The Lung Microbiome, Immunity, and the

Pathogenesis of Chronic Lung Disease

David N. O'Dwyer, Robert P. Dickson and Bethany B.
Moore
This information is current as
of May 21, 2018. J Immunol 2016; 196:4839-4847; ;
doi: 10.4049/jimmunol.1600279
http://www.jimmunol.org/content/196/12/4839

Downloaded from http://www.jimmunol.org/ by guest on May 21, 2018

References This article cites 124 articles, 38 of which you can access for free at:
http://www.jimmunol.org/content/196/12/4839.full#ref-list-1

Why The JI? Submit online.

• Rapid Reviews! 30 days* from submission to initial decision
• No Triage! Every submission reviewed by practicing scientists
• Fast Publication! 4 weeks from acceptance to publication
*average

Subscription Information about subscribing to The Journal of Immunology is online at:

http://jimmunol.org/subscription
Permissions Submit copyright permission requests at:
http://www.aai.org/About/Publications/JI/copyright.html
Email Alerts Receive free email-alerts when new articles cite this article. Sign up at:
http://jimmunol.org/alerts

The Journal of Immunology is published twice each month by

The American Association of Immunologists, Inc.,
1451 Rockville Pike, Suite 650, Rockville, MD 20852
Copyright © 2016 by The American Association of
Immunologists, Inc. All rights reserved.
Print ISSN: 0022-1767 Online ISSN: 1550-6606.
 The Journal of
Brief Reviews Immunology
The Lung Microbiome, Immunity, and the Pathogenesis of
Chronic Lung Disease
David N. O’Dwyer,* Robert P. Dickson,* and Bethany B. Moore*,†
The development of culture-independent techniques it is well established that alterations of the gut microbiome can
for microbiological analysis has uncovered the previ- influence immune responses at distal sites. Antibiotic treatment,
ously unappreciated complexity of the bacterial micro- which disrupts gut microbiota accompanied by increases in
biome at various anatomic sites. The microbiome of fungal colonization, can greatly exaggerate the allergic response
the lung has relatively less bacterial biomass when com- to intranasal challenge with the mold spore Aspergillus fumigatus.
pared with the lower gastrointestinal tract yet displays With antibiotic treatment, mice showed increased levels of eo-
considerable diversity. The composition of the lung sinophils, mast cells, IL-5, IL-13, IFN-g, IgE, and mucus-
microbiome is determined by elimination, immigration, secreting cells (4). More recently, modulation of gut micro-
and relative growth within its communities. Chronic biota through the use of probiotics has been shown to increase

Downloaded from http://www.jimmunol.org/ by guest on May 21, 2018

the frequency of B cells expressing IgA in the colon and lymph
lung disease alters these factors. Many forms of chronic
nodes, likely secondary to increased lymph node T follicular
lung disease demonstrate exacerbations that drive disease
helper cells and IL-23–expressing dendritic cells (5), all changes
progression and are poorly understood. Mounting evi- that are likely to improve host defense at mucosal sites or re-
dence supports ways in which microbiota dysbiosis can sponse to vaccination. Conversely, antibiotic treatment can limit
influence host defense and immunity, and in turn may development of T follicular helper cells (6). The response of
contribute to disease exacerbations. Thus, the key to un- pathogen recognition receptors (PRRs) of the innate immune
derstanding the pathogenesis of chronic lung disease may response in the lung is well described. We know that defective
reside in deciphering the complex interactions between components of the innate response can predispose to over-
the host, pathogen, and resident microbiota during stable whelming infection and mortality and in some cases reduce in-
disease and exacerbations. In this brief review we discuss jury from pathogens (7–9). The relationship between resident
new insights into these labyrinthine relationships. The microbiota and this flagship innate response and the subsequent
Journal of Immunology, 2016, 196: 4839–4847. adaptive immune response in the lung is poorly understood.
With this backdrop, we have chosen to explore what is known
about the potential role of the microbiota (both gut and lung)

T
he microbiome is defined as the “ecological community
and host interaction in regulating the pathogenesis of several
of commensal, symbiotic and pathogenic organisms
important lung diseases.
that share our body space” (1). Most studies of host
and microbiome interaction in the human have focused al-
most exclusively on bacteria, biotic factors, and the host. Origins of lung microbiome and debunking lung sterility
These complex communities of microbiota that inhabit en- The lung is an organ constantly exposed to microbiota either
vironments such as the lung, skin, or gut are now appreci- through inhalation or subclinical microaspiration from birth.
ated for their role in maintaining organ, tissue, and immune Historically, medical texts allude to a sterile lung environment,
homeostasis. One striking example is the early observation and this dogma has persisted in contemporary medicine. In the
that germ-free mice have absent/impaired secondary lym- last decade, a revolution of sorts has taken place in our un-
phoid architecture with resulting loss of lymphoid cells (2). derstanding of how the lung and microbiota interact and exist.
Additionally, commensal microbiota can have both systemic This revolution stems from new knowledge that the lung is
and site-specific autonomous immune effects. For example, not sterile (10) and, in fact, harbors an abundance of diverse
Staphylococcus epidermidis colonization of the skin promotes interacting microbiota. As mentioned above, the gut microbiome
CD4 cell IFN-g production, which protects against infection modulates host mucosal defense (11, 12); however, there is a
with the parasite Leishmania major. In contrast, colonization of paucity of information regarding the potential role of lung
the gut with S. epidermidis had no effect (3). In other situations, microbiota to regulate immunity and homeostasis.

*Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Address correspondence and reprint requests to Dr. Bethany B. Moore, University of
University of Michigan Health System, Ann Arbor, MI 48109; and †Department of Michigan, 109 Zina Pitcher Place, 4053 BSRB, Ann Arbor, MI 48109-2200. E-mail
Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, address: bmoore@umich.edu
MI 48109
Abbreviations used in this article: CF, cystic fibrosis; COPD, chronic obstructive
ORCIDs: 0000-0003-3214-380X (D.N.O.); 0000-0002-6875-4277 (R.P.D.); 0000- pulmonary disease; IPF, idiopathic pulmonary fibrosis; PRR, pathogen recognition
0003-3051-745X (B.B.M.). receptor.
Received for publication February 16, 2016. Accepted for publication March 24, 2016.
Copyright Ó 2016 by The American Association of Immunologists, Inc. 0022-1767/16/$30.00
This work was supported in part by National Institutes of Health Grants HL115618 and
AI117229 (to B.B.M.) and HL130641 and UL1TR000433 (to R.P.D.).

www.jimmunol.org/cgi/doi/10.4049/jimmunol.1600279
4840 BRIEF REVIEWS: MICROBIOME DRIVING PATHOGENESIS OF LUNG DISEASE

The lung is not sterile, contrary to centuries of dogma species, some of which are more susceptible to cell disruption
asserting the same. Throughout the 1900s this inference was than others. This discrepancy can lead to overrepresentation of
reinforced by respiratory culture-based protocols that sought some species over others. Further steps that may alter the ac-
only to identify clinically significant pathogens and by a spurious curacy and reliability of acquired data include the generation of
conclusion that upper respiratory tract microbes cultured from appropriate PCR primers, data normalization, the choice of
the lung represented contamination (10). The lung is a warm reference database, and divergent measures of diversity (25). The
environment exposed to 7000 l of diverse microbe-ridden air use of 16S rRNA sequencing remains a pillar step in the sample
every day (13). Microbes adapt and exist in hostile environ- processing; however, 16S rRNA sequencing may not be able to
ments similar to polar ice sheets of Antarctica and hot sulfur differentiate between species with varying immunogenicity and
springs of Japan, yet the idea the human lung existed in a sterile pathogenicity (26). The microbiome is subject to a number of
state was “cultivated” in the medical literature for decades (14, factors that are known to change its composition, including age,
15). The upper respiratory tract and oropharynx, where mi- diet, ethnicity, and study design, and in humans requires careful
crobes are found in abundance (16), is in direct communica- management of these potential influences (27–29). However, in
tion with the lung, and subclinical aspiration of oropharyngeal tandem, researchers are developing novel and ingenious methods
contents occurs universally in humans (17, 18). Thus, the lung to limit any possible error in microbiome studies. For example,
is subject to a constant level of microbe immigration and as an alternate process to 16S rRNA sequencing and primer
elimination through host mucosal defense and mucociliary choice, metagenomic data are being generated through the
clearance. Modern studies employing sequence-based bacterial sequencing of all DNA from a sample (shotgun sequencing),
identification techniques support the presence of a consistently which may be even more informative (30). Culture-based

