The Microbial Ecology of Acute Lung Injury: How the Microbiome Affects (And Is Affected By) Alveolar Leak

Abstract

Acute lung injury is a lethal pulmonary condition that causes over 75,000 deaths per year in the United States, and millions of additional deaths worldwide during the past several years as the severe manifestation of SARS-CoV-2 infection. Recently, it has been established that injured lungs across multiple etiologies contain microbial communities altered from those present during health. While impaired immunity in acutely injured lungs has been heavily studied, the effects of microbial community changes on lung injury pathogenesis, and conversely, the features of acutely injured lungs that alter microbial communities, are poorly understood. Given our incomplete understanding of the role of respiratory microbiota in acute lung injury, and our lack of targeted therapies for acute lung injury and its infectious sequelae, it is imperative to determine the factors that perpetuate detrimental microbial community changes in the context of acute lung injury.

Therefore, the objective of this dissertation is to determine how the acutely injured lung microenvironment and its associated microbial communities interact during acute lung injury pathogenesis. To evaluate our central hypothesis – that the microbiota influence and are influenced by the injured lung microenvironment to participate in acute lung injury pathogenesis – we employed a multifaceted approach to accomplish the following three aims: 1) optimize a sampling strategy for examining the lung microbiome in murine models of lung injury, 2) interrogate the causal relationship of the microbiome to the pathogenesis of acute lung injury, and 3) determine which soluble factors in the injured lung enhance survival of pneumonia-associated bacteria by serving as bacterial nutrient sources.

In healthy mice, whole lung tissue contained greater bacterial signal and less evidence of contamination than BALF. The superiority of whole lung tissue as a sample type was defined by a greater quantity of bacterial DNA, distinct community composition, decreased sample-to-sample variation, and greater biological plausibility; all of these are key criteria for rigorous, low-biomass microbiome studies. In murine models of acute lung injury, microbiome modulation with antibiotics or germ-free status modified susceptibility to lung pathogenesis. These modulatory effects included altered alveolar leak and mortality in a sterile injury model of hyperoxia and altered bacterial burden in an infectious injury model of Klebsiella pneumoniae pneumonia, effects that may be attributable to the interventions’ disruption of gut anaerobe populations. In an ex vivo model of secondary bacterial pneumonia, changes in the metabolic microenvironment contributed to pneumonia pathogenesis via increased availability of serum-derived nutrients in the airspace, including injury-specific, systemic metabolites. The growth of Pseudomonas aeruginosa (the most prominent respiratory pathogen in a retrospective cohort of patients with ARDS) was enhanced by the availability of ALI/ARDS-associated airspace metabolites both in mice and humans.

Together, these findings help refine our understanding of the injured lung microenvironment as a microbial ecosystem by improving methodological approaches for studying low-biomass microbial communities, enhancing understanding of host-microbe interactions during critical illness, and providing a mechanistic basis for the development of clinical interventions for patients with acutely injured lungs.