Ecology and evolution of commensal and pathogen species within the gut microbiota

The rise of antimicrobial resistance threatens animal and human health. An alternative to antimicrobials is urgently needed in the fight against infection. The commensal species of bacteria that form a healthy gut microbiota in mammals and birds provide their host with 'colonisation resistance' against invading pathogens. Administering specific consortia of probiotic species to boost colonisation resistance has great potential to protect against infectious disease. But a key question has yet to be asked: what are the long-term consequences of using probiotics? One of the big advantages that probiotics have over antibiotics lies in their potential to evolve in response to pathogens. In this way, probiotics could overcome the problem of resistance. Drug-resistant Salmonella is a 'serious threat' (CDC 2019) to both the food industry (for example in swine and poultry) and medicine. I will use experimental evolution in vitro and in vivo to test whether the well-studied model pathogen Salmonella enterica can evolve to invade a minimal community of probiotic gut bacteria, and whether the community can evolve in response to resist it. Additionally, I will carry out competition experiments to decipher the types of ecological interactions between commensals and other important harmful bacteria (such as Pseudomonas aeruginosa, Klebsiella pneumoniae and Candida spps.) carried in the gut. My ultimate goal is to determine the potential for using probiotic commensal species to expel these opportunistic pathogens from animal guts, thereby preventing infections.