The Airway Microbiome.
Michael G Surette
Canada Research Chair in Interdisciplinary Microbiome Research, Farncombe Family Digestive Health
Research Institute, McMaster University, Hamilton ON Canada (surette@mcmaster.ca)
Abstract
The respiratory tract is home to a diverse collection of microbes that include not only commensal
organisms but many pathogens carried asymptomatically. With the advent of molecular methods for
studying the microbiome our understanding of the composition of the microbial communities that
colonize the airways in both health and disease has exploded. The upper airways contain some of the
most diverse microbiome populations in the body. The lower airways (lungs) have also been the
focused of research and it has now been demonstrated that in most lower airways diseases, there is a
complex polymicrobial community present. Perhaps most surprising is the observation that obligate
anaerobic bacteria make up a significant proportion of this community. What role these organisms play
in disease is not yet clear. There has also been evidence to suggest that the lungs in healthy individuals
may be colonized by bacteria although the data is not conclusive. The relative ease and decreasing cost
of microbiome methodology has made this area of research widely accessible. These methods are
readily applied to the microbiomes of any host animal. However it is not without limitations and some
of the technical challenges are often overlooked. The discrepancy in results between very similar
studies may in part be accounted for by differences in methods used. Nonetheless microbiome profiling
is becoming an important approach in respiratory infections and diagnostics.
The description of microbes in close association with their animal hosts goes back to Hooke and van
Leeuwenhoek and the invention of the microscope in the 1600s (1). The importance of these organisms
to human health were being discussed early in the last century by Ilya Mechnikov (2). However it has
largely be the advances in DNA sequencing technology that has resulted in renewed interested in the
microbiomes associated with their animal (and plant) hosts. In a timely and provocative letter to science
in the issue after the publications of the first human genome sequences, Julian Davies reminded us that
the human genome is incomplete without including that of our microbial symbionts (3). The
microbiome includes not only eubacteria, but also archaebacteria, fungi and viruses (including
bacteriophage) living in close association with their hosts. Most of the research has focused on the
bacteria primarily because of the ease of the methodology for bacteria compared to the other microbes.
Our understanding of the microbiome has been accelerated by several large funding initiatives (such as
NIH’s Human Microbiome Project, the European MetaHIT Consortium, and Canadian Microbiome
Initiative) largely focused on humans and experimental animals. In the last decade or so, the human
microbiome has been implicated in almost all aspect of human health and disease (4,5). The greatest
focus has been on the microbiome of the gut where the greatest number of bacterial cells reside. But all
mucosal surfaces and the skin harbor distinct microbial populations. The upper respiratory tract,
including the nose, throat and oral cavities, is colonized by a rich microbial community. Collectively the
upper airways, in particular the oral cavity, represents the most diverse microbiome site in the body,
even harbouring more different bacterial types than the gastrointestinal tract (6,7,8). This is also the site
of initial interactions with many environmental microbes through breathing and ingestion. This
community of bacteria is dominated by a core microbiome of diverse Streptococcus, Gemella,
Veillonella, Prevotella and Fusobacterium (8). Importantly the resident microbiota of the upper airways
includes many pathogenic bacteria that colonize asymptomatically such as Streptococcus pneumoniae,
Staphylococcus aureus, Moraxella catarrhalis, and Haemophilus influenzae (9). For these organisms, the
distinction between commensal and pathogen is blurred.
The lower airways were generally considered to be a sterile site in healthy individuals or more
appropriately an effectively sterile site. The lower airways in an adult human are exposed to 105
microorganisms per day through aerosols during normal breathing. These were generally thought to be
effectively dealt with by the airway immune defense (10). In the case of chronic lower airway disease
[such as in cystic fibrosis (CF), chronic obstructive pulmonary disease and asthma] and even in more
acute infections, it is now widely accepted that the lower airway colonization is polymicrobial (10).
