The microbiome and the lung

Abstract

Investigation of the human microbiome has become an important field of research facilitated by advances in sequencing technologies. The lung, which is one of the latest body sites being explored for the characterization of human-associated microbial communities, has a microbiome that is suspected to play a substantial role in health and disease. In this review, we provide an overview of the basics of microbiome studies. Challenges in the study of the lung microbiome are highlighted, and further attention is called to the optimization and standardization of methodologies to explore the role of the lung microbiome in health and disease. We also provide examples of lung microbial communities associated with disease or infection status and discuss the role of fungal species in the lung. Finally, we review studies demonstrating that the environmental microbiome can influence lung health and disease, such as the finding that the diversity of microbial exposure correlates inversely with the development of childhood asthma.

Keywords: HIV/AIDS; asthma; chronic obstructive pulmonary disease; lung; microbiome.

Figure 1.

16S ribosomal DNA hypervariable regions. Nine hypervariable regions (V1–V9) were labeled on the secondary structure of 16 rDNA. Among them, both V1–V3 and V3–V5 regions are commonly used to characterize the bacterial microbiome. Reprinted by permission from Reference .

Figure 2.

Interaction between the mycobiome and the immune system. The mycobiome shapes the immune response by the recognition between pathogen-associated molecular patterns (PAMPs) and pattern recognition receptors (PRRs) and the stimulation of the complement system and immune cell maturation. IFN = interferon; Ig = immunoglobulin; IL = interleukin; Th = T helper; TNF = tumor necrosis factor. Reprinted by permission from Reference .

Figure 3.

Relative abundance of fungal taxa in the respiratory mycobiome after lung transplant. Oropharyngeal washes and bronchoalveolar lavages were collected from each patient. Pyrosequencing data of the internal transcribed spacer (ITS) were clustered into operational taxonomic units, which were then assigned to taxonomic classes. The colors represent the relative abundance of the fungal taxon within each sample. The top row is the concentration of ITS DNA post–polymerase chain reaction for each sample. Reprinted by permission from Reference .