The Human Respiratory Microbiome Current Understandings and Future Directions

Microorganisms colonize the human body. The lungs and respiratory tract, previously believed to be sterile, harbor diverse microbial communities and the genomes of bacteria (bacteriome), viruses (virome), and fungi (mycobiome). Recent advances in amplicon and shotgun metagenomic sequencing technologies and data-analyzing methods have greatly aided the identification and characterization of microbial populations from airways. The respiratory microbiome has been shown to play roles in human health and disease and is an area of rapidly emerging interest in pulmonary medicine. In this review, we provide updated information in the field by focusing on four lung conditions, including asthma, chronic obstructive pulmonary disease, cystic fibrosis, and idiopathic pulmonary fibrosis. We evaluate gut, oral, and upper airway microbiomes and how they contribute to lower airway flora. The discussion is followed by a systematic review of the lower airway microbiome in health and disease. We conclude with promising research avenues and implications for evolving therapeutics.

Automated summary

Microorganisms inhabit the human body, including the previously thought sterile lungs and respiratory tract. Recent advances in sequencing technologies have enabled the identification and characterization of microbial populations in the airways. The respiratory microbiome has been found to influence human health and disease, making it an emerging area of interest in pulmonary medicine. This review focuses on four lung conditions and examines the contribution of gut, oral, and upper airway microbiomes to the lower airway flora. The review concludes with potential research directions and implications for therapeutics.