These communities include many members of the upper airway microbiome in addition to the expected
pathogens. Importantly obligate anaerobes make up a significant portion of these lower airway
microbiomes. The role of these additional microbes in disease is not understood. The studies have also
led to investigations of the lower airways in healthy individuals and whether there may be a viable
microbial colonization of the lungs. The challenge in these studies is contamination of the sample during
bronchoscopy and the suggestion that the diverse community observed represents contamination
rather than true colonization of the lower airways. To address this, oral microbiota profiles are
compared to bronchoalveolar lavage (BAL). If there is a true lower airway community it should look
different than the oral microbiota in the sample individuals. Assuming the lower airways would be
colonized from the upper airways but represent a different ecological environment, some but not all
species would be similar and their relative abundances differ. The data from recent studies suggests a
lower airway microbiome, but it is certainly not convincing in all samples (11,12). In disease states, such
as in CF, several studies have shown that the sputum or BAL microbiome is distinct in microbial
composition and relative abundance compared to the oral microbiome (13) ruling out contamination as
a major source of the organisms. It is likely that all lower airway infections will be accompanied by
polymicrobial colonization of the lower airways even in acute pneumonias. Whether this will influence
the progression of disease is not known. Using animal models, we have shown that bacteria isolated
from the airways of CF patients that themselves have little or no pathogenic potential, can synergize
with pathogens to enhance virulence suggesting a role for polymicrobial interactions in disease
progression (14).
The microbial characterization of the airway microbiome has been carried out primarily using cultureindependent molecular methods. The bacterial gene encoding the small ribosomal subunit, 16S rRNA
gene, is widely used to define the composition of microbial communities. Taxonomy can be inferred
from direct sequencing of the amplified 16s rRNA gene fragment using clone libraries and now more
commonly using massively paralleled DNA sequencing methods (15). These approaches cans provide
hundreds to millions of sequences and provide in depth analysis of community composition. The steps
involved are outlined in Figure 1. There are significant technical challenges associated with each of
these steps. Differences reported by different studies on similar samples may be attributed to
differences in one or more of these steps rather than the actual microbial communities. To date most
groups use different extraction protocols, regions of the 16S rRNA, sequencing technologies and
bioinformatics analysis. This limits our ability to make direct comparisons between the predicted
communities in these various studies. Furthermore, the taxonomic resolution of these methods is often
not good enough to distinguish recognized pathogens from closely related avirulent relatives. There are
two additional caveats of the culture-independent approaches that can bias the inferred community.
The airways contain a significant amount of DNA from dead cells which can accumulate in the thick
mucus, particularly in disease states. This DNA can persist and may not accurately reflect levels of viable
bacteria. In the studies of BAL fluid noted above, whether the DNA isolated from the healthy lower
airways represented viable bacteria is not known. This issue may also limit the use of these molecular
approaches to measure efficacy of antibiotic therapy over the short term. Second, DNA extraction
protocols vary widely and some organisms can be under represented by some methods (16). This may
account for some difference in relative abundances of some organisms between studies.
Despite these caveats, culture-independent methods provide a relatively straight forward means to
study these complex communities. Beyond these descriptions of “who’s there”, metagenomic,
metatranscriptomic and metabolomic approaches are required to understand the functional biology of
the airway microbiome. Whether or not there is a stable viable microbiome in healthy lungs, it is clear
that the lungs are constantly exposed to microbes from the upper airways including known and
potential pathogens. Any compromise in innate defense such as through infection, stress, or trauma can
lead to rapid onset of acute lung infections. Whether or not there are protective microorganisms in the
upper airways that can reduce the risk (airway probiotics) and how the gut microbiota influences these
processes through its modulation of the immune system are important areas of investigation.
Microbiome
Community
Sample Collection
and Processing
Nucleic Acid
Extraction
16S rRNA gene PCR
and Sequencing
?
Inferred Community
Composition
Taxonomic
Profile
Data Analysis
Figure 1. The multiple steps in molecular profiling of bacterial communities. Each step in the processes has
limitations and technical challenges. The assumption is that the final inferred community accurately reflects the
original composition of the sample community (adapted from 17).
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