The Respiratory System Microbiome: Diversity, Function and Health

It is now clear that the respiratory system of humans and other vertebrates, once thought to constitute a sterile environment, possesses a microbiome. The study of the respiratory system microbiome is in its infancy, and that presents challenges and opportunities. The challenges include 1) separating the true microbiome community from the organisms present because of incidental inhalation or laboratory contamination, 2) distinguishing a typical healthy respiratory system microbiome from one that results from pathology, 3) the problem of sampling tissues in minimally invasive ways, 4) linking the respiratory system microbiome to immune health and immune responses, and 5) understanding the interplay between host immune responses and the ability of microorganisms to evade or exploit immune responses. Opportunities in this field include the uncharted territory of understanding the potential benefits of a healthy respiratory system microbiome and the consequences of dysbiosis.

The respiratory system provides an important port of entry for airborne viruses, bacteria, fungi, and parasites. It is unsurprising that certain microorganisms have adapted to colonize the respiratory system. Early studies of the human respiratory system microbiome focused on individuals with respiratory system diseases, including cystic fibrosis, tuberculosis, and pneumonia among other infections. Recent studies have also addressed the importance of COVID-19 causing dysbiosis, resulting in secondary infections. Meanwhile, only a handful of studies have addressed the complex microbial environment present in healthy respiratory system tissues. Diverse research approaches are needed to better understand the nature and consequences of the respiratory system microbiome. We welcome articles of original research and reviews regarding historical and current topics in this field.

For this Research Topic we encourage the submission of articles of original research or review that include but are not limited to the following:

• Approaches to improve characterization and understanding of the respiratory system microbiome.
• The respiratory system microbiome and health (human or animal), including longitudinal studies to understand microbial turnover versus long term microbial residents.
• The consequences of diseases such as COVID-19, Valley fever, and bacterial or fungal pneumonia in disrupting the normal respiratory system microbiome.
• The importance of respiratory pathogens and host spillover.
• Studies of the respiratory system immune response to bacteria, fungi, and viruses in the context of the respiratory system microbiome.
• Factors that affect the transition of respiratory system commensals (e.g., species of Pneumocystis, Candida and Streptococcus) to pathogenic states.