Yingzi Cong, PhD, the Stanley Gradowski Professor of Gastroenterology and a professor of Microbiology-Immunology and of Pathology, was senior and co-corresponding author of the study.

The researchers say the results support the idea that beneficial compounds made by gut microbes can effectively “train” the intestinal lining, helping it preserve immune tolerance over time.

“Our laboratory has long been interested in how the gut microbiota regulates immune responses at intestinal mucosal surfaces,” said first and co-corresponding author of the study Tianming Yu, PhD, research assistant professor of Medicine in the Division of Gastroenterology and Hepatology. “Short-chain fatty acids (SCFAs), which are produced by gut bacteria during the fermentation of dietary fiber, are known to have anti-inflammatory effects in the intestine.”

How Butyrate May Influence Gut Immunity

One major question, however, has remained unresolved, Yu said.

“A large proportion of butyrate in the gut is rapidly absorbed and metabolized by intestinal epithelial cells (IECs), which limits the amount of free butyrate that can directly reach underlying immune cells,” Yu said. “This led us to ask whether butyrate might act through IECs to regulate intestinal immunity.”

To investigate, the researchers supplied mice with butyrate in their drinking water for a set period and then ended the treatment. Two weeks after the butyrate had been withdrawn, CD4+ T-cells were still producing elevated levels of IL-10, an important anti-inflammatory cytokine that helps control intestinal inflammation.

The treated mice were also more resistant to chemically induced colitis. Compared with untreated animals, they lost less weight, had lower levels of inflammatory markers, and developed less severe tissue damage. According to the study, this protection depended on IL-10 signaling.

The researchers also determined that the lasting effect did not result from changes to the gut microbiome itself. In experiments involving germ-free mice, which lack all microbes, butyrate still created a persistent immune-regulating environment.

“We found that oral butyrate treatment induces a sustained immunoregulatory response in the intestine, characterized by increased IL-10 production in CD4+ T-cells and protection from intestinal inflammation even after butyrate treatment is stopped,” Yu said. “This effect was also observed in germ-free mice, suggesting that butyrate can establish a lasting intestinal environment that does not depend on continuous microbial stimulation.”

Intestinal Cells May Store a Lasting Biological Signal

Yu and his colleagues next focused on intestinal epithelial cells (IECs), which form the physical boundary between the body and the microbiome. In laboratory experiments, epithelial cells exposed to butyrate caused a strong increase in IL-10 production in both mouse and human T-cells.

“We further found that conditioned medium from butyrate-treated IECs strongly induced IL-10-producing CD4+ T-cells in both mouse and human T-cell culture systems,” Yu said. “These findings suggest that IECs secrete some immunoregulatory factors after butyrate treatment, and these factors can act on T-cells.”

The team then used metabolomic analysis to search for molecules that might be carrying this signal. One likely candidate was N1-acetylspermidine. The compound increased IL-10 production in T-cells and appeared to account for part of the immune-regulating activity generated by epithelial cells exposed to butyrate, Yu said.

“Mechanistically, we found that butyrate acts on IECs and induces sustained transcriptional and epigenetic activation of Sat1, an acetylpolyamine biosynthetic enzyme,” Yu said. “This promotes production of the metabolite N1-acetylspermidine, which contributes to the ability of butyrate-treated IEC-conditioned medium to induce IL-10 production in CD4⁺ T-cells.”

The results challenge the traditional idea that intestinal epithelial cells are primarily temporary responders whose main role is to serve as a barrier. Instead, the findings suggest that these cells may retain a longer-lasting molecular record of beneficial signals from the microbiome.

“The significance of this work is that it identifies a mechanism by which a microbiota-derived metabolite can create durable epithelial T-cell crosstalk,” Yu said. “The intestinal epithelium is often viewed as a short-lived barrier that responds rapidly to luminal stimuli. Our findings suggest that it can also retain a lasting imprint of a microbial metabolite signal. The study also introduces the idea that beneficial microbial metabolites may ‘train’ the IECs to maintain immune tolerance over time.”

Potential Implications for Inflammatory Bowel Disease

More research will be necessary to confirm the findings and determine whether the same mechanism operates in people, but Yu said the work could eventually have implications for inflammatory bowel disease.

“One important next step is to determine how this epithelial metabolic pathway operates in human intestinal disease, especially in patients with inflammatory bowel disease,” Yu said. “We are interested in testing whether the butyrate-Sat1-N1-acetylspermidine pathway is altered in human IECs and whether it correlates with immune regulation or disease activity.”

The researchers also intend to investigate other metabolites that may contribute to the effect. N1-acetylspermidine by itself did not fully account for all of the immune-regulating activity observed in the experiments.

Over the longer term, Yu said the findings may expand scientists’ understanding of the relationship among diet, metabolites produced by gut microbes and the intestinal lining.

“Many studies have focused on how inflammation can leave harmful memory in epithelial cells, but our findings suggest that beneficial microbial metabolites may also establish protective epithelial programs,” he said. “Understanding how diet, microbiota-derived metabolites and inflammation shape intestinal epithelial memory could open new directions for restoring intestinal immune tolerance in inflammatory bowel disease.”

Wenjing Yang, MD, PhD, research assistant professor of Medicine in the Division of Gastroenterology and Hepatology, was co-first author of the study.

Additional Feinberg co-authors include Suxia Yao, MD, research associate professor of Medicine in the Division of Gastroenterology and Hepatology; and Parambir Dulai, MD, associate professor of Medicine in the Division of Gastroenterology and Hepatology.

Cong, Yu, Yang, Yao, and Dulai are members of the Center for Human Immunobiology.

The study was supported by National Institutes of Health grants DK135193, DK124132 and DK145439.