Effects of defined gut microbial ecosystem components on virulence determinants of Clostridioides difficile

Abstract

Many cases of Clostridioides difficile infection (CDI) are poorly responsive to standard antibiotic treatment strategies, and often patients suffer from recurrent infections characterized by severe diarrhea. Our group previously reported the successful cure of two patients with recurrent CDI using a standardized stool-derived microbial ecosystem therapeutic (MET-1). Using an in vitro model of the distal gut to support bacterial communities, we characterized the metabolite profiles of two defined microbial ecosystems derived from healthy donor stool (DEC58, and a subset community, MET-1), as well as an ecosystem representative of a dysbiotic state (ciprofloxacin-treated DEC58). The growth and virulence determinants of two C. difficile strains were then assessed in response to components derived from the ecosystems. CD186 (ribotype 027) and CD973 (ribotype 078) growth was decreased upon treatment with DEC58 metabolites compared to ciprofloxacin-treated DEC58 metabolites. Furthermore, CD186 TcdA and TcdB secretion was increased following treatment with ciprofloxacin-treated DEC58 spent medium compared to DEC58 spent medium alone. The net metabolic output of C. difficile was also modulated in response to spent media from defined microbial ecosystems, although several metabolite levels were divergent across the two strains examined. Further investigation of these antagonistic properties will guide the development of microbiota-based therapeutics for CDI.

Antibacterial Activity of Bifidobacterium breve Against Clostridioides difficile

“…After that, the cell pellets were collected by centrifugation (12,000 r/min for 5 min), and washed twice in PBS (pH 7.4). The pellets were resuspended in 0.5 mL of PBS in the last wash. Spores were enumerated by serially diluting the samples in PBS and plating onto BHI agar plates with 0.1% sodium taurocholate (Sigma) (Carlucci et al, 2019). All these plates were incubated at 37°C anaerobically for 72 h, and the resultant CFU/mL values were considered to represent the relative numbers of viable spores produced.…”

1D 1H NMR as a Tool for Fecal Metabolomics

“…When analyzing more than two sample sets, color-coordinating sample sets may be helpful in distinguishing between shifts and sample relationships. As an example, Figure 8, from Carlucci et al (2019), displays the independent clustering of three microbial ecosystems based on metabolic output.…”

Precision medicine and gut dysbiosis

“…Patients who are infected with C difficile experience significant alterations to their gut flora (microbiota) due to shifts and changes instigated by the antibiotic(s) in majority of cases. 1,3,10 With the distortion of healthy microbiota, C difficile is able to colonize, multiply, and produce toxins which are responsible for causing symptoms and signs of the infection. [2][3][4][5] Of particular notice are the changes in overall bacterial abundances which are shown to be greatly decreased in CDI patients, suggesting a depletion of healthy microbes and overall diversity.…”