The Human Respiratory Microbiome: Implications and Impact

Alicia B. Mitchell, BMedSci (Hons); Allan R. Glanville, MBBS, MD, FRACP


Semin Respir Crit Care Med. 2018;39(2):199-212. 

In This Article

Summary and Conclusions

In a very real sense, our understanding of the component parts of the microbiome and, in particular, the human respiratory microbiome is just beginning. New tools, including NGS, are now available to assist in the exploration of this exciting field of knowledge; however, much work remains. Essentially, we need to define the constituents of the human respiratory microbiome in health and in disease states. Furthermore, we need to develop an understanding of what the normal range is throughout different phases of life and between different communities. In the human respiratory virome, in particular, it is vital to appreciate the concept of resident species such as anelloviruses and the impact of transient species such as community acquired respiratory viruses to underpin future research given the ubiquitous nature of the latter. Mapping the spatial architecture within the lung could also prove critical in localizing pathology to lung regions and providing potential targeted therapeutic options. Similarly, the ability to detect pathological alterations in the respiratory microbiome will depend on a deep understanding of the dynamics and inter-relationships between bacteria, viruses, fungi, and archaea. The study of these relationships will perhaps become a field unto itself. To date, there are little data in this area as a silo mentality has prevailed which has allowed a focus on one component at a time, perhaps reflecting individual interests and experience, as well as the limits of technology available, not to mention financial constraints. The challenge, therefore, for funding bodies, especially, is to see and appreciate the whole, and not just the component parts. Only then will the workings of the integrated machine become clear and our contemporary knowledge, which has been beset by false premises of microbial sterility of the lung, be cast aside to permit a revised vision of the complex microbial basis of this precious organ that allows us to breathe. Transplanting the human respiratory microbiome, as perforce is integral to lung transplantation, is a bold endeavor replete with its own special challenges where early exploratory evidence based on serial monitoring is showing promise of recognizing causes and outcomes of dysbiosis related to immune suppression. Whether real-time analysis will permit therapeutic adjustments to facilitate better outcomes remains to be tested in the crucible of clinical practice.