Clostridium difficile infection (CDI) represents a major healthcare concern that causes diarrhea and usually affects people who have recently been treated with antibiotics or have had an extended stay in a healthcare setting. It can also spread easily to others. Although previous experimental research has shown that a fiber-deprived diet leads to a disturbed host colonic epithelium and has an impact over generations, little is known about whether dietary fiber could affect the course of CDI.

A new study, led by Dr. Justin L. Sonnenburg from the Department of Microbiology and Immunology at Stanford University School of Medicine (USA), has found that microbiota-accessible carbohydrate-utilizing bacteria and short-chain fatty acids generated during their fermentation prevent C. difficile infection perpetuation in mice.

Microbiota-accessible carbohydrates (MACs) found in plants are a main source of energy for gut bacteria, which means their abundance can modulate gut microbial composition and function. The researchers used an experimental model of antibiotic-induced CDI in germ-free mice colonized with the gut microbiota of a healthy human donor to study the impact of a MAC-enriched diet on CDI outcomes. Humanized mice were fed a diet containing a complex mixture of MACs or two diets that were MAC-deficient.

While mice fed the MAC-deficient diets showed persistent CDI, those fed with the MAC diet cleared the pathogen below detection within 10 days of infection and CDI suppression was correlated with an increase in gut microbiota alpha diversity (the model of antibiotic-induced CDI used typically resolves within 12 days of infection). In mice fed the MAC-deficient diets, CDI remained unresolved until dietary transition to the MAC diet at day 36, which shifted the gut microbiota to resemble that of other MAC-fed mice, supported with a decrease in C. difficile burdens. MAC-dependent suppression did not depend on a specific gut microbiota profile or host genotype, as the same results were found when using conventional mice and germ-free mice colonized with conventional mouse microbiota.

The researchers also found that after the MAC dietary intervention, the mice’s gut microbiota resembled the gut microbiota of mice shifted from a MAC-deficient diet to a MAC diet. These data suggest that both diet and antibiotic treatment are relevant drivers of gut microbial communities involved in supporting or excluding C. difficile in this experimental model.

In order to explore whether diet effects on C. difficile burdens may be related to other dietary components, the researchers found in a second experimental setting that a diet shift from a MAC-deficient diet to a diet containing inulin as the only MAC source reduced C. difficile burdens without increasing microbial alpha diversity. However, the overall gut microbiota composition was different between mice fed the MAC diet and the inulin-containing diet. These results demonstrate that MAC reduction of C. difficile burdens is independent of gut microbiota diversity.

In order to explore MAC-mediated suppression of CDI, acetate, propionate and butyrate levels were measured in the cecal contents of mice fed the MAC-deficient, MAC and inulin-containing diets. Acetate and butyrate levels were elevated in the ceca of mice fed the MAC and inulin diets compared with the MAC-deficient diet, whereas propionate levels were elevated in the ceca of MAC-fed mice compared with the MAC-deficient and inulin diets. Interestingly, acetate, propionate and butyrate had concentration-dependent negative effects on C. difficile growth despite having concentration-dependent positive effects on the expression of toxin B, which is essential for C. difficile virulence. These data may indicate that diet may play a role in creating a gut microbiota profile and metabolome setting involved in controlling CDI, despite C. difficile responding to the MAC diet by increasing its toxin B production.

To better understand the inflammatory response during MAC-dependent suppression of CDI, humanized mice fed the MAC-deficient diet were infected and switched to either the MAC or inulin diet at 7 days post-infection. Inflammation was increased on proximal colon tissue from all mice infected when compared with uninfected control mice fed the MAC or inulin diets. In the group of mice fed the MAC-deficient diet, the levels of inflammation were comparably elevated in both infected and uninfected mice, which is in agreement with previous research in mice showing the pro-inflammatory effect of a limitation of dietary MACs. For mice switched to the MAC and inulin diets, toxin B abundance increased from day 0 to day 4, whereas the overall abundance of toxin B decreased. These results support the role of a MAC-deficient diet on facilitating inflammation that leads to C. difficile growth in the gut, which responds by elevating toxin B expression. In the end, however, it is unable to maintain its presence in the gastrointestinal tract upon the continued consumption of MACs by the host.

In conclusion, this is the first experimental study that has provided a rationale for the role of MAC-utilizing commensal microorganisms and derived short-chain fatty acids in clearing CDI despite increased C. difficile toxin B expression in the gut. Further research will provide a comprehensive picture of the role of fiber deficiencies in mitigating opportunistic enteric pathogens such as C. difficile.




Hryckowian AJ, Van Treuren W, Smits SA, et al. Microbiota-accessible carbohydrates suppress Clostridium difficile infection in a murine model. Nat Microbiol. 2018. doi: 10.1038/s41564-018-0150-6.