Downloaded from http://www.jimmunol.org/ by guest on May 21, 2018

detected diverse bacterial signal in the lung of healthy humans techniques remain highly relevant as complements to culture-
(19–22). Therefore, the notion of lung sterility has been independent techniques in determination of viability, in spe-
debunked. ciation, and in microbial phenotyping.
This new understanding was animated by the discovery of
culture-independent techniques for bacterial identification. Microbiome development and composition in healthy lung
The most commonly used approach involves high-throughput The human microbiota inhabits several organs and is pri-
sequencing of amplicons of the 16S rRNA gene, a highly marily colonized by six phyla: Firmicutes, Bacteroidetes,
conserved locus in the bacterial genome. Sequences are Proteobacteria, Actinobacteria, Fusobacteria, and Cyanobacteria
then categorized and classified according to publically available (31–34). Murine studies have demonstrated that bacterial load
prior knowledge taxonomic databases to allow for measures of in the lungs increases during the first 2 wk of life, and the phyla
total and relative abundance and diversity. The first appli- of organisms found in the lung shifted from Gammaproteo-
cation of culture-independent techniques was undertaken in bacteria and Firmicutes toward Bacteriodetes (35). Such
a cohort of healthy controls and asthma patients. Hilty et al. developmental changes in the microbiota were associated with
(20) reported that healthy airways contain bacteria similar accumulation of a PD-L1–dependent T regulatory cell population
to, but distinct from, the upper respiratory tract, and air- that could promote tolerance to allergen challenge (35). These
ways of asthma patients were enriched with the phylum data suggest that acquisition of a lung microbiome is an impor-
Proteobacteria. tant early life event necessary to protect the lung from injurious
Sampling the lung for microbiome sequencing is technically responses to inhaled Ags. In humans, studies have largely focused
challenging given the relatively low biomass. Furthermore, on gut microbiota and shown that newborns acquire microbiota
sampling lower airways by bronchoscopy requires passage of that resembles their mother quickly and in a manner specific to
the instrument through the oral or nasal route. This course the method of delivery. Dominguez-Bello et al. (36) reported that
allows for a theoretical risk of pharyngeal contamination of infants born by vaginal delivery acquired bacterial commu-
samples. Importantly, the mouth and nose microbiota are nities resembling their mother’s vaginal microbiota, dominated
markedly different and studies have not identified any de- by Lactobacillus, Prevotella, or Sneathia species. Infants born
tectable influence on the reported microbiota based on scope by cesarean section acquired skin-predominant Staphylococcus,
insertion site (22, 23). Additionally, if pharyngeal carryover Corynebacterium, and Propionibacterium species. These com-
from the bronchoscope insertion site was heavily influencing munities were undifferentiated across multiple body habitats in
the reported microbiota, then serial dilutions of samples should the infants, in contrast to the diverse communities evident in the
result in dilution of bacterial communities and signal. Several mothers. No studies to date have examined the dynamic changes
studies have established that this is not the case (19, 24). The that may occur in the lower respiratory tract microbiota as
evidence thus supports minimal contamination from pharyn- childhood progresses. However, it is likely from studies of the
geal sources acquired by bronchoscopic methods. upper respiratory tract and intestinal microbiota that these bac-
terial communities are dynamic (37, 38). There is relatively low
Methodology and limitations in studies of the microbiota bacterial biomass in the human lung. Bacterial loads from
Accurate and relevant studies of the microbiome require con- bronchoalveolar lavage have reported ranges from 4.5 to 8.25 log
sideration of several principles. Representative samples must be copies/ml (39, 40). Further analysis of lung tissue samples dem-
acquired from the distal airways, and, as discussed above, the onstrates some 10–100 bacterial cells per 1000 human cells (41).
possibility of contamination from other niche microbiota The healthy lung has been studied using culture-independent
must be addressed. Furthermore, contamination can occur techniques, and the predominant phyla are Bacteroidetes and
during sample processing; use of “no template” controls is es- Firmicutes (21, 24). Although individuals exhibit some spatial
sential in low-biomass studies to assess the effects of reagent variation in the microbiota of their respiratory tract, intrasubject
contamination. The extraction of nucleic acid requires lysis of variation is significantly less than that of intersubject variation (39).
The Journal of Immunology 4841

Dynamic changes in lung microbiome in health and disease Table I. Factors that impact the lung microbiota during acute and chronic
disease
The lung is a relatively low nutrient resource compared with
the intestinal tract for supporting microbiome development. Influences
Furthermore, physiological conditions are regionally variable
Architectural
even in healthy lungs. Conditions that affect bacterial pro- Airway obliteration (lung transplant, IPF)
liferation include oxygen tension, blood flow, local pH, Terminal bronchiole destruction (COPD)
temperature, effector inflammatory cell disposition, and Honeycombing and fibrosis (IPF)
Impaired mucociliary clearance (COPD, asthma)
epithelial cell architecture (42, 43). Coupled to this variable Immunologic
biogeography of the lung microbiome are the factors that Innate immune cell impairment
influence microbe immigration and elimination from the Altered PRR signaling
lower respiratory tract. Taken together, these factors de- Release of antimicrobial peptides
Apoptosis/autophagy
termine the dynamic change of the microbial ecosystem of Inflammation
the lung. Cytokine alterations
Lung disease alters the population dynamics through Microbiologic
Overgrowth of limited bacterial species (IPF, CF)
effects on immigration/elimination and the local conditions Antibiotic use (especially in CF)
of the microbial ecosystem of the lung (Table I). Chronic Lytic viral infection (COPD, asthma)
lung disease in many forms results in heterogeneous ar- Latent viral infection (IPF?)
Biofilm formation (CF, COPD)
chitectural distortion of the lung, including upper lobe Pathologic

Downloaded from http://www.jimmunol.org/ by guest on May 21, 2018

predominant destruction of the terminal bronchioles in Osmotic changes (CF)
emphysema and lower lobe predominant distortion of the Thickened mucus (CF)
parenchyma by honeycombing in idiopathic pulmonary Damaged cilia (COPD)
Changes in oxygen tension, ventilation, and perfusion
fibrosis (IPF) (44). Changes in the viscosity of the mucus (IPF, COPD, CF, asthma)
and pH occur in cystic fibrosis (CF) (45). The resultant Microaspiration (IPF)
changes in oxygen tension, ventilation, perfusion, inflam-
matory cells, and other local factors exert pressure on
COPD. The relationship between COPD exacerbation and
population dynamics. Immigration of microbiota from the
acute bacterial infection of the airway remains disputed. Po-
upper respiratory to the lower respiratory tract is primarily
tential pathogens cultured from sputum during COPD ex-
promoted by subclinical aspiration, which occurs in both
acerbations are less frequently cultured during periods of
health and disease, and overt clinical infection occurs when
clinical stability (49). Sethi et al. (50) identified similar cul-
local defense is blunted or overwhelmed (17, 18). Chronic
ture densities of Haemophilus influenzae and lower densities
lung disease is commonly associated with gastroesophageal
of Moraxella catarrhalis and Streptococcus pneumoniae in
reflux, which may result in elevated volumes of microaspiration sputum collected during acute exacerbations compared with
(46, 47). Elimination is achieved by cough and mucociliary samples during clinical stability. The use of antibiotic therapy
clearance. Host inflammatory cells are responsible for in COPD exacerbations also lacks clarity. Recent work
eradication of pathogens, and the type and number of reported a clear role in reducing the rate of treatment failure
effector cells are associated with certain features of the for severe disease in hospitalized patients, but the role is un-
microbiome. In a comparison of inflammatory cells and clear for mild to moderate disease (51). Culture-independent
microbiota detected in bronchoalveolar lavage fluid, Segal techniques have identified a diverse and abundant pulmonary
et al. (24) demonstrated increased community abundance microbiota in exacerbations from a variety of sampling types
of Prevotella and Veillonella species (common anaerobic (41, 52–54), and exacerbations are definitively associated with
oral commensals) associated with higher levels of lymphocyte changes in respiratory microbiota and airway inflammation.
and neutrophil inflammation. Therefore, the lung microbiome Millares et al. (52) analyzed sputum from COPD patients
has a potential role to play in the pathogenesis of chronic during exacerbations with paired sampling from periods of
lung disease through both the ability of lung microbiota clinical stability and found increases in the relative abundance
to modulate local inflammatory responses and the in- of bacteria associated with exacerbations, namely Haemophilus,
fluence of chronic lung diseases on the lung microbiome Pseudomonas, and Moraxella. Huang et al. (53) reported an
in turn. alteration in community content toward the Proteobacteria
Chronic lung diseases include asthma, chronic obstructive phylum during COPD exacerbations, including nontypical
pulmonary disease (COPD), CF, and IPF. Interestingly, these COPD pathogens. Additionally, the influence of viral exposure
diseases are all characterized by natural histories that are punc- may trigger COPD exacerbations (55) but the relationship
tuated by periods of acute exacerbations. Exacerbations are between viral infection, microbiome composition, and host
characterized by acute worsening of pulmonary symptoms and a defense is poorly understood. Patients experimentally infected
decline in pulmonary function. Such exacerbations are respon- with rhinovirus develop clinical features of COPD exacerbation,
sible for significant mortality and morbidity. The onset of ex- and culprit viruses have been isolated in respiratory samples
acerbation may herald accelerated disease progression, and many from 36 to 56% of patients with exacerbations versus 6–19%
patients fail to return to their previous functional and physio- of patients at clinical baseline (56–59). Interestingly, Molyneaux
logical baselines (48). Studies of these events may reveal key data et al. (60) compared sputum in COPD patients at baseline
that reanimate our current understanding of the pathogenesis of and during exacerbations and noted that sputum acquired
chronic lung disease, and it is likely that these exacerbations are after viral exposure demonstrated a shift toward the
accompanied or induced by microbiota dysbiosis. Proteobacteria phylum, a potential explanation for the
4842 BRIEF REVIEWS: MICROBIOME DRIVING PATHOGENESIS OF LUNG DISEASE

