The discovery of novel antimicrobial molecules is vital to combat the increasing prevalence of antimicrobial resistance in bacterial pathogens around the world. The ability to now cultivate the previously “unculturable” members of the human gastrointestinal microbiota, together with computational evidence of putative antimicrobial molecules within the gut microbiome, offers a promising approach in exploring antimicrobial production by the human gut microbiome.
A panel of human gastrointestinal commensal bacteria were screened for antimicrobial activity against eight multi-drug resistant strains of gastrointestinal pathogens: Clostridiodes difficile, Escherichia coli, Enterococcus faecium, and Klebsiella pneumoniae. Of the 95 bacterial isolates screened, 75% exhibited inhibition of at least one of the pathogens tested. Specifically, a Bacteroides faecis, was selected for further investigation. To identify the inhibitory molecule produced by the B faecis candidate, assays with the cell-free supernatant of the isolate were performed. However, inhibition was unable to be replicated in the cell-free supernatant, and further exploration of the environment and stimuli required for secretion of a bioactive antimicrobial in B. faecis was conducted. The B. faecis candidate did not exhibit antimicrobial activity in these assays, and additional experiments are required to confirm the source of the pathogen inhibition caused by the B. faecis candidate, and the environment needed for potential production of antimicrobial molecules.
This study demonstrated that members of the human gut microbiota have inhibitory effects against multi-drug resistant gastrointestinal pathogens. Further investigation is required to determine the requirements for antimicrobial production in these commensal strains.