EDITORIALS epoxygenase overexpression and soluble epoxide hydrolase disruption attenuate acute vascular inflammatory responses in mice. FASEB J 2011;25:703–713. 10. Morisseau C, Hammock BD. Impact of soluble epoxide hydrolase and epoxyeicosanoids on human health. Annu Rev Pharmacol Toxicol 2013;53:37–58. 11. Lara A, Khatri SB, Wang Z, Comhair SA, Xu W, Dweik RA, Bodine M, Levison BS, Hammel J, Bleecker E, et al.; National Heart, Lung, and Blood Institute’s Severe Asthma Research Program. Alterations of the arginine metabolome in asthma. Am J Respir Crit Care Med 2008;178:673–681. 12. Holguin F, Comhair SA, Hazen SL, Powers RW, Khatri SS, Bleecker ER, Busse WW, Calhoun WJ, Castro M, Fitzpatrick AM, et al. An association between L-arginine/asymmetric dimethyl arginine balance, obesity, and the age of asthma onset phenotype. Am J Respir Crit Care Med 2013;187:153–159. 13. Planaguma` A, Pfeffer MA, Rubin G, Croze R, Uddin M, Serhan CN, Levy BD. Lovastatin decreases acute mucosal inflammation via 15-epilipoxin A4. Mucosal Immunol 2010;3:270–279.
14. Bhavsar P, Hew M, Khorasani N, Torrego A, Barnes PJ, Adcock I, Chung KF. Relative corticosteroid insensitivity of alveolar macrophages in severe asthma compared with non-severe asthma. Thorax 2008;63:784–790. 15. Bhavsar PK, Levy BD, Hew MJ, Pfeffer MA, Kazani S, Israel E, Chung KF. Corticosteroid suppression of lipoxin A4 and leukotriene B4 from alveolar macrophages in severe asthma. Respir Res 2010; 11:71. 16. Wang L, Yang J, Guo L, Uyeminami D, Dong H, Hammock BD, Pinkerton KE. Use of a soluble epoxide hydrolase inhibitor in smokeinduced chronic obstructive pulmonary disease. Am J Respir Cell Mol Biol 2012;46:614–622. 17. Smith KR, Pinkerton KE, Watanabe T, Pedersen TL, Ma SJ, Hammock BD. Attenuation of tobacco smoke–induced lung inflammation by treatment with a soluble epoxide hydrolase inhibitor. Proc Natl Acad Sci USA 2005;102:2186–2191.
Copyright © 2014 by the American Thoracic Society
The Lung Microbiome in Idiopathic Pulmonary Fibrosis What Does It Mean and What Should We Do about It? Idiopathic pulmonary fibrosis (IPF) is a devastating, progressive lung disease. Despite years of investigation, the cause of IPF remains enigmatic. The disease is likely multifactorial, with contributions of genetics and environment that determine both the development and the trajectory of the disease. A potential role for infections as a cofactor in fibrosis initiation and progression or as a trigger in exacerbations has been postulated, but in most cases, traditional culture methods in IPF patients are unrevealing. High-throughput DNA sequencing technologies now allow examination of complex microbial communities, including organisms that cannot be cultured. The microbiome refers to the entire set of microbes and microbial genes contained in an environment (1). Metagenomic tools (i.e., approaches that comprehensively analyze microbes as they exist in their natural environmental niche, rather than after isolation or culture in vitro) have been extensively applied to understanding microbial communities in gut, skin, genital tract, the oropharyngeal cavity, and other easily accessible sites. Only recently have studies begun to address bacterial communities in the lung. These studies show extensive alterations in cystic fibrosis and lung transplantation, with evidence supporting an emerging concept that more subtle changes are present in chronic obstructive pulmonary disease, but little is known about the lung microbiome in other lung diseases. In this issue of the Journal, Molyneaux and colleagues (pp. 906–913) applied these metagenomic techniques to investigating the bacterial burden and composition in bronchoalveolar lavage (BAL) of individuals with IPF (2). The BAL microbiome in IPF was compared with that in healthy subjects and among individuals with stable or progressive IPF. Using 16S ribosomal RNA gene quantitative polymerase chain reaction, the authors found a statistically significant twofold higher bacterial burden in BAL of individuals with IPF compared with that of healthy control patients or individuals with chronic obstructive pulmonary disease. Furthermore, although there was no 850