increased presence of Pseudomonas spp. noted in COPD Idiopathic pulmonary fibrosis. IPF is a chronic fatal remodeling
exacerbations (52). Sequencing-based studies of tissue disease of the lung parenchyma of unknown etiology (72). The
from COPD patients have demonstrated an increase in natural history of IPF is characterized by exacerbations that
the Firmicutes community in severe disease (GOLD stage contribute greatly to disease-related morbidity and mortality.
4) attributable to an increase in the Lactobacillus genus (41). Recent work has highlighted a potential role for both viral and
Phagocytosis of Lactobacillus spp. by human macrophages bacterial infection in the pathogenesis of IPF (73–77). Unlike
reduces the effects of cigarette smoke–related inflammation, with asthma or COPD, the current definition of acute
potentially suggesting that these species are beneficial modifiers exacerbations of IPF excludes active infectious pathogens (78).
of smoking-related lung disease (61). Animal models of Disease progression in IPF is characterized by an alteration in the
respiratory syncytial virus infection have demonstrated microbiome with a relative increased abundance of Streptococcus
that the antiviral response within the lung mucosa can and Staphylococcus taxonomic groups (79). This has particular
be modulated by the administration of Lactobacillus relevance given recent work identifying pneumolysin, a
rhamnosus species prior to infection (62). Thus, changes Pneumococcus-produced toxin, that mediates fibrotic progression
in the microbiome may represent an adaptation to try in animal models via injury of the alveolar epithelium (73).
to protect the lung from respiratory viral infection. However, Further study by Molyneaux et al. (76) described an increased
we speculate that, as suggested above, once pathogenic bacterial burden in the bronchoalveolar lavage fluid of IPF
infection does occur, these beneficial changes may be patients compared with controls using culture-independent
lost. techniques. These communities were enriched with Haemophilus,
Asthma. Studies of airway microbiota in asthma have estab-
Streptococcus, Neisseria, and Veillonella. The greater the bacterial

Downloaded from http://www.jimmunol.org/ by guest on May 21, 2018

lished that composition is altered when compared with con- burden in these patients, the greater the independent association
with IPF disease progression. Recent trials of trimethoprim/
trols. Hilty et al. (20) identified asthma patients with more
sulfamethoxazole have demonstrated benefit with improved
frequent Proteobacteria (particularly Haemophilus) in the
Medical Research Council dyspnea scores, quality of life, and
bronchial tree compared with controls. The authors also
even all-cause mortality (hazard ratio, 0.21; 95% confidence
noted a decrease in Bacteroidetes, especially Prevotella species,
interval, 0.06–0.78; p = 0.02) (80). This further supports a
in asthmatic airways. Studies of asthma severity identified
role for bacterial burden in disease progression. Aspects of host
similar altered microbiomes with a predominance of
defense and innate immunity also have putative roles in IPF
Proteobacteria and found that the airway microbiome of
disease progression (81–86). We have previously suggested that
asthmatic patients was more diverse that of nonasthmatic
defective TLR3 signaling promotes IPF disease progression (81).
controls (63). Huang et al. (64) reported an association between The L412F polymorphism (rs3775291) of TLR3 results in a
bronchial hyperresponsiveness and community diversity and functional defect in primary lung fibroblasts from IPF
composition, secondary to an increased abundance of patients. This defect leads to aberrant inflammation and
Proteobacteria. Bronchial hyperresponsiveness is accentuated blunted IFN responses to TLR3 activation by synthetic dsRNA
during exacerbation and is an accurate predictor of future (and likely pathogen-associated molecular patterns, although
exacerbations (65). Alterations to the microbiome appear this was not directly examined). Genotyping studies of two
similar in both mild and severe disease and are specifically independent cohorts of IPF patients confirmed an association
associated with features of the disease. No studies have between this polymorphism with increased mortality and
analyzed the airway microbiome in asthma exacerbations. functional decline. However, the interaction between the
However, an estimated 80% of asthma exacerbations are pulmonary microbiome, host defense, acute infection, and
associated with viral infection (66, 67). The host microbiome IPF disease progression remains unclear. Ultimately, the
interaction may be crucial in the development of asthma. questions of whether chronic lung disease promotes microbiome
Ege et al. (68) have demonstrated that children with broad alterations or microbiome changes modify chronic lung disease
microbial exposures (i.e., traditional farming) were protected remain to be answered.
from asthma and atopy in childhood. Further studies reported Cystic fibrosis. The manifestations of CF in the lung involve the
an association with high-fiber diet and a reduced risk of asthma progressive development of bronchiectasis and obstructive
(69). The proposed mechanism was related, in part, to an lung disease. Central to disease progression are exacerbations
altered immune response. Mice fed a low-fiber diet exhibited of CF bronchiectasis, which are responsible for significant
reduced levels of short-chain fatty acids with increased allergic mortality, morbidity, and accelerated disease progression (87).
inflammation, whereas mice with a high-fiber diet had elevated Exacerbations of disease are attributed to infection by specific
levels of short-chain fatty acids and were protected against pathogens that are cultured from sputum during exacerba-
allergic inflammation. Short-chain fatty acid propionate tions and clinical stability. These pathogens commonly in-
treatment of mice resulted in the generation of macrophages clude Staphylococcus aureus and Pseudomonas aeruginosa (88).
and dendritic cells with enhanced phagocytic properties but The evidence to support the use of antibiotics directed against
an attenuated capacity to initiate a Th2 response, a crucial these pathogens is sparse. The bacterial density of sputum is
component of allergic inflammation (69). Furthermore, studies not altered during CF exacerbations when antibiotics are
have suggested that resident microbiota may promote Th17- administered (89). Clinical trials have not reported an asso-
dependent neutrophil inflammation in a murine model of ciation between the clinical response during antibiotic therapy
OVA-induced asthma (70). Similarly, an experimental model of and the in vitro susceptibility of the cultured bacteria to
allergic airway inflammation is exacerbated by the administration the administered antibiotics (90, 91). Indeed, culture-
of antibiotics during early life. This correlated with a reduction in independent analysis has primed a revision of our long-held
microbial load and diversity (71). understanding of the bacterial pathogenesis of CF lung
The Journal of Immunology 4843

disease. Studies have consistently reported that CF exacerbations resulting pathogenesis could be the result of dysbiosis leading to
are not associated with increased bacterial density or attenuated altered airway microbiota and disproportionate inflammation.
diversity (92–94). However, evidence would support a loss of Although loss of gut commensal signaling may impair lung
diversity with increasing age and disease severity, which was innate immunity in this disorder, cigarette smoke directly and
strongly associated with cumulative antibiotic exposure (95, indirectly contributes to impaired innate immunity in the lung
96). The emergence of new pathogens may have implications via alterations in ciliary function, mucus, innate immune cell
for our understanding of the microbiome and lung disease phagocytosis, and via direct enhancement of bacterial virulence
interaction in CF. Nontuberculosis Mycobacterium, in particular (e.g., enhanced biofilm formation) (reviewed in Ref. 112).
M. abscessus, is associated with increased mortality and These changes could impact the ability of respiratory pathogens
morbidity in CF (97–99). Guidelines for the management of to exacerbate COPD.
M. abscessus have been published, and long-term treatment with Given the propensity for viruses to precipitate lung disease
broad-spectrum antibiotics is required in these cases (100). The exacerbations, it is interesting to note the potential impact of
consequences for the lung microbiome for this treatment remain respiratory viral infection on the intestinal microbiota. Wang
unknown. This is of particular relevance given the limited et al. (113) reported that influenza infection may lead to alter-
treatment benefit for M. abscessus infection in CF (100). The ations in intestinal microbiota with a reduction in Lactobacillus
relationship between the microbiome, antibiotic exposure, and Lactococcus and an outgrowth of Enterobacteriaceae. As
exacerbation, and ultimate disease progression will thus noted above, this may lead to a loss of beneficial microbiota for
require further careful study in CF. smoking-related disease. The authors demonstrated that these
shifts in intestinal microbiota were not secondary to lytic influ-

