Turning Fermented Plant-Based Foods into Precision-Nutrition for Oral and Gut Health

PHILADELPHIA – Fermented plant-based foods such as kimchi and sauerkraut may offer more than bold flavors. According to a review paper published online in Nature Reviews Microbiology on June 23, these traditional foods could help inspire a new generation of microbiome-informed dietary strategies for supporting oral and gut health.

The review, led by investigators at Penn and Jeonbuk National University in South Korea, examines how fermented foods interact with the microbes that live in the mouth and gut. The authors focus on plant-based fermented foods, which can carry diverse communities of live microorganisms, microbial metabolites, fiber-rich food structures, and plant-derived bioactive compounds. Recognizing these distinctive features, the authors set out a roadmap for developing fermented foods into microbiome-based precision nutrition strategies to support health.

Fermented plant-based foods carry diverse microbial populations along with their metabolites, and in principle could be tailored to support oral and gastrointestinal health,” said study co-corresponding author Hyun Koo, DDS, MS, PhD, professor in the Departments of Endodontics and Bioengineering, and co-founding director of the Center for Innovation & Precision Dentistry (CiPD) at Penn Dental Medicine. “The goal is not to claim that these foods are treatments today, but to understand how they could be developed and tested as part of precision nutrition.”

The other co-corresponding author was Dongyeop Kim, PhD, associate professor in the Department of Preventive Dentistry, School of Dentistry, Jeonbuk National University, Jeonju, South Korea. Also collaborating on the paper were Gary Wu, MD, the Ferdinand G. Weisbrod Professor in Gastroenterology at the University of Pennsylvania’s Perelman School of Medicine, and Charlene Compher, PhD, Professor of Nutrition Science at the University of Pennsylvania’s School of Nursing, both of whom participated in this project with institutional support from the Penn Center for Nutritional Science and Medicine (PenNSAM).

“This is the first collaboration between CiPD and PenNSAM, and we look forward continuing this partnership to address common issues in oral and gut health through nutrition science,” Koo said.

Fermentation is a process in which microbes such as bacteria and yeasts convert some compounds in foods into other compounds, creating foods with unique flavors, textures, and nutritional characteristics. Humans have used fermentation for thousands of years to preserve and enhance food and drink and create new foods. Even in modern society, the list of dietary items involving fermentation is extensive and includes yogurt, kefir, kombucha, soy sauce, coffee, chocolate, bread, cheese, alcoholic beverages, sauerkraut and kimchi.

Yogurt and other liquid probiotics are already used widely to modify the gut microbiome to promote better digestion. But the researchers note that the potential health benefits of fermented foods could extend beyond dairy products, and that solid, plant-based fermented foods have distinct features over liquid ones. Kimchi, for example, a fermented form of cabbage, contains not just a small number of bacterial strains from a defined starter culture—as yogurts typically do—but a diverse community or “consortium” of native bacteria, along with many bioactive metabolites. In principle, this diverse microbial population could be tailored for specific gut or oral health applications.

“Vegetable-based fermented foods have fiber-rich structures that help protect the microbes they carry and allow them to stay longer on mucosal surfaces,” Kim said. “This could create more opportunities for short-term microbial interactions in the mouth and gastrointestinal tract.”

“Plant-based fermented foods may have an advantage not only in their efficiency of delivering microbes to the host but also by providing unique benefits via bioactive phytochemicals that have been shown to promote human health,” Wu added.

The review emphasizes that many questions remain. Scientists still need to determine which microorganisms and metabolites are most important, how long food-derived microbes persist after ingestion, how individual microbiomes influence responses, and whether specific fermented foods can produce reproducible health benefits in controlled clinical trials.

The authors propose a roadmap for moving the field forward. Key steps include building better databases of food microbiomes, using advanced tools to profile microbial strains and metabolites, and developing plant-based fermented food products with defined microbial and chemical features. These approaches could eventually help match specific fermented foods to individual microbiome profiles or health needs.

“The science behind fermented foods is exciting because it brings together diet, beneficial microbes, and bioactive metabolites that may interact with the microbiomes of the mouth and gut,” said Koo. “The next step is to test these ideas rigorously.”

Ultimately, experimental fermented-food products could be tested in clinical trials with standardized protocols and outcomes. The team is now working to build a collaborative research program to follow the roadmap described in the paper.