Environmental Influences on the Lung and Gut Microbiomes

Over the past few hundred years humans have been evolving into a primarily urban species. This evolution has coincided with an increase in allergy that may be caused by an underdeveloped immune system. Increasingly, research suggests this underdevelopment may be caused through loss of contact with beneficial, health promoting microorganisms known as the old friend’s hypothesis. This is of particular interest as humans continue to urbanize and begin spending more time indoors. there still exists several questions that need to be answered. Thus, it has become imperative to understand how exposure to diverse microbial populations changes the composition the lung and gut microbiomes and whether exposure through soils results in beneficial health outcomes. The first objective of this dissertation was to quantify the relative impacts of the different environmental media on the lung microbiome using a pig model. Using 16S rRNA gene amplicon sequencing, the microbiomes of the lungs, soil, water, feed, and air were determined at two different farms. Using the environmental data, a support vector machine model was created that could accurately classify the upper respiratory lung microbiome samples but not the alveolar samples. This suggests that while the upper respiratory system is regulated by the surrounding environment, this is a distinct community at the alveolar level that is regulated by selective pressures within the lung. The second objective utilized a mouse model exposed to three different soil types over 5 weeks to determine how the gut and lung microbiomes changed in response to the environmental alteration. This objective utilized 16S rRNA gene amplicon sequencing to determine the bacterial community within the cage, gut, and lung microbiomes. The differentially abundant amplicon sequence variants (ASVs) were identified to determine whether differentially abundant features in the soils were also found in the gut and lungs. This objective found that soils had a significant effect on both the gut and lung microbiomes that was driven largely by ASVs belonging to the family Lachnospiracae. The third objective explores whether exposure to the diverse microbial communities through soils resulted in a differential immune response when challenged with influenza A. To measure the differential immune response, RNA-seq was conducted with RNA extracted from whole lung tissue. From the differential expression data, the River soil exposed mice showed a significant increase in anti-inflammatory cytokines and lower overall neutrophil and macrophage cell counts. To determine what may be mediating this response, metagenome function was inferred from the 16S rRNA amplicon which showed several of the higher abundance Lachnospiracae ASVs were implicated in an upregulated propionate producing pathway, a small chain fatty acid associated with lower lung inflammation.