Downloaded from http://www.jimmunol.org/ by guest on May 21, 2018

Evidence and implications for a gut/lung axis and the regulation of enza gut infection. This injury was mediated by Th17 cells, and
host defense for chronic lung disease exacerbations IL-17 neutralization resulted in attenuated injury. Additionally,
Exactly how microbiota may regulate innate immunity in antibiotic-mediated depletion of intestinal microbiota led to at-
health and disease is an area of active investigation, and very tenuated intestinal injury. Interestingly, this study also high-
little is known about how the lung microbiota may specifically lighted the importance of an effector T cell that arose in the lung
regulate lung immunity or the development of bronchial- after infection and then migrated to the small intestine to pro-
associated lymphoid tissue. There is growing appreciation vide IFN-g to alter the gut microbiome. Ultimately the alter-
for the fact that the gut commensal microbiota is an impor- ations in the gut microbiota stimulated epithelial-derived IL-15
tant regulator of the innate immune system (101, 102). The to promote the Th17 response. It is possible that IL-17 responses
bacterial biomass of the intestine dwarfs the relative mass seen arising in the gut may further impact lung disease (114). IL-17 is
in the lung (103). In healthy adults the intestine microbiota involved in the elimination of certain pathogens (115) and is
consists predominantly of three phyla: Bacteroides, Prevotella, implicated in the pathogenesis of several pulmonary pathologies
and Ruminococcus (104). There is evidence to support a including asthma, sarcoidosis, obliterative bronchiolitis, CF, and
crucial early period during life where intestinal microbiome bone marrow transplant–related pneumonitis (116–120).
development is important for the regulation of an appro- IL-17 may also play a central role in the dynamic change that
priate immune response in the lung. CF and asthma are occurs within the pulmonary microbiota of COPD. Yadava
examples of chronic lung disease where disease course and et al. (121) reported the impact of experimental change on the
susceptibility are influenced by shifts in the composition of lung microbiota in an emphysema animal model. Specific
the gut microbiota (105, 106). Furthermore, in the absence pathogen-free and axenic mice were challenged with LPS/
of normal gut biota, the host is more susceptible to pul- elastase for 4 wk. Microbiota diversity and abundance was
monary infections, including Listeria monocytogenes (107), decreased in the LPS/elastase model with an abundance of
Klebsiella pneumoniae (108), and viruses (109). This raises Pseudomonas, Lactobacillus, and a depletion of Prevotella. Loss
the interesting possibility that exacerbations of chronic lung of bacterial load was associated with attenuated IL-17 pro-
disease may arise from impaired innate and adaptive im- duction. The intranasal application of microbiota-enriched
mune function secondary to alterations in the host gut fluid to axenic mice enhanced IL-17 production. The neutral-
microbiota. As mentioned above, patients with progressive ization of IL-17 in mice harboring microbiota led to dampened
IPF show evidence of enhanced burden of Streptococcus and inflammation and reduced disease burden. Several studies have
Staphylococcus species in the lung, and previous studies have implicated IL-17 in hepatic fibrosis, and certain experimental
shown that the ability of neutrophils from microbiota- models of pulmonary fibrosis are IL-17A–dependent (120, 122,
depleted mice to kill S. pneumoniae and S. aureus are reduced 123). Furthermore, studies examining the development of in-
(110). It is not known at present whether the accumulation of testinal fibrosis have reported an association with alterations in
these species in the lung correlates with loss of gut microbial the microbiota and Th17 responses (124). The intestine is a
communities during IPF disease progression, but this is an known source of Th17 cells through binding of segmented
interesting area for future study (Fig. 1). Support for such a filamentous bacteria to intestinal epithelial cells (125). The case
concept comes from recent work showing that bacterial acti- may be similar in the lung. Gauguet et al. (126) have demon-
vation of Nod-like receptors in the gut leads to enhanced strated that intestinal segmented filamentous bacteria have the
production of reactive oxygen species within alveolar macro- ability to promote pulmonary innate immunity through the
phages, the sentinel innate immune cell within the lung (101), induction of IL-17 to provide resistance to S. aureus pneumonia
implying that conditions associated with loss of gut bacterial in animal models. This constitutes further evidence to support a
homeostasis (e.g., antibiotic use) could provide a window of gut/lung microbiome axis that may be pivotal in modulating
opportunity for lung immunity to be impaired. In COPD, the innate immune response of the lung. However, direct evi-
exacerbations can occur due to viral infections (60, 111), and dence of a gut/lung axis promoting exacerbation of chronic lung
4844 BRIEF REVIEWS: MICROBIOME DRIVING PATHOGENESIS OF LUNG DISEASE

Downloaded from http://www.jimmunol.org/ by guest on May 21, 2018

FIGURE 1. Proposed regulation of disease exacerbation by the gut/lung axis. During normal homeostasis, the lung microbiome is primarily characterized by low
biomass, but prominent diversity in microbial species. In contrast, the healthy gut microbiome is characterized by high diversity and high biomass. In homeostasis,
the gut microbiome helps shape development of lymphoid architecture and appropriate immune responsiveness. Loss of gut diversity (e.g., as a result of viral
infection or antibiotic use) may cause dysregulation of IL-17 or bacterial killing mechanisms systemically, potentially leading to impaired alveolar macrophage
function and the overgrowth of selective organisms with pathogenic potential that may result in disease exacerbation. Alternatively, some forms of chronic lung
disease exacerbations may be due to translocation and/or expansion of bacterial contents from the gut. Direct insults to the lung (e.g., viral infection or aspiration)
may exacerbate disease in part via their effects on the lung or gut microbiota. Alterations in systemic cytokines (e.g., Th2 or Th17 induction) may promote
pathologic fibrotic remodeling as well.

disease is limited to experimental data to date and requires the need for careful future human studies that will characterize
further study. not only the lung, but also the gut microbiota during periods
of disease stability versus exacerbations. Additionally, murine
models may allow us to interrogate the PRRs and cytokine
Conclusions signaling pathways that promote exacerbations.
Growing evidence suggests that alterations in the lung and/or
gut microbiota characterize chronic lung diseases and may
allow for exacerbations caused by endogenous microbiota al- Disclosures
terations or susceptibility to new infection (Fig. 1). We spec- The authors have no financial conflicts of interest.
ulate that impairment in lung innate immunity caused by
microbial dysbiosis may promote susceptibility of the host to References
infections that can exacerbate chronic lung diseases. Further- 1. Lederberg, J., and A. T. McCray. 2001. ’Ome sweet ’omics—a genealogical
more, shifts in cytokine profiles mediated by changes in the treasury of words. Scientist 15: 8.
2. Bauer, H., R. E. Horowitz, S. M. Levenson, and H. Popper. 1963. The response of
microbiota may also promote epithelial injury and fibrotic the lymphatic tissue to the microbial flora. Studies on germfree mice. Am. J. Pathol.
outcomes. Overall, there appears to be a vital cross-talk be- 42: 471–483.
3. Naik, S., N. Bouladoux, C. Wilhelm, M. J. Molloy, R. Salcedo, W. Kastenmuller,
tween the gut and lung mucosa and the microbial communities C. Deming, M. Quinones, L. Koo, S. Conlan, et al. 2012. Compartmentalized
within. The device through which this cross-talk may be control of skin immunity by resident commensals. Science 337: 1115–1119.
achieved remains unknown. Possible instruments include trans- 4. Noverr, M. C., R. M. Noggle, G. B. Toews, and G. B. Huffnagle. 2004. Role of
antibiotics and fungal microbiota in driving pulmonary allergic responses. Infect.
location of gut microbiota (including potential pathogens) Immun. 72: 4996–5003.
through blood or lymphatics, modulation of circulating or 5. Manuzak, J. A., T. Hensley-McBain, A. S. Zevin, C. Miller, R. Cubas, B. Agricola,
J. Gile, L. Richert-Spuhler, G. Patilea, J. D. Estes, et al. 2016.Enhancement of
lung-resident effector immune and inflammatory cells, or al- microbiota in healthy macaques results in beneficial modulation of mucosal and
terations in systemic cytokine profiles. These results highlight systemic immune function. J. Immunol. 196: 2401–2409.
The Journal of Immunology 4845

