Idiopathic pulmonary fibrosis (IPF) is a progressive and fatal fibrotic lung disease of unknown
aetiology. There is growing evidence that the lung microbiota may play a role in IPF. However, no
study has investigated the functional impact of the short-chain fatty acids (SCFAs) on disease
pathogenesis. The aim of this thesis was to characterise the respiratory microbiome and
metabolome in healthy controls and subjects with IPF and to investigate the influence of the SCFAs
on human primary bronchial epithelial cells (PBECs) and human lung fibroblasts (HLFs) from these
individuals.
Subjects diagnosed with IPF (n=201) and healthy controls (n=40) were prospectively recruited and
underwent bronchoscopy. Bacterial DNA was isolated and 16S rRNA gene sequencing undertaken
to characterise bacterial communities. Untargeted 1H nuclear magnetic resonance spectroscopybased
metabolomics and targeted gas chromatography-mass spectrometry captured the metabolic
profile of these samples. PBECs, differentiated at air-liquid interface, and HLF from healthy controls
and subjects with IPF were either left untreated or exposed to the SCFAs.
Compared to healthy controls, the IPF microbiota was less diverse (P<0.01), and had increased
proportions of Firmicutes (P<0.01), Streptococcus and Staphylococcus (P<0.05). Relative
concentrations of the SCFAs were increased in IPF compared to healthy controls, and in IPF,
propionate positively correlated with the bacterial burden (rho=0.47, P=8 x 10-5). Treatment of
PBECs from IPF subjects but not healthy controls with the SCFAs led to morphological changes, a
dose-dependent release of pro-inflammatory mediators in the cell supernatant, and a decrease in
transepithelial electrical resistance (TEER) over time. Compared to baseline, exposure of IPF PBECs
to 1 mM of propionate led to a 40% reduction in TEER and a significant increase (P<0.05) in the
secretion of IL-6. Treatment of HLFs with 5 mM of propionate or butyrate was found to increase cell
proliferation at 72 hours.
Subjects with IPF display an altered microbiome which is associated with a distinct metabolic
signature in the lower airways. Differences in bacterial genera and an increased bacterial burden in
IPF results in changes in the SCFAs in the airways. In vitro work demonstrates the potential of these
SCFAs to shape immunological responses in the lung, mediating the pathogenesis of fibrosis.