relationship between 16S levels and disease severity at baseline, 16S levels were significantly higher in participants with progressive IPF compared with those with stable disease. Using high-density pyrosequencing, the authors also reported modest differences in microbiome composition in individuals with IPF compared with control patients. This study complements another very recent report that identified higher abundances of Staphylococcus and Streptococcus sequences in progressive compared with stable IPF (3). To put the current study in context, it is worth reviewing what is known about lung bacteria in healthy individuals. In individuals without lung disease, bacteria found in the lung closely match those in the upper respiratory tract, with similar composition and relative abundances of individual taxa, but at overall much lower bacterial quantities (4, 5). Several taxa have been found at somewhat higher relative abundances in lung compared with the upper respiratory tract. Although these findings suggest that limited local replication and enrichment in the lung may occur, the close relationship in composition, but difference in quantities of microbial communities in the upper respiratory tract and the lung, suggest the majority of the lung microbiome may be derived from the upper respiratory tract, largely by microaspiration, which occurs even in healthy people. Thus, one potential explanation for the study’s findings of a higher bacterial burden in patients with IPF than in control patients, and in patients with progressive rather than stable disease, could be increased microaspiration (or decreased clearance) of normally aspirated upper respiratory tract bacteria. IPF has previously been associated with gastroesophageal reflux and aspiration (6–8), so this is a plausible explanation for why bacterial quantities may be higher in IPF (Figure 1). Alternatively, the higher relative abundance of Haemophilus, Streptococcus, Neisseria, and Veillonella species in IPF compared with control patients reported here could reflect local replication within the lower respiratory tract, but the absence of matched upper respiratory tract samples
American Journal of Respiratory and Critical Care Medicine Volume 190 Number 8 | October 15 2014
EDITORIALS
B
4C/FPO
A
C
Figure 1. Schematic of possible mechanisms by which lung bacteria may contribute to idiopathic pulmonary fibrosis (IPF) pathogenesis and progression. (A) Increased lung bacterial burden resulting from chronic microaspiration of oropharyngeal contents or limited local replication within the lower respiratory tract results in chronically increased exposure of distal lung to bacterial stimuli. (B) Alternatively, genetic polymorphisms of genes that regulate local management of or responses to bacteria such as MUC5B or TOLLIP result in increased local exposure at the alveolar region or aberrant cellular responses to bacterial stimuli. (C) Resulting chronic low-level inflammation and damage contribute to progressive fibrosis and lung injury.
limits the ability to distinguish this possibility from passive aspiration. This point is significant, as even if higher bacterial loads in IPF were found to be causal in disease progression, any therapeutic approach to bacterial aspiration from the upper respiratory tract versus endogenous replication within the lung would necessarily be different. The association with higher bacterial burden was seen only in patients with IPF who lacked the MUC5B promoter polymorphism, which suggests another mechanism for bacteria in IPF pathogenesis (Figure 1). This polymorphism has been linked to higher IPF risk but, paradoxically, slower disease progression (9, 10). Patients with IPF without the MUC5B polymorphisms had a significantly higher 16S bacterial burden in BAL and more rapid progression than those with the polymorphism. MUC5B is a protein that is more highly expressed in the lung of patients with IPF compared with control patients, and the polymorphism is associated with higher levels of MUC5B expression (10, 11). In addition to mucus production, MUC5B plays an important role in airway defense. Editorials
Curiously, given the current findings, it is the absence of MUC5B that has been associated with increased bacteria in the lungs and defective airway defense (12). The findings of this study raise the possibility that there may be two distinct pathways that lead to bacterially induced tissue injury: one involving higher bacterial overall burden in those without the MUC5B polymorphism and another in which bacterial burden is not increased overall, but MUC5B overexpression at the distal airway/alveolar junction results in, perhaps, adequate airway clearance, but aberrant entry into the alveolar region (Figure 1). IPF risk or progression has also been associated with single nucleotide polymorphisms in microbially linked genes such as TOLLIP, which serves as an adaptor protein for Toll-like receptors that mediate microbe–host interactions (13). Whatever the mechanisms responsible for altered abundance and composition of bacteria in lungs in IPF, the key question is whether this serves as a marker for disease or disease progression, is a covariant of other pathogenic factors (such as aspiration, which 851
