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Targeting C. difficile Infection with Next-Generation Probiotics


Antibiotic use can disrupt your body’s protective microbial barrier and open the door to pathogens and illness. Our research focuses on developing next-generation probiotics that would selectively prevent infection by the bacterium Clostridium difficile, a gastrointestinal pathogen that produces toxins resulting in watery diarrhoea and in severe cases, pseudomembrane colitis, toxemia, sepsis and death.

C. difficile infection (CDI) is the leading hospital-associated infection in the U.S., causing thousands of deaths and billions of dollars in healthcare expense each year. A healthy gastrointestinal microbiome is usually sufficient to protect against this pathogen, but when patients take antibiotics for unrelated illnesses they are 7-10 times more likely to become infected with C. difficile than those not taking antibiotics.

The current standard of care for CDI is additional antibiotic therapy with one of only three drugs effective against C. difficile. Treatment failure occurs in approximately 35% of patients, who then require further antibiotic therapy. This perpetuates a vicious cycle whereby the microbiome cannot recover and results in increased morbidity and mortality. Patients require microbiome replacement by faecal microbial transplant (FMT) as a last resort to survive. FMT typically resolves recurrent CDI, but the long-term health risks associated with transferring processed fecal matter into the GI tracts of patients are largely unknown.

The introduction of antibiotics over 70 years ago revolutionised health care to the point where minor cuts and burns no longer came with the threat of death by infection. Yet, after decades of antibiotic misuse, we are witnessing a global health crisis, fuelled by multi-drug resistant organisms that pose fatal threats at levels significantly greater than the pre-antibiotic era. The threat of antimicrobial resistance to global health has scientists racing to develop novel therapeutics that not only prevent or treat microbial infection, but also diminish the rate at which new resistant organisms arise.

Although C. difficile is not antibiotic resistant per se, its intimate relationship with antibiotic exposure and limited antibiotic treatment options rank this pathogen as one of the greatest health threats of the 21st century. With only three antibiotics currently available to treat CDI and the unknown long-term health risks of FMT, non-traditional therapeutics like toxin binding agents, immunotherapies, defined microbial therapies, to replace FMT, and probiotics are ideal alternatives worthy of exploration.

Fighting Microbes with Microbes

Ultimately, a healthy microbiome prevents CDI and the fact that the re-population of a disrupted GI microbiota by FMT cures recurrent CDI suggests that protection against this deadly infection could be harnessed from beneficial microbes or probiotics. The use of probiotics to prevent antibiotic associated diarrhoea is not a new concept and recent meta-analysis indicates that patients that are at high risk of developing CDI benefit the most from using probiotics as adjunct therapy to antibiotics. However, clear recommendations for clinical use of probiotics in CDI prevention are hindered, due to the lack of evidence on specific probiotic strains, doses and patient populations. Regardless, microbiome research has catapulted a public interest in probiotics and physicians are making general recommendations for probiotic use, especially in cases of GI disease and antibiotic associated diarrhoea. These general recommendations stand to benefit from clear and concise scientific evidence supporting mechanistic means by which specific probiotics prevent disease.

Probiotics have long been defined by the World Health Organisation as live microbes that confer health benefits when administered in adequate quantities. They have been regulated as ‘GRAS’ (Generally Regarded as Safe) by the FDA. Therefore, they cannot be associated with health claims. Next-generation probiotics are beneficial microbes that are intended to target disease as therapies and will require increased regulation by the FDA as drugs, and in doing so should provide us with the required evidence to make clear clinical recommendations for their use.

Selective Decolonisation Of Pathogens By Next-generation Probiotics

Many of our microbial counterparts produce antimicrobial agents that aid in niche adaptation and promote a natural barrier to pathogen colonisation and infection.  Efforts into harnessing this activity can be used to counter antimicrobial resistance and selectively decolonise pathogen reservoirs to decrease disease incidence. Our studies have focused on characterising the antimicrobial activity of probiotic L. reuteri  and we are on the cusp of defining a rationally designed next-generation probiotic formulation with specific activity against C. difficile.

Specific human-derived probiotic L. reuteri strains produce reuterin, an isomeric mixture of 3-hydroxypropionaldehyde, with antimicrobial activity against C. difficile. The production of reuterin by L. reuteri is a vitamin B12-dependent process that results in the conversion of glycerol (substrate) to reuterin (antimicrobial compound). This process is not trivial by any means. Genomes of reuterin-producing strains contain a horizontally acquired 57-gene cluster that enables (1) vitamin B12 synthesis de novo, (2) formation of intracellular microcompartments required for reuterin sequestration, and (3) fermentation of glycerol. Understanding the requirements for this intricate process has enabled us to postulate probiotic formulations capable of selectively decolonising enteric pathogens.

While reuterin activity against single pathogens has been documented, our most recent work has highlighted the substrate requirements for anti-pathogenic activity in a microbial community setting.  Using multiple continuous culture systems, or mini-bioreactor arrays, we showed that L. reuteri has specific activity against C. difficile only when glycerol is provided to drive reuterin production; L. reuteri alone is not sufficient. Microbiome analysis confirmed specificity to C. difficile in a mixed microbial community supporting the use of a L. reuteri/glycerol formulation as a selective decolonisation agent to decrease CDI. Future next-generation probiotic applications could include prophylactic administration before and during antibiotic exposure to prevent C. difficile growth.


Jennifer Spinler is an instructor at Baylor College of Medicine in the Texas Children’s Microbiome Center (TCMC).


To find out more about probiotics and their role in personalised nutrition, infant health, and colonic bacteria, join us at the Probiotics Congress: USA in San Diego. Find out more about the event here

2 Responses to “Targeting C. difficile Infection with Next-Generation Probiotics”

  1. Julia Oldham

    Has Baylor/Spinler’s divison said whether this been tried with humans yet? If so, effective dosing please. If not, should it be safe to just try taking some reuteri and glycerol since they’re both available “otc” ? I did google up a recommended glycerol to water ratio; was on a sports supplements site (blog?). Thanks

  2. I was searching to find out the propertions/dosage of lactobacillus reuteri and glycerol for treating Clostridium difficile as well. Did you have any luck?


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