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Clostridioide (formerly Clostridium) difficile’s success as a pathogen is rooted in the . The bacterial pathogen’s time as a toxin-producing vegetative cell is flanked by periods as a tough, metabolically dormant spore. C. difficile’s transition from one life stage to the next depends on specific nutrients and metabolic compounds derived from its host and other gut microbiota. By understanding what C. difficile needs (or eats, for that matter) to survive and thrive in the gut, we can develop strategies to prevent or treat C. difficile infection (CDI) at various stages of the pathogen’s life cycle.

Current Treatments Encourage C. difficile Recurrence

in the United States alone every year. This diarrhea-inducing bacterium can do some serious damage, both in and outside the gut. Indeed, the economic costs associated with per year. It is no surprise that C. difficile has landed a spot on the .

Most of the time, our by hogging nutrients and space in the intestine, releasing metabolic by-products that inhibit C. difficile growth and secreting compounds that directly target and kill this nasty bug. However, perturbations to the microbial community, often as a result of antibiotic treatment, weaken these barriers to C. difficile colonization. Indeed, antibiotic treatment is the primary risk factor for developing CDI, thanks to its microbiota-obliterating powers. and having a weakened immune system or pre-existing condition, like .

Clinical syndromes resulting from CDI range from mild diarrhea to life-threatening colitis (inflammation of the lining of the colon). Unfortunately, the primary treatment for CDI also happens to be the key risk factor: antibiotics. As a result, as . These patients take , largely because their microbiota is depleted and fails to return to its pre-infectious, C. difficile-resistant state. To this end, fecal microbiota transplants (FMTs), in which the microbiota from a healthy donor is transmitted to a CDI patient, are currently the gold standard for treating recurrent CDI. Though effective, FMTs are a black box in terms of their microbial composition. They can , that lead to disease and complications in FMT recipients.

The problem of recurrent CDI, coupled with concern for the and potential for adverse FMT-associated outcomes, has prompted interest in developing novel preventive and therapeutic strategies for managing CDI. Luckily, C. difficile’s life cycle offers a number of potential targets.

The Beginning of C. difficile Colonization: Germination

As an anaerobic bacterium, C. difficile survives the oxygen-rich world outside the gut by forming spores. Spores are shed through feces. Without good hygienic practices (e.g., proper hand-washing), they can contaminate food or surfaces, where they are inadvertently passed from one person to the next. While , one is most likely to pick them up in CDI hot-spots, like or .

Similar to the seeds of a plant, , like DNA and enzymes, encased in multiple membranes and protein-rich shells. Upon ingestion and safe passage into the host’s intestine, the spores germinate into vegetative cells. During this process, they rehydrate and metabolism kicks into gear. Whether or not germination occurs, however, depends on interactions between the spores and small molecules, called germinants, within the gut. In C. difficile’s case, these germinants come in the form of host-derived primary bile acids.

Primary are synthesized from cholesterol in the liver and secreted into the digestive tract. Like soap cutting through grease, bile acids are detergent-like molecules that help break down fats in the gut. There are several types of bile acids that differ in their molecular structure. Because of this, not all bile acids support C. difficile germination. For example, ; it to initiate the germination process. , on the other hand, can , but does not induce the downstream signalling required for germination to occur.

While certain spore-bile acid interactions are critical for initiating germination, they are not enough by themselves. Co-germinants, like the , and are also required. The exact roles of these compounds, which are presumably derived from host diet, are not well-defined. However, they likely signal to C. difficile spores that there are enough nutrients in the gut to support the generation and proliferation of vegetative cells. Indeed, , while . Thus, bile acids and co-germinants collectively send a message to C. difficile spores that a) they are in the gut and b) there will be enough food to support their transformation into metabolically active, free-living cells.

In addition to host-associated compounds, germination is tightly linked to the metabolic output of the gut microbiota. Some gut bacteria can convert primary bile acids into , such as lithocholate and deoxycholate, which inhibit C. difficile germination and outgrowth into vegetative cells, respectively. Under normal circumstances, secondary bile acids constitute a barrier to C. difficile intestinal colonization. However, antibiotic treatment kills members of the microbiota that produce these inhibitory molecules. As a result, primary bile acids, some of which act as germinants, increase in concentration and increase the likelihood for C. difficile spore germination and expansion in the gut.

