Annette Nguyen

Background: Clostridioides difficile (C. difficile) is one of the most reported nosocomial pathogens, accounting for 12% of healthcare-associated infections.¹ While colonization by C. difficile is common, infection occurs primarily when gut microbiota dysbiosis disrupts colonization resistance, allowing the bacterium to proliferate and produce toxins that damage the intestinal epithelium^1,2. Antibiotic therapy—the common cause of gut dysbiosis—paradoxically serves as the primary treatment for Clostridioides difficile infection (CDI)^1,3,4, frequently leading to recurrent infections and an urgent need for alternative therapeutic approaches.  Recent research suggests that diversity in gut microbiota protects the gut barrier integrity, conferring resistance to CDI. Studies indicate that gut microbiota-derived metabolites, such as secondary bile acids and short-chain fatty acids, play crucial roles in suppressing C. difficile spore germination and reinforcing host immune defenses⁵. However, the mechanistic details of this microbiota-host interplay are incompletely understood.

Objective: In this review, the relationship between gut microbiota and host immunity is mechanistically explored.

Search Methods: An online search in the PubMed database was conducted from 2018 to 2025 using the following keywords: “Clostridioides difficile“, “gut microbiota”, ” innate immune system”, and ”colonization resistance”

Results: Fecal microbiota transplantation (FMT) was found to effectively reduce multidrug-resistant organism (MDRO) colonization in renal transplant recipients⁶, a population prone to opportunistic infections due to antibiotic prophylaxis. Shotgun metagenomic sequencing revealed a significant decrease in antimicrobial resistance genes after FMT, with strain-level analysis confirming antibiotic-resistant bacterial strains were replaced competitively by antibiotic-susceptible strains⁶. Notably, one of the most consistent donor taxa to engraft after FMT was Phascolarctobacterium spp.⁶, leading to exclusion of C. difficile.  Another study demonstrated that interleukin-22 (IL-22) induced by the gut microbiota causes host glycoylation, promoting Phascolarctobacterium expansion and creating innate resistance against CDI⁷. Using germ-free Rag1^−/− mice colonized with human microbiota, researchers identified microbiota-driven IL-22 expression as a critical factor in colonization resistance, independent of host T and B cell immunity⁷. Innate lymphoid cell type 3 (ILC3)-derived IL-22 is also essential in the late phase of CDI⁸. Additionally, ILC3s were found to facilitate early CDI defense through granulocyte-macrophage colony-stimulating factor (GM-CSF), enhancing neutrophil maturation and activation⁸.  Metabolic interactions within the microbiota were explored as an independent mechanism of CDI resistance. Butyrate, a short-chain fatty acid produced by the gut microbiome, was shown to impair C. difficile fitness via energetically unfavorable metabolic pathways, leading to autolysis⁹. Moreover, experiments in major histocompatibility complex-related protein 1-deficient mice indicated microbiota-derived metabolites shape immune recognition, with fecal microbiota transplantation confirming microbiota-mediated colonization resistance to CDI¹⁰.

Conclusions: The gut microbiota interacts with the host immune system by inducing IL-22 expression and ILC3-derivied GM-CSF, both in turn promoting innate resistance for C. difficile. Furthermore, microbiota-derived metabolites influence resistance against C. difficile and how the immune system recognizes the gut microbiota. These interactions demonstrate the intricate synergism of the host immune system and gut microbiota that can be used for future potential treatments against CDI.

Works Cited:

1. Bella SD, Sanson G, Monticelli J, et al. Clostridioides difficile infection: history, epidemiology, risk factors, prevention, clinical manifestations, treatment, and future options. Clinical Microbiology Reviews; 2024:37(2):e00135-23. doi:doi:10.1128/cmr.00135-23
2. Khoruts A, Staley C, Sadowsky MJ. Faecal microbiota transplantation for Clostridioides difficile: mechanisms and pharmacology. Nature Reviews Gastroenterology & Hepatology; 2021:18(1):67-80. doi:10.1038/s41575-020-0350-4
3. Normington C, Chilton CH, Buckley AM. Clostridioides difficile infections; new treatments and future perspectives. Curr Opin Gastroenterol; 2024:40(1):7-13. doi:10.1097/mog.0000000000000989
4. Czepiel J, Dróżdż M, Pituch H, et al. Clostridium difficile infection: review. Eur J Clin Microbiol Infect Dis; 2019:38(7):1211-1221. doi:10.1007/s10096-019-03539-6
5. Kayama H, Okumura R, Takeda K. Interaction Between the Microbiota, Epithelia, and Immune Cells in the Intestine. Annu Rev Immunol; 2020:38:23-48. doi:10.1146/annurev-immunol-070119-115104
6. Woodworth MH, Conrad RE, Haldopoulos M, et al. Fecal microbiota transplantation promotes reduction of antimicrobial resistance by strain replacement. Science Translational Medicine; 2023:15(720):eabo2750. doi:10.1126/scitranslmed.abo2750
7. Nagao-Kitamoto H, Leslie JL, Kitamoto S, et al. Interleukin-22-mediated host glycosylation prevents Clostridioides difficile infection by modulating the metabolic activity of the gut microbiota. Nature Medicine; 2020:26(4):608-617. doi:10.1038/s41591-020-0764-0
8. Fachi JL, Oliveira Sd, Gilfillan S, et al. NKp46⁺ ILC3s promote early neutrophil defense against Clostridioides difficile infection through GM-CSF secretion. Proceedings of the National Academy of Sciences; 2024:121(45):e2416182121. doi:10.1073/pnas.2416182121
9. Pensinger DA, Dobrila HA, Stevenson DM, Hryckowian ND, Amador-Noguez D, Hryckowian AJ. Exogenous butyrate inhibits butyrogenic metabolism and alters virulence phenotypes in Clostridioides difficile. mBio; 2024:15(3):e0253523. doi:10.1128/mbio.02535-23
10. Smith AD, Foss ED, Zhang I, et al. Microbiota of MR1 deficient mice confer resistance against Clostridium difficile infection. PLoS One; 2019:14(9):e0223025. doi:10.1371/journal.pone.0223025