Developing communities of commensal bacteria to enhance immune defences to infection

Abstract

The microbiota is the collective term referring to the diverse range of microorganisms which colonise the human body and other forms of higher life. This complex and dynamic community contains trillions of bacteria and other microbes; it has evolved alongside the host and inhabits all environmentally exposed surfaces within the body. As a result, the microbiota plays a critical role in host health and disease. In particular, the microbiota has been shown to be invaluable for a normal functioning immune system, with disruption to the microbiota resulting in increased susceptibility to pathogenic infection, as well as a multitude of inflammatory or autoimmune diseases. Microbiota-mediated regulation of the innate immune system is facilitated through the production of pattern recognition receptor (PRR) ligands and short-chain fatty acids (SCFAs). While both mechanisms of immune regulation are well-studied independently, the combine effect of these two pathways is far less well understood, despite occurring constantly during homeostasis. In this thesis, we show that the effect of PRR ligands and SCFAs on macrophages in isolation is distinct compared to their combined effect. We demonstrate that SCFAs modulate cytokine production induced by PRR activation, resulting from co-stimulation of macrophages with a wide range of commensal bacteria and different SCFAs. These SCFAs elicit either a pro- or anti-inflammatory effect depending on the sequential order of treatments. We also show that stimulation of PRRs by certain commensal bacteria is able to rescue macrophages from the cytotoxic concentrations of SCFAs, found within the host. Finally, using a Clostridium difficile infection (CDI) mouse model, we demonstrate that a combination of SCFA treatment and commensal bacteria inoculation, significantly reduces C. difficile load and increases expression of the antimicrobial peptide Reg3γ, in comparison to each treatment in isolation. The work outlined in this thesis provides a foundation for novel microbiome-based therapeutics, which can harness the combined potential of both PRR- and SCFA-mediated immune regulation, to enhance immune defences to infection.