Researchers have identified a microbiota metabolite that is depleted by the antibiotic clindamycin and replaced with fecal microbiota transplantation (FMT), mediating its effects on recurrent Clostridioides difficile (Clostridium difficile) infection (CDI). Reporting in the November issue of Gastroenterology, the researchers propose that this bacterial metabolite, valerate, might be used in safer and more effective treatments for CDI.
Exposure to antibiotics kills microbes that perform important functions in the intestinal ecosystem—the resulting dysbiosis creates an environment that promotes C difficile germination and growth. FMT is believed to reverse these effects by restoring microbes and their metabolic functions. However, transferring undefined living bacteria involves uncontrollable risks for infectious and metabolic or malignant diseases—particularly in immune-compromised patients.
Sterile fecal filtrate (bacterial debris, proteins, antimicrobial compounds, metabolic products, and oligonucleotides/DNA) from healthy stool donors also causes remission of patients with recurrent CDI. This filtrate is believed to contain bacterial metabolites or enzymes that are sufficient to inhibit C difficile spore germination and vegetative growth. Julie A.K. McDonald et al aimed to identify factors in fecal filtrate that are effective in patients with CDI.
They performed 16S rRNA gene sequencing, proton nuclear magnetic resonance spectroscopy, and ultra-performance liquid chromatography and mass spectrometry bile acid profile analyses of FMT mixtures prepared from fresh fecal samples provided by donors enrolled in an FMT program in the United Kingdom.
McDonald et al found that clindamycin decreased valerate and deoxycholic acid concentrations and increased C difficile total viable counts and valerate precursors, taurocholic acid, and succinate concentrations. After the authors stopped adding clindamycin, levels of bile acids and succinate recovered, whereas levels of valerate and valerate precursors did not.
Valerate is a short-chain fatty acid produced through amino acid fermentation by members of the gut microbiota.
In a chemostat model of CDI, the authors found that increasing valerate concentrations reduced C difficile total viable counts (94% decrease), spore counts (86% decrease), and valerate precursor concentrations; concentrations of bile acids were unchanged. Furthermore, valerate significantly decreased C difficile growth in mice with CDI.
In stool samples from patients with CDI, valerate was depleted before FMT but restored after FMT (at 1, 4, and 12 weeks). There were no significant differences in the levels of valerate in stool samples from healthy donors compared with those collected at any of the time points from patients with CDI after FMT.
McDonald et al performed batch culture experiments to directly study the effects of specific metabolites on C difficile germination and vegetative growth. These experiments confirmed that valerate decreased vegetative growth, and that taurocholic acid was required for germination but had no effect on vegetative growth. Furthermore, valerate decreased C difficile growth by 95% in mice with CDI compared with mice given phosphate buffered saline.
The authors propose that maintaining or restoring the levels of valerate in the intestinal microbiota of patients with CDI will inhibit the vegetative growth of C difficile. Valerate is a well-defined small molecule that is normally present in the healthy gut. Its restoration could be accomplished by directly supplying the gut with valerate (such as in the form of glycerol trivalerate) or by administering bacteria capable of transforming valerate precursors into to valerate.
Other options include supplementation with bile salt hydrolase enzymes (to degrade TCA and prevent C difficile pore germination) and succinate-degrading enzymes (to degrade succinate and give C difficile vegetative cells a competitive disadvantage). McDonald et al state that these proposed interventions are well defined and are safer options that will avoid all the risks involved with administering live micro-organisms to patients and will not promote antimicrobial resistance.