Key Clinical Summary

• In a University of Michigan study, 10 of 11 ulcerative colitis (UC) fecal microbiomes were susceptible to Clostridioides difficile colonization in vitro, compared with 5 of 12 healthy donor microbiomes (P=.027).
• Susceptibility occurred in samples from both active and quiescent UC despite similar overall microbial diversity between groups.
• Increasing inulin in the culture medium from 0.1% to 1% significantly reduced C difficile colonization in UC samples. In vivo evaluation is underway.

University of Michigan researchers reported that inulin increased resistance to C difficile colonization in laboratory cultures of fecal microbiomes from adults with UC. The findings, presented October 12, 2026, at ACG 2026, address a potential gap in UC care: according to the investigators, medications that induce remission do not restore colonization resistance in most patients.

Study Findings

The investigators collected fecal samples from adults with and without UC who had not received antibiotics in the preceding 3 months. They tested whether the samples’ microbial communities resisted C difficile colonization using an anaerobic cultivation system with peristaltic flow designed for long-term growth of complex communities.

Samples from patients with either active or quiescent UC were more often susceptible than healthy donor samples: 10 of 11 (91%) versus 5 of 12 (42%; P=.027). Mean Shannon diversity scores were similar between groups, at 5.12 for UC and 5.36 for healthy donors (P=.265). The susceptibility difference therefore was not accompanied by a statistically significant difference in this measure of overall diversity.

Susceptibility was associated with higher levels of Dialister species and lower prevalence of Collinsella and Lachnoclostridium species. Compared with resistant healthy donor samples, susceptible UC samples also had different metabolomic profiles in vitro, including lower 3-hydroxybutyrate and higher succinate, deoxycholic acid, and glycolithocolic acid levels.

To assess inulin, the researchers increased its concentration in the culture medium from 0.1% to 1%. They measured colonization by plating on selective agar and reported a significant reduction in C difficile colonization in UC samples after the increase. The abstract did not provide an effect size for this comparison.

Clinical Implications

The findings identify a potential way to support colonization resistance in UC microbiomes, including those from patients with quiescent disease. They also suggest that overall microbial diversity alone may not capture the differences associated with susceptibility in this experimental system.

For clinicians, the distinction between the laboratory result and a patient outcome is central. The study tested fecal microbial communities in vitro; it did not establish that taking inulin prevents C difficile colonization, infection, or UC flares in patients. The reported taxonomic and metabolomic differences are associations within the tested samples, while the inulin result comes from changing the culture medium. The investigators stated that work is underway to evaluate colonization susceptibility in vivo.

Expert Commentary

Presenting author Kira L. Newman, MD, PhD, of the University of Michigan in Ann Arbor, and colleagues wrote that the response to inulin suggests resistance-associated taxa “may be present but at low levels without prebiotic support.” Their interpretation remains a proposed explanation for the laboratory finding; the abstract does not report a patient treatment study.

The study points to inulin as a candidate for further investigation in UC-associated C difficile susceptibility. Whether its effect in cultured microbiomes translates to colonization resistance in patients remains to be determined.

Reference: Newman KL, James G, Standke AK, et al. Inulin restores colonization resistance against C difficile of ulcerative colitis patient microbiomes in vitro. Presented at: ACG 2026; October 12, 2026. Abstract 7.