6. Block, K. E., Z. Zheng, A. L. Dent, B. L. Kee, and H. Huang. 2016. Gut 35. Gollwitzer, E. S., S. Saglani, A. Trompette, K. Yadava, R. Sherburn,
microbiota regulates K/BxN autoimmune arthritis through follicular helper T but K. D. McCoy, L. P. Nicod, C. M. Lloyd, and B. J. Marsland. 2014. Lung
not Th17 cells. J. Immunol. 196: 1550–1557. microbiota promotes tolerance to allergens in neonates via PD-L1. Nat. Med. 20:
7. Ishizaki, Y., M. Takemoto, R. Kira, K. Kusuhara, H. Torisu, Y. Sakai, M. Sanefuji, 642–647.
N. Yukaya, and T. Hara. 2008. Association of Toll-like receptor 3 gene poly- 36. Dominguez-Bello, M. G., E. K. Costello, M. Contreras, M. Magris, G. Hidalgo,
morphism with subacute sclerosing panencephalitis. J. Neurovirol. 14: 486–491. N. Fierer, and R. Knight. 2010. Delivery mode shapes the acquisition and
8. Netea, M. G., C. Wijmenga, and L. A. O’Neill. 2012. Genetic variation in Toll- structure of the initial microbiota across multiple body habitats in newborns. Proc.
like receptors and disease susceptibility. Nat. Immunol. 13: 535–542. Natl. Acad. Sci. USA 107: 11971–11975.
9. Khor, C. C., S. J. Chapman, F. O. Vannberg, A. Dunne, C. Murphy, E. Y. Ling, 37. Yatsunenko, T., F. E. Rey, M. J. Manary, I. Trehan, M. G. Dominguez-Bello,
A. J. Frodsham, A. J. Walley, O. Kyrieleis, A. Khan, et al. 2007. A Mal functional M. Contreras, M. Magris, G. Hidalgo, R. N. Baldassano, A. P. Anokhin, et al.
variant is associated with protection against invasive pneumococcal disease, bac- 2012. Human gut microbiome viewed across age and geography. Nature 486:
teremia, malaria and tuberculosis. Nat. Genet. 39: 523–528. 222–227.
10. Dickson, R. P., J. R. Erb-Downward, F. J. Martinez, and G. B. Huffnagle. 2016. 38. Biesbroek, G., E. Tsivtsivadze, E. A. Sanders, R. Montijn, R. H. Veenhoven,
The microbiome and the respiratory tract. Annu. Rev. Physiol. 78: 481–504. B. J. Keijser, and D. Bogaert. 2014. Early respiratory microbiota composition
11. Caballero, S., and E. G. Pamer. 2015. Microbiota-mediated inflammation and determines bacterial succession patterns and respiratory health in children. Am. J.
antimicrobial defense in the intestine. Annu. Rev. Immunol. 33: 227–256. Respir. Crit. Care Med. 190: 1283–1292.
12. Martin, C., P. R. Burgel, P. Lepage, C. Andréjak, J. de Blic, A. Bourdin, J. Brouard, 39. Erb-Downward, J. R., D. L. Thompson, M. K. Han, C. M. Freeman,
P. Chanez, J. C. Dalphin, G. Deslée, et al. 2015. Host-microbe interactions in distal L. McCloskey, L. A. Schmidt, V. B. Young, G. B. Toews, J. L. Curtis,
airways: relevance to chronic airway diseases. Eur. Respir. Rev. 24: 78–91. B. Sundaram, et al. 2011. Analysis of the lung microbiome in the “healthy” smoker
13. Winslow, C. E. 1908. A new method of enumerating bacteria in air. Science 28: and in COPD. PLoS One 6: e16384.
28–31. 40. Charlson, E. S., J. M. Diamond, K. Bittinger, A. S. Fitzgerald, A. Yadav,
14. Thomas, D. N., and G. S. Dieckmann. 2002. Antarctic Sea ice—a habitat for A. R. Haas, F. D. Bushman, and R. G. Collman. 2012. Lung-enriched organisms
extremophiles. Science 295: 641–644. and aberrant bacterial and fungal respiratory microbiota after lung transplant. Am.
15. Yamamoto, H., A. Hiraishi, K. Kato, H. X. Chiura, Y. Maki, and A. Shimizu. J. Respir. Crit. Care Med. 186: 536–545.
1998. Phylogenetic evidence for the existence of novel thermophilic bacteria in hot 41. Sze, M. A., P. A. Dimitriu, S. Hayashi, W. M. Elliott, J. E. McDonough,
spring sulfur-turf microbial mats in Japan. Appl. Environ. Microbiol. 64: 1680– J. V. Gosselink, J. Cooper, D. D. Sin, W. W. Mohn, and J. C. Hogg. 2012. The
1687. lung tissue microbiome in chronic obstructive pulmonary disease. Am. J. Respir.

Downloaded from http://www.jimmunol.org/ by guest on May 21, 2018

16. Wilson, M. T., and D. L. Hamilos. 2014. The nasal and sinus microbiome in Crit. Care Med. 185: 1073–1080.
health and disease. Curr. Allergy Asthma Rep. 14: 485. 42. Ingenito, E. P., J. Solway, E. R. McFadden, Jr., B. Pichurko, H. F. Bowman,
17. Gleeson, K., D. F. Eggli, and S. L. Maxwell. 1997. Quantitative aspiration during D. Michaels, and J. M. Drazen. 1987. Indirect assessment of mucosal surface
sleep in normal subjects. Chest 111: 1266–1272. temperatures in the airways: theory and tests. J. Appl. Physiol. 63: 2075–2083.
18. Huxley, E. J., J. Viroslav, W. R. Gray, and A. K. Pierce. 1978. Pharyngeal aspi- 43. West, J. B. 1978. Regional differences in the lung. Chest 74: 426–437.
ration in normal adults and patients with depressed consciousness. Am. J. Med. 64: 44. Nishimura, K., M. Kitaichi, T. Izumi, S. Nagai, M. Kanaoka, and H. Itoh. 1992.
564–568. Usual interstitial pneumonia: histologic correlation with high-resolution CT. Ra-
19. Dickson, R. P., J. R. Erb-Downward, C. M. Freeman, L. McCloskey, J. M. Beck, diology 182: 337–342.
G. B. Huffnagle, and J. L. Curtis. 2015. Spatial variation in the healthy human 45. Collawn, J. F., and S. Matalon. 2014. CFTR and lung homeostasis. Am. J. Physiol.
lung microbiome and the adapted island model of lung biogeography. Ann. Am. Lung Cell. Mol. Physiol. 307: L917–L923.
Thorac. Soc. 12: 821–830. 46. Raghu, G., T. D. Freudenberger, S. Yang, J. R. Curtis, C. Spada, J. Hayes,
20. Hilty, M., C. Burke, H. Pedro, P. Cardenas, A. Bush, C. Bossley, J. Davies, J. K. Sillery, C. E. Pope, II, and C. A. Pellegrini. 2006. High prevalence of ab-
A. Ervine, L. Poulter, L. Pachter, et al. 2010. Disordered microbial communities in normal acid gastro-oesophageal reflux in idiopathic pulmonary fibrosis. Eur. Respir.
asthmatic airways. PLoS One 5: e8578. J. 27: 136–142.
21. Morris, A., J. M. Beck, P. D. Schloss, T. B. Campbell, K. Crothers, J. L. Curtis, 47. Robinson, N. B., and E. DiMango. 2014. Prevalence of gastroesophageal reflux in
S. C. Flores, A. P. Fontenot, E. Ghedin, L. Huang, et al; Lung HIV Microbiome cystic fibrosis and implications for lung disease. Ann. Am. Thorac. Soc. 11: 964–
Project. 2013. Comparison of the respiratory microbiome in healthy nonsmokers 968.
and smokers. Am. J. Respir. Crit. Care Med. 187: 1067–1075. 48. Ryerson, C. J., V. Cottin, K. K. Brown, and H. R. Collard. 2015. Acute exac-
22. Bassis, C. M., J. R. Erb-Downward, R. P. Dickson, C. M. Freeman, erbation of idiopathic pulmonary fibrosis: shifting the paradigm. Eur. Respir. J. 46:
T. M. Schmidt, V. B. Young, J. M. Beck, J. L. Curtis, and G. B. Huffnagle. 2015. 512–520.
Analysis of the upper respiratory tract microbiotas as the source of the lung and 49. Monsó, E., J. Ruiz, A. Rosell, J. Manterola, J. Fiz, J. Morera, and V. Ausina. 1995.
gastric microbiotas in healthy individuals. MBio 6: e00037. Bacterial infection in chronic obstructive pulmonary disease. A study of stable and
23. Dickson, R. P., J. R. Erb-Downward, C. M. Freeman, N. Walker, B. S. Scales, exacerbated outpatients using the protected specimen brush. Am. J. Respir. Crit.
J. M. Beck, F. J. Martinez, J. L. Curtis, V. N. Lama, and G. B. Huffnagle. 2014. Care Med. 152: 1316–1320.
Changes in the lung microbiome following lung transplantation include the 50. Sethi, S., R. Sethi, K. Eschberger, P. Lobbins, X. Cai, B. J. Grant, and
emergence of two distinct Pseudomonas species with distinct clinical associations. T. F. Murphy. 2007. Airway bacterial concentrations and exacerbations of chronic
PLoS One 9: e97214. obstructive pulmonary disease. Am. J. Respir. Crit. Care Med. 176: 356–361.
24. Segal, L. N., A. V. Alekseyenko, J. C. Clemente, R. Kulkarni, B. Wu, Z. Gao, 51. Vollenweider, D. J., H. Jarrett, C. A. Steurer-Stey, J. Garcia-Aymerich, and
H. Chen, K. I. Berger, R. M. Goldring, W. N. Rom, et al. 2013. Enrichment of M. A. Puhan. 2012. Antibiotics for exacerbations of chronic obstructive pulmo-
lung microbiome with supraglottic taxa is associated with increased pulmonary nary disease. Cochrane Database Syst. Rev. 12: CD010257.
inflammation. Microbiome 1: 19. 52. Millares, L., R. Ferrari, M. Gallego, M. Garcia-Nuñez, V. Pérez-Brocal,
25. Rogers, G. B., D. Shaw, R. L. Marsh, M. P. Carroll, D. J. Serisier, and M. Espasa, X. Pomares, C. Monton, A. Moya, and E. Monsó. 2014. Bronchial
K. D. Bruce. 2015. Respiratory microbiota: addressing clinical questions, microbiome of severe COPD patients colonised by Pseudomonas aeruginosa. Eur. J.
informing clinical practice. Thorax 70: 74–81. Clin. Microbiol. Infect. Dis. 33: 1101–1111.
26. Zhu, B., D. Xiao, H. Zhang, Y. Zhang, Y. Gao, L. Xu, J. Lv, Y. Wang, J. Zhang, and 53. Huang, Y. J., S. Sethi, T. Murphy, S. Nariya, H. A. Boushey, and S. V. Lynch.
Z. Shao. 2013. MALDI-TOF MS distinctly differentiates nontypable Haemophilus 2014. Airway microbiome dynamics in exacerbations of chronic obstructive pul-
influenzae from Haemophilus haemolyticus. PLoS One 8: e56139. monary disease. J. Clin. Microbiol. 52: 2813–2823.
27. O’Toole, P. W., and I. B. Jeffery. 2015. Gut microbiota and aging. Science 350: 54. Pragman, A. A., H. B. Kim, C. S. Reilly, C. Wendt, and R. E. Isaacson. 2012. The
1214–1215. lung microbiome in moderate and severe chronic obstructive pulmonary disease.
28. David, L. A., C. F. Maurice, R. N. Carmody, D. B. Gootenberg, J. E. Button, PLoS One 7: e47305.
B. E. Wolfe, A. V. Ling, A. S. Devlin, Y. Varma, M. A. Fischbach, et al. 2014. Diet 55. Hewitt, R., H. Farne, A. Ritchie, E. Luke, S. L. Johnston, and P. Mallia. 2016.
rapidly and reproducibly alters the human gut microbiome. Nature 505: 559–563. The role of viral infections in exacerbations of chronic obstructive pulmonary
29. Mason, M. R., H. N. Nagaraja, T. Camerlengo, V. Joshi, and P. S. Kumar. 2013. disease and asthma. Ther. Adv. Respir. Dis. 10: 158–174.
Deep sequencing identifies ethnicity-specific bacterial signatures in the oral 56. Papi, A., C. M. Bellettato, F. Braccioni, M. Romagnoli, P. Casolari, G. Caramori,
microbiome. PLoS One 8: e77287. L. M. Fabbri, and S. L. Johnston. 2006. Infections and airway inflammation in
30. Shah, N., H. Tang, T. G. Doak, and Y. Ye. 2011. Comparing bacterial com- chronic obstructive pulmonary disease severe exacerbations. Am. J. Respir. Crit.
munities inferred from 16S rRNA gene sequencing and shotgun metagenomics. Care Med. 173: 1114–1121.
Pac. Symp. Biocomput. 2011: 165–176. 57. Rohde, G., A. Wiethege, I. Borg, M. Kauth, T. T. Bauer, A. Gillissen, A. Bufe, and
31. Eckburg, P. B., E. M. Bik, C. N. Bernstein, E. Purdom, L. Dethlefsen, M. Sargent, G. Schultze-Werninghaus. 2003. Respiratory viruses in exacerbations of chronic
S. R. Gill, K. E. Nelson, and D. A. Relman. 2005. Diversity of the human in- obstructive pulmonary disease requiring hospitalisation: a case-control study.
testinal microbial flora. Science 308: 1635–1638. Thorax 58: 37–42.
32. Grice, E. A., and J. A. Segre. 2011. The skin microbiome. Nat. Rev. Microbiol. 9: 58. Mallia, P., S. D. Message, V. Gielen, M. Contoli, K. Gray, T. Kebadze,
244–253. J. Aniscenko, V. Laza-Stanca, M. R. Edwards, L. Slater, et al. 2011. Experimental
33. Frank, D. N., L. M. Feazel, M. T. Bessesen, C. S. Price, E. N. Janoff, and rhinovirus infection as a human model of chronic obstructive pulmonary disease
N. R. Pace. 2010. The human nasal microbiota and Staphylococcus aureus carriage. exacerbation. Am. J. Respir. Crit. Care Med. 183: 734–742.
PLoS One 5: e10598. 59. Seemungal, T., R. Harper-Owen, A. Bhowmik, I. Moric, G. Sanderson,
34. Kim, T. K., S. M. Thomas, M. Ho, S. Sharma, C. I. Reich, J. A. Frank, S. Message, P. Maccallum, T. W. Meade, D. J. Jeffries, S. L. Johnston, and
K. M. Yeater, D. R. Biggs, N. Nakamura, R. Stumpf, et al. 2009. Heterogeneity of J. A. Wedzicha. 2001. Respiratory viruses, symptoms, and inflammatory markers
vaginal microbial communities within individuals. J. Clin. Microbiol. 47: 1181– in acute exacerbations and stable chronic obstructive pulmonary disease. Am. J.
1189. Respir. Crit. Care Med. 164: 1618–1623.
4846 BRIEF REVIEWS: MICROBIOME DRIVING PATHOGENESIS OF LUNG DISEASE

