Defining the members of the microbiota that regulate innate immunity and protect against respiratory infection

Abstract

Humans are colonised by myriad bacteria, viruses and fungi, which constitute the microbiota. The majority reside in the gut and provide benefits to the host including regulating the development and maturation of the immune system. How the host’s innate immune system detects and responds to individual commensal species, and what the contributions of specific species are to immune regulation are poorly defined. This thesis investigates the immuno-stimulatory capacity of commensals from major phyla in the human gut by analysing cytokine induction and PRR activation by each species, thereby revealing their individual immunological fingerprint. Potent NOD2-activating commensal bacteria were identified and found, as a consortium, to boost resistance to a pulmonary S. pneumoniae infection. Protection was mediated by a GM-CSF-dependent mechanism which potentiated the bactericidal activity of alveolar macrophages. Signalling pathways activated downstream of PRRs by gut commensals were defined and found to vary between species, which may tailor the immune response to the specific stimulus. Important signalling nodes, common to all commensals such as ERK, RIP2 and the negative regulators MSK1 and MSK2, were also identified. Commensal gut bacteria were shown to induce memory, termed ‘trained immunity’, in innate cells and this altered the cytokine response to subsequent stimulations. An mTOR/AKT/HIF1-α-dependent mechanism of metabolic changes was identified to be important for most species to produce memory, however a reliance on glutaminolysis and cholesterol synthesis was also shown for certain commensals. The importance of epigenetic modifications facilitated by methyltransferase enzymes was demonstrated and supports the requirement for open chromatin, produced by histone methylation, at inflammatory cytokine promoters during innate immune training. This thesis establishes the variance in detection of, and immediate and long-term responses to, gut commensal bacteria by the innate immune system. Key species have been identified as major regulators of immunity and which protect the host against infection. These organisms could be investigated as novel therapeutics to manipulate innate immunity in diseases characterised by hypo- or hyper-inflammatory responses.