UC Berkeley

Like all sites on the human body that are open to the outside world, the human lungs are colonized by microbial life. The advent of culture-independent sequencing in the 90’s led to the knowledge of this site as a rich and diverse microbial ecosystem. In recent years, the dysbiosis or eubiosis of this community has been linked to the occurrence of a variety of respiratory diseases including infection. With increasing concerns over antimicrobial resistance amongst respiratory pathogens, tuning of the human lung microbiome in favor of health may serve as an alternative therapeutic strategy for preventing and treating respiratory infections. Tuning of the lung microbiome could be achieved through numerous avenues such as administration of substrates that can augment health-promoting organisms or supplementation of those health promoting organisms themselves.

Here, I explore the concept of supplementing the native community with probiotics, or health-promoting organisms, to prevent respiratory infection. Specifically, I hypothesize that organisms isolated from the native lung community will be efficacious probiotics as they will be adapted to the lower airway environment. I survey the ability of these host-derived candidate probiotics to directly compete with a model pathogen, Burkholderia thailandensis, to ultimately exclude it from the lung niche. I also investigate the mechanisms by which this antagonism may be achieved, through the use of specialized metabolites (Chapter 1) or resource competition (Chapter 2). This investigation ultimately allows me to begin to develop a pipeline for nomination of single and multi-organism probiotics for preventing Burkholderia infection. Finally, we show that prophylactic administration of some of these candidate probiotics to the lower airway of mice significantly protects them from death due to infection.

In the last two chapters, I delve into the ability of these same candidate probiotics to be repurposed as diagnostic sensors and tools for studying the native lung microbiome. In Chapter 3, I make inroads towards development of probiotic biosensors for detecting infectious agents in the lower airway. I show that some of these host-derived organisms are genetically tractable and propose experimental strategies to test their functionality in vitro and in vivo. Finally, in Chapter 4, I show progress towards the design of a model lung fabricated ecosystem using the candidate probiotics which will have utility for in vitro study of microbial interactions in a lung-like environment.

Ultimately, the work presented in this thesis underscores the potential of manipulating the lung microbiome as a promising strategy for preventing respiratory diseases. It has also shown the vast complexity of microbial interactions in the lung and has generated numerous questions about how the fundamental principles herein apply broadly to preventing other lower airway disease states. As such, tools for investigation of these interactions in biologically relevant systems are needed. If a fine-grained knowledge of the lower airway microbiome can be achieved, genetic manipulation could be used to predictably tune this environment towards a number of desired states.