60. Molyneaux, P. L., P. Mallia, M. J. Cox, J. Footitt, S. A. Willis-Owen, D. Homola, 82. Trujillo, G., A. Meneghin, K. R. Flaherty, L. M. Sholl, J. L. Myers,
M. B. Trujillo-Torralbo, S. Elkin, O. M. Kon, W. O. Cookson, et al. 2013. E. A. Kazerooni, B. H. Gross, S. R. Oak, A. L. Coelho, H. Evanoff, et al. 2010.
Outgrowth of the bacterial airway microbiome after rhinovirus exacerbation of TLR9 differentiates rapidly from slowly progressing forms of idiopathic pulmonary
chronic obstructive pulmonary disease. Am. J. Respir. Crit. Care Med. 188: 1224– fibrosis. Sci. Transl. Med. 2: 57ra82.
1231. 83. Lafyatis, R., and A. Farina. 2012. New insights into the mechanisms of innate
61. Mortaz, E., I. M. Adcock, F. L. Ricciardolo, M. Varahram, H. Jamaati, immune receptor signalling in fibrosis. Open Rheumatol. J. 6: 72–79.
A. A. Velayati, G. Folkerts, and J. Garssen. 2015. Anti-Inflammatory Effects of 84. Margaritopoulos, G. A., K. M. Antoniou, K. Karagiannis, K. D. Samara,
Lactobacillus rahmnosus and Bifidobacterium breve on cigarette smoke activated I. Lasithiotaki, E. Vassalou, R. Lymbouridou, H. Koutala, and N. M. Siafakas. 2010.
human macrophages. PLoS One 10: e0136455. Investigation of Toll-like receptors in the pathogenesis of fibrotic and granulomatous
62. Tomosada, Y., E. Chiba, H. Zelaya, T. Takahashi, K. Tsukida, H. Kitazawa, disorders: a bronchoalveolar lavage study. Fibrogenesis Tissue Repair 3: 20.
S. Alvarez, and J. Villena. 2013. Nasally administered Lactobacillus rhamnosus 85. Papanikolaou, I. C., K. A. Boki, E. J. Giamarellos-Bourboulis, A. Kotsaki,
strains differentially modulate respiratory antiviral immune responses and in- K. Kagouridis, N. Karagiannidis, and V. S. Polychronopoulos. 2015. Innate im-
duce protection against respiratory syncytial virus infection. BMC Immunol. munity alterations in idiopathic interstitial pneumonias and rheumatoid arthritis-
14: 40. associated interstitial lung diseases. Immunol. Lett. 163: 179–186.
63. Marri, P. R., D. A. Stern, A. L. Wright, D. Billheimer, and F. D. Martinez. 2013. 86. Samara, K. D., K. M. Antoniou, K. Karagiannis, G. Margaritopoulos,
Asthma-associated differences in microbial composition of induced sputum. J. I. Lasithiotaki, E. Koutala, and N. M. Siafakas. 2012. Expression profiles of Toll-
Allergy Clin. Immunol. 131: 346–352.e1-3. like receptors in non-small cell lung cancer and idiopathic pulmonary fibrosis. Int.
64. Huang, Y. J., C. E. Nelson, E. L. Brodie, T. Z. Desantis, M. S. Baek, J. Liu, J. Oncol. 40: 1397–1404.
T. Woyke, M. Allgaier, J. Bristow, J. P. Wiener-Kronish, et al; National Heart, 87. Stenbit, A. E., and P. A. Flume. 2011. Pulmonary exacerbations in cystic fibrosis.
Lung, and Blood Institute’s Asthma Clinical Research Network. 2011. Airway Curr. Opin. Pulm. Med. 17: 442–447.
microbiota and bronchial hyperresponsiveness in patients with suboptimally 88. Ramsey, B. W. 1996. Management of pulmonary disease in patients with cystic
controlled asthma. J. Allergy Clin. Immunol. 127: 372–381.e1-3. fibrosis. N. Engl. J. Med. 335: 179–188.
65. Gonem, S., I. Umar, D. Burke, D. Desai, S. Corkill, J. Owers-Bradley, 89. Gold, R., S. Carpenter, H. Heurter, M. Corey, and H. Levison. 1987. Ran-
C. E. Brightling, and S. Siddiqui. 2012. Airway impedance entropy and exacer- domized trial of ceftazidime versus placebo in the management of acute respiratory
bations in severe asthma. Eur. Respir. J. 40: 1156–1163. exacerbations in patients with cystic fibrosis. J. Pediatr. 111: 907–913.
66. Nicholson, K. G., J. Kent, and D. C. Ireland. 1993. Respiratory viruses and ex- 90. Hurley, M. N., A. H. Ariff, C. Bertenshaw, J. Bhatt, and A. R. Smyth. 2012.
acerbations of asthma in adults. BMJ 307: 982–986. Results of antibiotic susceptibility testing do not influence clinical outcome in

