Persisting in an unfriendly environment: the case of being difficile

A bactericidal bile salt that protects against C. diff infections could also help this bacterium hide

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Infections caused by Clostridium difficile are typically associated with antibiotic treatments that disrupt the healthy intestinal microbiota, called dysbiosis. Recent studies demonstrate that C. difficile can be found in healthy people’s intestinal tracts. While these people only become sick when they receive antibiotic treatments, they act as carriers and might spread the disease when they are admitted in a healthcare setting. Bacteria that form part of the healthy microflora help defend you against C. difficile infection by converting primary bile salts (e.g. cholate and chenodeoxycholate) to secondary bile salts (e.g. deoxycholate and lithocholate) that will prevent the growth of undesirable bacteria (1, 2, 3). Metabolites, such as short chain fatty acids resulting from dietary fibre digestion, produced by the microbiota also limit colonization of undesirable bacteria (4, 5, 6). Therefore, the question we wanted to answer in this study was: how does C. difficile persist in the intestinal tract in the presence of these anti-infective metabolites?

Spore formation by C. difficile was initially hypothesized to be responsible for its persistence in the intestinal tract. An alternate hypothesis also exists, where C. difficile grows as part of a biofilm in the large intestine and that this mode of growth allows vegetative cells, as well as spores, to tolerate different attacks from the microbial communities and antibiotic treatment.

When this project began in the laboratory, we first looked at molecules that are present in the intestinal tract, especially those found in the caecal area of the large intestine where C. difficile colonizes. We next focused on bile salts, as they impact the physiology and pathogenicity of C. difficile and are also known to induce biofilm-formation by other intestinal pathogens. We started with a complex mixture of bile salts and found that they induce C. difficile biofilm formation. We then wanted to identify which bile salt(s) were responsible and found that sub-inhibitory concentrations of deoxycholate induced robust biofilm formation. The transition to a biofilm mode of growth was associated with a large metabolic shift in the bacteria in addition to increased bacterial viability during late stationary phase. Growth as a biofilm allowed C. difficile to tolerate concentration of deoxycholate and antibiotics that would typically stall growth or kill the bacteria. Growth in the presence of deoxycholate also decreased the production of two major infection determinants: toxins and spores.

Given that a secondary bile salt (deoxycholate) induces biofilm formation, we wanted to know if the conversion of primary bile salts into secondary bile salts by bacteria that normally form part of the microbiota are involved. Therefore, we tested whether the conversion of cholate into deoxycholate by resident microflora member Clostridium scindens induces C. difficile biofilm formation. We show that not only does C. scindens induce C. difficile biofilm formation, they actually co-operate to form one together!

Together, our findings provide a mechanism used by C. difficile to persist in the intestinal tract of people with a healthy microbiota. This study contributes to the understanding of the complex relationship between C. difficile and the host environment.

For more details, please see the paper in npj Biofilms and Microbiomes by clicking the Read the Paper button at the top.


1. Solbach P, et al. baiCD gene cluster abundance is negatively correlated with Clostridium difficile infection. PLoS One (2018) 13:e0196977. doi:10.1371/journal.pone.0196977

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5. Seekatz AM, et al. Restoration of short chain fatty acid and bile acid metabolism following fecal microbiota transplantation in patients with recurrent Clostridium difficile infection. Anaerobe (2018) 53:64. doi: 10.1016/j.anaerobe.2018.04.001.

6. Theriot CM, Young VB. Microbial and metabolic interactions between the gastrointestinal tract and Clostridium difficile infection. Gut Microbes (2014) 5:86. doi: 10.4161/gmic.27131.

Yannick Tremblay

Research Associate, Institut Pasteur