C. difficile Growth: The Vegetative Phase

After germination, C. difficile enters its hungry phase. , in part by inhibiting the pathogen’s access to nutrients or by releasing inhibitory metabolic compounds, like secondary bile acids.

However, if the microbial community is disrupted, a to eat. C. difficile is not picky when it comes to food, and depending on the at a given time. However, there are some nutrients that are critical for efficient growth, including . These substrates , a set of amino acid , in which electrons are transferred from one amino acid to another to produce adenosine triphosphate (ATP) and other molecular drivers of life.

Many of the nutrients C. difficile consumes are associated with a loss in gut bacterial diversity—the bugs that normally hoard the food C. difficile likes to eat are no longer there (likely due to antibiotic treatment). That being said, the pathogen can also exploit nutrients derived from the microbes that are present. For instance, , a sugar liberated from intestinal mucus by members of the microbiota, to expand in the gut. Other compounds associated with microbiota metabolism, such as . Thus, the gut microbiota can be both friend and foe when it comes to C. difficile nutrient acquisition.

Hunger and Destruction: C. difficile Toxin Production

C. difficile’s phase as a vegetative cell is marked by intestinal destruction. The that disrupt intestinal barrier integrity and promote inflammation. Interestingly, toxin production occurs not in the presence of specific nutritional or metabolic signals, but rather in the absence of such signals.

Several in vitro studies suggest that , . In fact, are . In other words, toxin production is C. difficile’s “”response. , like collagen, from host cells, while inhibiting expansion of bacteria that might compete with the pathogen for those same nutrients. This strategy is similar to what has been reported for other gut bacterial pathogens, like and , which exploit the host inflammatory response for food. Thus, C. difficile’s toxins may create a nutritional niche for the pathogen to occupy within the gut.

And So It Begins Again: C. difficile Sporulation

After its stint as a free-living cell, C. difficile reverts to its spore form. While the specific triggers of spore formation remain elusive, there is evidence to suggest that, like toxin production, . Indeed, and the and toxin production are also involved in sporulation. In any case, once the process is complete, the new spores are shed into the environment, where they bide their time until a new host comes along.

Managing CDI by Starving the Pathogen

The need for new methods for managing CDI fuels research into strategies that prevent or treat infection by targeting metabolically distinct phases of C. difficile’s life cycle. Some of these strategies focus on germination. After all, inhibiting germination of C. difficile spores saps the ability of the pathogen to do any damage. prevent C. difficile spore germination in vitro, . One competitive inhibitor of taurocholate-mediated germination, called in a mouse model of disease.

Other strategies restore a C. difficile-resistant gut microbiota. While FMTs are undefined in their microbial composition, recent work has focused on identifying and generating specific bacteria or defined bacterial “cocktails” that can inhibit C. difficile germination and growth. For example, Clostridium scindens is one of the gut bacteria that can convert primary bile acids into secondary bile acids. This bacterium is , in part by altering the bile acid pool within the gut.

Promoting microbial competition with C. difficile for nutrients is another viable option. for mucus-derived sugars and reduce its growth in the gut. Others have shown that , some of which are naturally occurring, can protect against subsequent infection by a toxigenic strain. While the mechanism underlying this protection is unclear, nutrient competition may play a role.

Still others have taken an indirect approach by assessing how host diet affects the microbiota and resistance to CDI. For instance, produced from and . To this end, , which were associated with reduced gut concentrations of C. difficile. and in mouse models of disease. Thus, tweaking diet may be one way to reduce the availability of C. difficile-preferred nutrients and enrich for microbes that resist the pathogen.

While the results from these studies are encouraging, many of the proposed strategies for managing CDI are still in the early phases of development—they have yet to become more than intriguing possibilities. Nevertheless, they emphasize that the key to managing CDI may rest in understanding the metabolic underpinnings of C. difficile’s life cycle.

Why have C. difficile infections increased over the past several decades? How do fecal transplants successfully treat recurrent CDI? Tune in as Dr. Vincent Young, a professor in the departments of Internal Medicine and Microbiology and Immunology at the University of Michigan Medical School, provides answers to these questions and more.