New Northwestern Medicine research published in Nature Communications suggests that a metabolite produced by gut bacteria when they digest dietary fiber can leave a lasting molecular imprint on intestinal cells, promoting immune tolerance and protecting against inflammatory bowel disease-like conditions long after exposure ends.

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.

Investigators describe the findings as evidence that beneficial microbial metabolites may be able to “train” the intestinal lining to maintain 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.”

However, a longstanding puzzle remained, 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 test the hypothesis, the scientists gave mice butyrate in drinking water for a period of time and then stopped treatment. Even after a two-week washout period, levels of CD4+ T-cell production of IL-10, a major anti-inflammatory cytokine against intestinal inflammation, remained elevated.

The animals also showed protection against chemically induced colitis, experiencing less weight loss, reduced inflammatory markers and milder tissue damage than untreated mice. The protective effect depended on IL-10 signaling, the study found.

Additionally, the effect was not driven by changes in the gut microbiome itself. Experiments in germ-free mice, which lack all microbes, demonstrated that butyrate could establish a durable immune-regulating environment even in the absence of microbes.

“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.”

Next, Yu and his collaborators then turned their attention to intestinal epithelial cells (IECs), which form the barrier between the body and the microbiome. They found that butyrate-treated epithelial cells strongly increased IL-10 production in both mouse and human T-cells in laboratory experiments.

“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.”

Using metabolomic analysis, the team identified a likely messenger: N1-acetylspermidine. The compound increased IL-10 production in T-cells and appeared to contribute to the activity of butyrate-conditioned epithelial cells, 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 findings challenge the traditional view of IECs as only short-lived responders that primarily serve as a barrier.

“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.”

While more work is needed to verify the findings, Yu said the work could 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 team also plans to search for additional metabolites involved in the response, since N1-acetylspermidine alone did not fully explain the immune-regulating activity observed.

In the longer term, Yu said the study could broaden scientific thinking about how diet, microbial metabolites and the gut lining interact.

“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.