The microbiota of the respiratory tract: gatekeeper to respiratory health

Wing Ho Man, Wouter Antonius Adrianus de Steenhuijsen Piters, Debby Bogaert

Research output: Contribution to journalArticlepeer-review


The respiratory tract is a complex organ system that is responsible for the exchange of oxygen and carbon dioxide. The human airways extend from the nostrils to the lung alveoli and are inhabited by niche-specific bacterial communities. The microbiota of the respiratory tract likely acts as gatekeeper to provide colonization resistance to respiratory pathogens. The respiratory microbiota might also be involved in maturation and maintenance of homeostasis of respiratory physiology and immunity. The ecological and environmental factors that direct the development of respiratory microbial communities, and how these communities affect respiratory health are the focus of current research. At the same time, the functions of the upper and lower respiratory tract microbiome in the physiology of the human host are being studied in detail. In this review, we will discuss the epidemiological, biological and functional evidence that support the physiological role of the respiratory microbiome in the maintenance of human health.

Microbial communities have co-evolved with humans and our ancestors for millions of years and they inhabit all surfaces of the human body, including the respiratory tract mucosa. Specific sites within the respiratory tract harbour specialized bacterial communities that are thought to play a major role in maintaining human health. In the previous decade, next generation sequencing has led to major advances in our understanding of possible functions of the resident microbiota. So far, research has largely focused on the gut microbiota, microbiota-derived metabolites and their influence on host metabolism and immunity. However, recent studies on microbial ecosystems of other body sites, including the respiratory tract, reveal an even broader role of the microbiota in human health1.
The respiratory tract is a complex organ system that is divided into the upper respiratory tract (URT) and lower respiratory tract (LRT). The URT includes the anterior nares, nasal passages, paranasal sinuses, the naso- and oropharynx, and the portion of the larynx above the vocal cords, whereas the LRT includes the portion of the larynx below the vocal cords, the trachea, smaller airways (i.e. bronchi and bronchioli) and alveoli. The primary role of the respiratory tract in human physiology is the exchange of oxygen and carbon dioxide. To this purpose, the human airways have a surface area of approximately 70 m2, 40 times the surface area of the skin2. This entire surface is inhabited by niche-specific bacterial communities, with the highest bacterial densities being observed in the URT (FIG. 1). Over the years, evidence for the role of URT bacterial communities in preventing respiratory pathogens from establishing an infection on the mucosal surface and spreading to the LRT has accumulated. For most respiratory bacterial pathogens, colonization of the URT is a necessary first step before causing an upper, lower or disseminated (respiratory) infection3. Inhibition of this first step of pathogenesis of respiratory infections by the resident microbiota, a process which is also called ‘colonization resistance’, might be paramount to respiratory health. Furthermore, if a pathogen has colonized the mucosal surface, it might be beneficial to both the microbial community and the host that these pathogens are kept at bay, preventing their overgrowth, inflammation and subsequent local or systemic spread4. In addition to this symbiotic relationship, the respiratory microbiota likely has a role in the structural maturation of the airways5 and in shaping local immunity6,7.
Current research questions address how the healthy respiratory microbiota is established and which ecological and environmental factors govern its development. At the same time, the broad palette of functions of the respiratory microbiome is starting to become clear. In this review, we focus on the role of the respiratory microbiota in the development and maintenance of human respiratory health.
Original languageEnglish
JournalNature Reviews Microbiology
Early online date20 Mar 2017
Publication statusE-pub ahead of print - 20 Mar 2017

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