Downloaded from http://www.jimmunol.org/ by guest on May 21, 2018

67. Johnston, S. L., P. K. Pattemore, G. Sanderson, S. Smith, F. Lampe, L. Josephs, children with cystic fibrosis. J. Cyst. Fibros. 11: 288–292.
P. Symington, S. O’Toole, S. H. Myint, D. A. Tyrrell, et al. 1995. Community 91. Smith, A. L., S. B. Fiel, N. Mayer-Hamblett, B. Ramsey, and J. L. Burns. 2003.
study of role of viral infections in exacerbations of asthma in 9–11 year old chil- Susceptibility testing of Pseudomonas aeruginosa isolates and clinical response to
dren. BMJ 310: 1225–1229. parenteral antibiotic administration: lack of association in cystic fibrosis. Chest 123:
68. Ege, M. J., M. Mayer, A. C. Normand, J. Genuneit, W. O. Cookson, C. Braun- 1495–1502.
Fahrländer, D. Heederik, R. Piarroux, and E. von Mutius, GABRIELA Transregio 92. Price, K. E., T. H. Hampton, A. H. Gifford, E. L. Dolben, D. A. Hogan,
22 Study Group. 2011. Exposure to environmental microorganisms and childhood H. G. Morrison, M. L. Sogin, and G. A. O’Toole. 2013. Unique microbial
asthma. N. Engl. J. Med. 364: 701–709. communities persist in individual cystic fibrosis patients throughout a clinical
69. Trompette, A., E. S. Gollwitzer, K. Yadava, A. K. Sichelstiel, N. Sprenger, exacerbation. Microbiome 1: 27.
C. Ngom-Bru, C. Blanchard, T. Junt, L. P. Nicod, N. L. Harris, and 93. Carmody, L. A., J. Zhao, P. D. Schloss, J. F. Petrosino, S. Murray, V. B. Young,
B. J. Marsland. 2014. Gut microbiota metabolism of dietary fiber influences al- J. Z. Li, and J. J. LiPuma. 2013. Changes in cystic fibrosis airway microbiota at
lergic airway disease and hematopoiesis. Nat. Med. 20: 159–166. pulmonary exacerbation. Ann. Am. Thorac. Soc. 10: 179–187.
70. Lemaire, M. M., L. Dumoutier, G. Warnier, C. Uyttenhove, J. Van Snick, M. de 94. Stressmann, F. A., G. B. Rogers, P. Marsh, A. K. Lilley, T. W. Daniels,
Heusch, M. Stevens, and J. C. Renauld. 2011. Dual TCR expression biases lung M. P. Carroll, L. R. Hoffman, G. Jones, C. E. Allen, N. Patel, et al. 2011. Does
inflammation in DO11.10 transgenic mice and promotes neutrophilia via bacterial density in cystic fibrosis sputum increase prior to pulmonary exacerba-
microbiota-induced Th17 differentiation. J. Immunol. 187: 3530–3537. tion? J. Cyst. Fibros. 10: 357–365.
71. Russell, S. L., M. J. Gold, B. P. Willing, L. Thorson, K. M. McNagny, and 95. Cox, M. J., M. Allgaier, B. Taylor, M. S. Baek, Y. J. Huang, R. A. Daly,
B. B. Finlay. 2013. Perinatal antibiotic treatment affects murine microbiota, im- U. Karaoz, G. L. Andersen, R. Brown, K. E. Fujimura, et al. 2010. Airway
mune responses and allergic asthma. Gut Microbes 4: 158–164. microbiota and pathogen abundance in age-stratified cystic fibrosis patients. PLoS
72. Raghu, G., B. Rochwerg, Y. Zhang, C. A. Garcia, A. Azuma, J. Behr, J. L. Brozek, One 5: e11044.
H. R. Collard, W. Cunningham, S. Homma, et al; American Thoracic Society; 96. Zhao, J., P. D. Schloss, L. M. Kalikin, L. A. Carmody, B. K. Foster,
European Respiratory society; Japanese Respiratory Society; Latin American J. F. Petrosino, J. D. Cavalcoli, D. R. VanDevanter, S. Murray, J. Z. Li, et al.
Thoracic Association. 2015. An official ATS/ERS/JRS/ALAT clinical practice 2012. Decade-long bacterial community dynamics in cystic fibrosis airways. Proc.
guideline: treatment of idiopathic pulmonary fibrosis. An update of the 2011 Natl. Acad. Sci. USA 109: 5809–5814.
clinical practice guideline. Am. J. Respir. Crit. Care Med. 192: e3–e19. 97. Aitken, M. L., A. Limaye, P. Pottinger, E. Whimbey, C. H. Goss, M. R. Tonelli,
73. Knippenberg, S., B. Ueberberg, R. Maus, J. Bohling, N. Ding, M. Tort Tarres, G. A. Cangelosi, M. A. Dirac, K. N. Olivier, B. A. Brown-Elliott, et al. 2012.
H. G. Hoymann, D. Jonigk, N. Izykowski, J. C. Paton, et al. 2015. Streptococcus Respiratory outbreak of Mycobacterium abscessus subspecies massiliense in a lung
pneumoniae triggers progression of pulmonary fibrosis through pneumolysin. transplant and cystic fibrosis center. Am. J. Respir. Crit. Care Med. 185: 231–232.
Thorax 70: 636–646. 98. Esther, C. R., Jr., D. A. Esserman, P. Gilligan, A. Kerr, and P. G. Noone. 2010.
74. Lasithiotaki, I., K. M. Antoniou, V. M. Vlahava, K. Karagiannis, D. A. Spandidos, Chronic Mycobacterium abscessus infection and lung function decline in cystic fi-
N. M. Siafakas, and G. Sourvinos. 2011. Detection of herpes simplex virus type-1 brosis. J. Cyst. Fibros. 9: 117–123.
in patients with fibrotic lung diseases. PLoS One 6: e27800. 99. Sanguinetti, M., F. Ardito, E. Fiscarelli, M. La Sorda, P. D’Argenio, G. Ricciotti,
75. Pulkkinen, V., S. Bruce, J. Rintahaka, U. Hodgson, T. Laitinen, H. Alenius, and G. Fadda. 2001. Fatal pulmonary infection due to multidrug-resistant My-
V. L. Kinnula, M. Myllärniemi, S. Matikainen, and J. Kere. 2010. ELMOD2, a cobacterium abscessus in a patient with cystic fibrosis. J. Clin. Microbiol. 39: 816–
candidate gene for idiopathic pulmonary fibrosis, regulates antiviral responses. 819.
FASEB J. 24: 1167–1177. 100. Floto, R. A., K. N. Olivier, L. Saiman, C. L. Daley, J. L. Herrmann, J. A. Nick,
76. Molyneaux, P. L., M. J. Cox, S. A. Willis-Owen, P. Mallia, K. E. Russell, P. G. Noone, D. Bilton, P. Corris, R. L. Gibson, et al. 2016. US Cystic Fibrosis
A. M. Russell, E. Murphy, S. L. Johnston, D. A. Schwartz, A. U. Wells, et al. Foundation and European Cystic Fibrosis Society consensus recommendations for
2014. The role of bacteria in the pathogenesis and progression of idiopathic the management of non-tuberculous mycobacteria in individuals with cystic fi-
pulmonary fibrosis. Am. J. Respir. Crit. Care Med. 190: 906–913. brosis. Thorax 71(Suppl. 1): i1–i22.
77. Folcik, V. A., M. Garofalo, J. Coleman, J. J. Donegan, E. Rabbani, S. Suster, 101. Clarke, T. B. 2014. Early innate immunity to bacterial infection in the lung is
A. Nuovo, C. M. Magro, G. Di Leva, and G. J. Nuovo. 2014. Idiopathic pul- regulated systemically by the commensal microbiota via Nod-like receptor ligands.
monary fibrosis is strongly associated with productive infection by herpesvirus Infect. Immun. 82: 4596–4606.
saimiri. Mod. Pathol. 27: 851–862. 102. Sassone-Corsi, M., and M. Raffatellu. 2015. No vacancy: how beneficial microbes
78. Collard, H. R., B. B. Moore, K. R. Flaherty, K. K. Brown, R. J. Kaner, T. E. King, cooperate with immunity to provide colonization resistance to pathogens. J.
Jr., J. A. Lasky, J. E. Loyd, I. Noth, M. A. Olman, et al; Idiopathic Pulmonary Immunol. 194: 4081–4087.
Fibrosis Clinical Research Network Investigators. 2007. Acute exacerbations of 103. Savage, D. C. 1977. Microbial ecology of the gastrointestinal tract. Annu. Rev.
idiopathic pulmonary fibrosis. Am. J. Respir. Crit. Care Med. 176: 636–643. Microbiol. 31: 107–133.
79. Han, M. K., Y. Zhou, S. Murray, N. Tayob, I. Noth, V. N. Lama, B. B. Moore, 104. Arumugam, M., J. Raes, E. Pelletier, D. Le Paslier, T. Yamada, D. R. Mende,
E. S. White, K. R. Flaherty, G. B. Huffnagle, and F. J. Martinez, COMET In- G. R. Fernandes, J. Tap, T. Bruls, J. M. Batto, et al; MetaHIT Consortium. 2011.
vestigators. 2014. Lung microbiome and disease progression in idiopathic pul- Enterotypes of the human gut microbiome. Nature 473: 174–180.
monary fibrosis: an analysis of the COMET study. Lancet Respir. Med. 2: 548–556. 105. Abrahamsson, T. R., H. E. Jakobsson, A. F. Andersson, B. Björkstén,
80. Varney, V. A., H. M. Parnell, D. T. Salisbury, S. Ratnatheepan, and R. B. Tayar. L. Engstrand, and M. C. Jenmalm. 2012. Low diversity of the gut microbiota in
2008. A double blind randomised placebo controlled pilot study of oral co- infants with atopic eczema. J. Allergy Clin. Immunol. 129: 434–440, 440.e1–440.
trimoxazole in advanced fibrotic lung disease. Pulm. Pharmacol. Ther. 21: 178– e2.
187. 106. Bruzzese, E., M. L. Callegari, V. Raia, S. Viscovo, R. Scotto, S. Ferrari, L. Morelli,
81. O’Dwyer, D. N., M. E. Armstrong, G. Trujillo, G. Cooke, M. P. Keane, V. Buccigrossi, A. Lo Vecchio, E. Ruberto, and A. Guarino. 2014. Disrupted
P. G. Fallon, A. J. Simpson, A. B. Millar, E. E. McGrath, M. K. Whyte, et al. intestinal microbiota and intestinal inflammation in children with cystic fibrosis
2013. The Toll-like receptor 3 L412F polymorphism and disease progression in and its restoration with Lactobacillus GG: a randomised clinical trial. PLoS One 9:
idiopathic pulmonary fibrosis. Am. J. Respir. Crit. Care Med. 188: 1442–1450. e87796.
The Journal of Immunology 4847

