8 The Respiratory Microbiome
The Respiratory Microbiome
The respiratory microbiome (specifically the lower portions) was once thought to be nonexistent, as many considered healthy lungs to be a sterile environment. Like other microbiomes though, the upper and lower respiratory system are environments rich with bacteria, fungi, archaea, and viruses, and because of the novelty of study many of the members in these groups have not been identified. However, it is known that many of such organisms are not only responsible for or exacerbate a number of pulmonary diseases, but that the respiratory microbiome can help to mitigate infection and influence treatment of certain illnesses (Unger and Bogaert, 2017, Watson et al., 2019).
The human respiratory system begins with the upper respiratory system; starting with the nose and nostrils, then proceeds to the nasal cavity, pharynx, and larynx. The lower respiratory system then starts with the trachea, moves to the bronchi and bronchioles, and ends with the lungs. Each of these structures and areas have their own microbial niche which serve various roles in maintaining health, but also have the potential to be compromised. The respiratory system is similar to the oral and digestive system, in that they interact intimately with external stimuli and bring in foreign matter and microbes during regular biological processes, like inhalation. These systems also have overlapping parts (e.g. oral cavity and pharynx), where their respective microbiomes serve similar roles such as resistance to disruptive environmental factors and host defense (Dickson et al., 2014, Zaura et al., 2014, Hakansson et al., 2018). The mucosal surfaces of the respiratory tract also have a natural healthy biofilm where the resident microbiota reside to maintain homeostatic functions, however, as an extension of dysbiosis, these biofilms can become altered and obtain pathogenic microbes which contribute to respiratory diseases (Hamilos, 2019).
Composition
Immediately after birth the respiratory microbiome becomes colonized, though the collection of microbes found here during infancy is not much different than other locations in the body, and generally reflect the mode of delivery (Dominguez-Bello et al., 2010). The respiratory microbiome, as well as others, become differentiated over time when the different species of microbes adapt and outcompete each other based on their niche, host genetics, and environmental factors (Bosch et al., 2016). Colonization additionally depends on microbial immigration, microbial elimination, and relative reproduction rates of its members (Figure 1) (Dickson and Huffnagle, 2015). With age, the respiratory microbiome of each particular individual reflects the aforementioned factors as well as other lifestyle habits, and so they can be vastly different between people. Although these respiratory microbiomes are unique, a core set of microbes can be defined, with most of them being aerobic or facultatively anaerob