conditions such as Multiple Sclerosis, Parkinson’s and Alzheimer’s Disease. “The hope is to identify microbial signatures within the gut to diagnose neurodegenerative conditions sooner,” she said.

In another serendipitous turn, her hire as a faculty member corresponds with the launch of Oregon State University’s new six-year strategic plan. Within the plan there’s a key focus on building collaborative multidisciplinary research utilizing “artificial intelligence, data science and research computing” within focus areas including “integrated health and biotechnology.” 

In the next few years, the Jen-Hsun and Lori Huang Collaborative Innovation Complex will be completed at the university and house an NVIDIA supercomputer that will be one of the worlds’ most powerful. This will allow researchers like Arnold to tap into the very best as they build their computational tools. 
It’s an exciting time to be part of the Oregon State University community. 

Arnold is actively recruiting students to join her lab and research team and build her own part of the community. The first students will be starting this fall on a project studying how the microbiome may be used in wild animals as a remote monitoring tool of ecosystem health. Arnold is drawing on her own experience at Oregon State to create an environment of curiosity and belonging.  

“I feel very humbled to have had the best training as a student, postdoc, and intern at OSU,” Arnold said. “Brianna Beechler and Anna Jolles, my postdoc advisors, are very supportive of a nontraditional career path. And Dr. Bermudez [department head of biomedical sciences] and Dr. Tornquist [dean of the college], I couldn’t have done it without them, because they’ve been very supportive of all these crazy ideas. And Dr. Tandi Ngwenyama [assistant professor of emergency and critical care] is an influential mentor for me in terms of thinking about how people learn and striving to provide an environment where continual learning is OK. There’s been so, so many supportive people here. It’s a good place.”