107. Inagaki, H., T. Suzuki, K. Nomoto, and Y. Yoshikai. 1996. Increased susceptibility 117. Tan, H. L., N. Regamey, S. Brown, A. Bush, C. M. Lloyd, and J. C. Davies. 2011. The
to primary infection with Listeria monocytogenes in germfree mice may be due to Th17 pathway in cystic fibrosis lung disease. Am. J. Respir. Crit. Care Med. 184: 252–258.
lack of accumulation of L-selectin+ CD44+ T cells in sites of inflammation. Infect. 118. Facco, M., A. Cabrelle, A. Teramo, V. Olivieri, M. Gnoato, S. Teolato, E. Ave,
Immun. 64: 3280–3287. C. Gattazzo, G. P. Fadini, F. Calabrese, et al. 2011. Sarcoidosis is a Th1/Th17
108. Fagundes, C. T., F. A. Amaral, A. T. Vieira, A. C. Soares, V. Pinho, J. R. Nicoli, multisystem disorder. Thorax 66: 144–150.
L. Q. Vieira, M. M. Teixeira, and D. G. Souza. 2012. Transient TLR activation 119. Vanaudenaerde, B. M., S. I. De Vleeschauwer, R. Vos, I. Meyts, D. M. Bullens,
restores inflammatory response and ability to control pulmonary bacterial infection V. Reynders, W. A. Wuyts, D. E. Van Raemdonck, L. J. Dupont, and
in germfree mice. J. Immunol. 188: 1411–1420. G. M. Verleden. 2008. The role of the IL23/IL17 axis in bronchiolitis obliterans
109. Abt, M. C., L. C. Osborne, L. A. Monticelli, T. A. Doering, T. Alenghat, syndrome after lung transplantation. Am. J. Transplant. 8: 1911–1920.
G. F. Sonnenberg, M. A. Paley, M. Antenus, K. L. Williams, J. Erikson, et al. 120. Zhou, X., H. Loomis-King, S. J. Gurczynski, C. A. Wilke, K. E. Konopka,
2012. Commensal bacteria calibrate the activation threshold of innate antiviral C. Ptaschinski, S. M. Coomes, Y. Iwakura, L. F. van Dyk, N. W. Lukacs, and
immunity. Immunity 37: 158–170. B. B. Moore. 2015. Bone marrow transplantation alters lung antigen-presenting
110. Clarke, T. B., K. M. Davis, E. S. Lysenko, A. Y. Zhou, Y. Yu, and J. N. Weiser. cells to promote TH17 response and the development of pneumonitis and fibrosis
following gammaherpesvirus infection. Mucosal Immunol. In press.
2010. Recognition of peptidoglycan from the microbiota by Nod1 enhances sys-
121. Yadava, K., C. Pattaroni, A. K. Sichelstiel, A. Trompette, E. S. Gollwitzer,
temic innate immunity. Nat. Med. 16: 228–231.
O. Salami, C. von Garnier, L. P. Nicod, and B. J. Marsland. 2015. Microbiota
111. MacDonald, M., T. Korman, P. King, K. Hamza, and P. Bardin. 2013. Exacer-
promotes chronic pulmonary inflammation by enhancing IL-17A and autoanti-
bation phenotyping in chronic obstructive pulmonary disease. Respirology 18:
bodies. Am. J. Respir. Crit. Care Med. In press.
1280–1281. 122. Tan, Z., X. Qian, R. Jiang, Q. Liu, Y. Wang, C. Chen, X. Wang, B. Ryffel, and
112. Jaspers, I. 2014. Cigarette smoke effects on innate immune mechanisms in the B. Sun. 2013. IL-17A plays a critical role in the pathogenesis of liver fibrosis
nasal mucosa. Potential effects on the microbiome. Ann. Am. Thorac. Soc. 11 through hepatic stellate cell activation. J. Immunol. 191: 1835–1844.
(Suppl. 1): S38–S42. 123. Wilson, M. S., S. K. Madala, T. R. Ramalingam, B. R. Gochuico, I. O. Rosas,
113. Wang, J., F. Li, H. Wei, Z. X. Lian, R. Sun, and Z. Tian. 2014. Respiratory A. W. Cheever, and T. A. Wynn. 2010. Bleomycin and IL-1b-mediated pulmo-
influenza virus infection induces intestinal immune injury via microbiota-mediated nary fibrosis is IL-17A dependent. J. Exp. Med. 207: 535–552.
Th17 cell-dependent inflammation. J. Exp. Med. 211: 2397–2410. 124. Ray, S., C. De Salvo, and T. T. Pizarro. 2014. Central role of IL-17/Th17 im-
114. Chewning, J. H., and C. T. Weaver. 2014. Development and survival of Th17 mune responses and the gut microbiota in the pathogenesis of intestinal fibrosis.
cells within the intestines: the influence of microbiome- and diet-derived signals. J. Curr. Opin. Gastroenterol. 30: 531–538.

Downloaded from http://www.jimmunol.org/ by guest on May 21, 2018

Immunol. 193: 4769–4777. 125. Atarashi, K., T. Tanoue, M. Ando, N. Kamada, Y. Nagano, S. Narushima,
115. Tan, H. L., and M. Rosenthal. 2013. IL-17 in lung disease: friend or foe? Thorax W. Suda, A. Imaoka, H. Setoyama, T. Nagamori, et al. 2015. Th17 cell induction
68: 788–790. by adhesion of microbes to intestinal epithelial cells. Cell 163: 367–380.
116. Kudo, M., A. C. Melton, C. Chen, M. B. Engler, K. E. Huang, X. Ren, Y. Wang, 126. Gauguet, S., S. D’Ortona, K. Ahnger-Pier, B. Duan, N. K. Surana, R. Lu,
X. Bernstein, J. T. Li, K. Atabai, et al. 2012. IL-17A produced by ab T cells drives C. Cywes-Bentley, M. Gadjeva, Q. Shan, G. P. Priebe, and G. B. Pier. 2015.
airway hyper-responsiveness in mice and enhances mouse and human airway Intestinal microbiota of mice influences resistance to Staphylococcus aureus pneu-
smooth muscle contraction. Nat. Med. 18: 547–554. monia. Infect. Immun. 83: 4003–4014.