Rebecca Wilkes: Turning microbes into precision biomanufacturing tools

Rebecca Wilkes is putting the best of nature to use today for tomorrow's biofactories, applying her synthetic biology skills to create microbes that can break down and convert complex mixtures like plant biomass into valuable chemicals and materials. Her research underpins a supply chain that supports the nation's agricultural sector while creating a secure, domestic source of advanced bioproducts.

Wilkes works in the Biosciences Division at the Department of Energy's Oak Ridge National Laboratory, and also serves as a Fellow with the University of Tennessee-Oak Ridge Innovation Institute (UT-ORII). The institute bridges the scientific expertise and capabilities of ORNL and UT to advance research and develop talent in areas of national need.

Wilkes is applying her skills to a UT-ORII Convergent Research Initiative focused on building a high-growth sector for the Tennessee economy.

She studies the metabolism of microbes that can break down and convert substances such as the natural polymers in plant biomass into valuable products. One of the organisms she focuses on is the bacterium Comamonas testosteroni, a stress-resistant microorganism with an appetite for polymers such as polyethylene terephthalate (PET) - one of the most commonly used plastics worldwide and an abundant feedstock for industry.

Wilkes honed her synthetic biology skills in projects focused on lignin biopolymer for the ORNL-headquartered Center for Bioenergy Innovation (CBI) while at one of the center's partners, the National Laboratory of the Rockies (NLR). She came onboard ORNL in 2025.

Microbes on a mission

Wilkes describes her work as taking complex mixtures from different feedstocks or waste streams, feeding them to bacteria, and then making a single product that can be used as-is or converted into another end-product. "The nice thing about bacteria," Wilkes said, "is they have this really cool, complex metabolism that can take these streams of complex material and convert them into a more purified compound of interest." There are many products that can be made with this biotechnology, including one of her current targets, glycolic acid - used in everything from paints and household cleaners to pharmaceuticals.

Wilkes is leveraging ORNL's expertise in synthetic biology and genome sequencing to learn more about Comamonas and to build new tools to customize the microbe. Non-model organisms such as Comamonas are useful for biomanufacturing as they've typically developed unique traits and enzymes by surviving harsh environments like waste streams. They also tend to have genetic and metabolic controls in place that allow them to rapidly adapt to changing feedstocks or challenging environments. That built-in 'fine-tuning' is complex, Wilkes noted, but it gives these non-model organisms an advantage in tolerating industrially relevant conditions.

Wilkes also continues to conduct research for CBI on topics such as lignin valorization. Her fluxomics expertise, for instance, helps explain how a microbe's genetic makeup influences the chemical reactions happening inside its cells, identifying the best pathways to rewire the organisms for specific conversion functions. She is using her background in modeling to build collaboration for computational modeling to better understand and harness fluxomics in microbes.

"I really like working on multidisciplinary teams at the national labs," Wilkes said. "You can access amazing research capabilities by working with people who are chemists, material scientists, computer scientists and economists. Working with a team geared this way is very exciting."

Rooted in science

Wilkes was inspired by her family to pursue a career in science. Her great-grandfather, Samuel A. Stouffer, was a pioneer of modern quantitative sociological research. Her grandmother, Ann Stouffer Bisconti, is a global expert on public opinion and communications research in the nuclear energy sector.

"Scientific exploration and hands-on learning were a large part of my education," Wilkes said of her family's influence. She was homeschooled while growing up and was encouraged to be flexible in her learning and interests. She wrote a fantasy adventure novel when she was 11, took online courses in graphic design and animation, and has adopted painting as a lifelong hobby.

Wilkes discovered her love of science as a teenager by taking community college courses in biology at Garrett College. She continued those studies at Washington & Jefferson College, where she earned a bachelor's in biology with minors in both chemistry and computing information studies as the class valedictorian. During her summers, she participated in two National Science Foundation Research Experience for Undergraduate programs, one at Donald Danforth Plant Science Center and one at Michigan State University, which gave her critical experience in experimental design and laboratory research.

As part of her honors coursework during college, she conducted a project on phytoremediation - the use of plants to bioaccumulate environmental contaminants. She analyzed how well certain wetland plants tolerated acid mine drainage and their uptake of metals from that environment. It was a prescient topic, Wilkes said, given the current focus on developing new domestic sources of critical minerals, including the use of biological means to hyperaccumulate and recover these materials.

Wilkes went on to earn both a master's and doctorate in biological and environmental engineering at Cornell University. She worked as a postdoc at Northwestern University and then at NLR, studying the ability of microbes to utilize polymers ranging from lignin to synthetic polymers like plastics, and developing biotechnology tools for American manufacturing success.

Throughout her education, Wilkes credits mentors who encouraged and supported her career in science, from her undergraduate advisors Peter Skylstad at Garrett College and Jason Kilgore at W&J college, to her PhD advisor Ludmilla Aristilde, to her postdoc advisors Gregg Beckham and Allison Werner. "I've been fortunate to have these people in my corner," Wilkes said.

Basic science, real-world impact

By working at the national labs, Wilkes has advanced fundamental scientific discovery with applications for the nation's economic success. "I've enjoyed the government lab environment because I like this kind of collaboration," Wilkes said. "You're a bit more on the applied side, and then you also get to work with a lot of academics and still answer some of the fundamental research questions that you wouldn't in industry."

One of her key interests is helping develop strategies for highly efficient biomanufacturing, taking advantage of every waste stream that comes out of a process as it's scaled. "Currently, biorefineries are typically built with one product in mind," Wilkes said. "But by diversifying and tapping into secondary output, refineries can generate even more profit."

Her advice for young scientists?

"The advice that you often hear about keeping balance in your life is very sound. It's also important to build resilience," Wilkes said. She recommends that young scientists "build a separation of self and science. It can be difficult if an experiment doesn't go as planned, or you get a bunch of edits back on a paper. It's important to be able to separate that out and view it as a learning experience that will make you better. Grit, I guess, is another term for it. Keep going in your science."

Wilkes also recommends students and early career scientists focus on building computational proficiency. "That skill set is really important, whether for modeling, automation, or robotics - those areas are integrating into pretty much every area of science. Having an understanding of the subject, even if you aren't directly doing it, allows you to communicate with colleagues and improve your research."

UT-Battelle manages ORNL for the DOE's Office of Science, the single largest supporter of basic research in the physical sciences in the United States. The Office of Science is working to address some of the most pressing challenges of our time. For more information, please visit energy.gov/science. - Stephanie Seay