The human gut microbiome harbours a community of microorganisms including many species of bacteria, viruses, and fungi. This diverse and complex community plays an essential role in both health and disease, with studies demonstrating interactions between bacteria and the immune system are critical for immune development. In addition to this immunomodulatory role, the human gut microbiome also provides direct colonisation resistance where a pathogen is inhibited from colonising the gut through direct or indirect processes.
The bacteriostatic and bactericidal properties of many bacterial species in the human gut microbiome that contribute to this colonisation resistance are only now being uncovered. These functions can involve the bacteria releasing antimicrobial products, including products formed as metabolic bi-products, hence, the human gut microbiome is considered as a potential source for novel therapeutics for bacterial infections. This project aims to discover novel antimicrobials by screening and characterising bacterial isolates from the human gut microbiome which inhibit the growth of four different pathogenic bacteria, all known to cause severe gastrointestinal disease; Eschericia coli, Klebsiella pneumoniae, Enterococcus faecium and Clostridium difficile. Applying high-throughput screening of 190 individually purified isolates representing 90 species, we have identified 10 strains that exhibit consistent inhibitory properties against these pathogenic strains. Notably these antimicrobial effects appear to exhibit strain specificity within the commensals providing a capacity to apply genomics, proteomics, and metabolomics in the specific characterisation of putative novel antimicrobials.