Unraveling the role of the gut and lung microbiome in pulmonary infection and inflammation

Bacteria were long considered to mainly be harmful. However, we now know that many microorganisms play important roles in the protection and functioning of the human body. This thesis provides an insight into the composition and function of the gut and lung microbiome during inflammation and infection. More specifically, we aimed to assess how these microbiomes can influence, or are influenced by, the host response to bacterial K. pneumoniae pneumonia and pulmonary LPS-induced inflammation. We focused on the effect of vendor, antibiotics and infection on the gut and lung microbiota and the gut-lung axis in murine models of K. pneumoniae infection. We found that although there was a marked variation in the gut microbiota composition of mice from different vendors, the impact on our models of pulmonary inflammation and severe pneumonia was limited. Whereas, antibiotics treatment of mice prior to a pulmonary challenge of LPS showed to have an immunomodulatory effect on experimental outcome. We also saw a change in the murine lung microbiota over-time during K. pneumoniae pneumonia and sepsis. These studies served to gain a greater understanding of how the microorganisms in the body function and change during bacterial pneumonia.