EDITORIALS may cause injury through various factors), or plays a direct causative role in tissue injury. It is not difficult to envision how increased exposure of distal lung tissue to bacterial products could augment tissue injury in the context of a susceptible host. Indeed, a central role for microbial agents as a driver of tissue injury could be part of the reason for the remarkable failure of immunosuppressive therapies to benefit IPF. Alternatively, more profound physiological derangement from other underlying processes in IPF could increase susceptibility to bacterial colonization that would then be a marker of other causative underlying processes. This study had many strengths. It reflects a relatively large group of patients with clearly defined IPF, had appropriate control patients, and paid attention to both the quantification and composition of the lung microbiome; however, several caveats are worth noting. First, the differences in bacterial burden are modest (approximately twofold) in measurements that can be substantially affected by sample collection technical factors. As noted earlier, the lack of upper respiratory tract samples makes it difficult to distinguish between lung-specific versus aspirationderived differences in microbiome composition. The overall BAL bacterial burden reported here (approximately 108 16S copies per microliter of BAL) is remarkably high, especially given the traditional estimate of 30-fold dilution of lung lining fluid in BAL. Although individual bacteria can have multiple 16S copies, the BAL quantities reported reflect numbers that exceed the 16S copy number associated with the small intestinal mucosa (14). As the authors correctly point out, laboratory-specific factors can affect absolute quantification levels in quantitative polymerase chain reaction. Thus, relative differences between groups identified here, rather than absolute quantities, are the principal relevant observation. Finally, bacteria are not the only constituents of the human microbiome, and further studies would be needed to investigate fungi and viruses. IPF is an intractable disease with a dismal prognosis that has so far eluded effective therapy. Thus, the identification of a mechanism by which respiratory tract bacteria contribute to IPF pathogenesis would be a welcome step forward in selecting avenues for further study. A previous trial of IPF treatment with the antibacterial co-trimoxazole failed to show an effect on disease progression, even though discrete infectious complications were reduced (14). Such a result would be consistent with upper respiratory tract aspiration-derived lung bacteria in IPF, which would not likely be globally reduced by antibiotic treatment, even if the bacteria themselves were playing a causal role in injury. Nevertheless, this study supports the need for future work examining the relationship of bacteria with IPF progression and suggests antibacterial therapy may be a promising avenue for treatment of this currently untreatable disease. n Author disclosures are available with the text of this article at www.atsjournals.org. Alison Morris, M.D., M.S. Kevin Gibson, M.D. Department of Medicine University of Pittsburgh School of Medicine Pittsburgh, Pennsylvania
852
Ronald G. Collman, M.D. Department of Medicine University of Pennsylvania School of Medicine Philadelphia, Pennsylvania
References 1. Ley RE, Lozupone CA, Hamady M, Knight R, Gordon JI. Worlds within worlds: evolution of the vertebrate gut microbiota. Nat Rev Microbiol 2008;6:776–788. 2. Molyneaux PL, Cox MJ, Willis-Owen SAG, Mallia P, Russell KE, Russell A-M, Murphy E, Johnston SL, Schwartz DA, Wells AU, et al. The role of bacteria in the pathogenesis and progression of idiopathic pulmonary fibrosis. Am J Respir Crit Care Med 2014;190:906–913. 3. Han MK, Zhou Y, Murray S, Tayob N, Noth I, Lama VN, Moore BB, White ES, Flaherty KR, Huffnagle GB, et al.; COMET Investigators. Lung microbiome and disease progression in idiopathic pulmonary fibrosis: an analysis of the COMET study. Lancet Respir Med 2014;2:548–556. 4. Charlson ES, Bittinger K, Haas AR, Fitzgerald AS, Frank I, Yadav A, Bushman FD, Collman RG. Topographical continuity of bacterial populations in the healthy human respiratory tract. Am J Respir Crit Care Med 2011;184:957–963. 5. Morris A, Beck JM, Schloss PD, Campbell TB, Crothers K, Curtis JL, Flores SC, Fontenot AP, Ghedin E, Huang L, et al.; Lung HIV Microbiome Project. Comparison of the respiratory microbiome in healthy nonsmokers and smokers. Am J Respir Crit Care Med 2013; 187:1067–1075. 6. Tobin RW, Pope CE II, Pellegrini CA, Emond MJ, Sillery J, Raghu G. Increased prevalence of gastroesophageal reflux in patients with idiopathic pulmonary fibrosis. Am J Respir Crit Care Med 1998;158: 1804–1808. 7. Lee JS, Ryu JH, Elicker BM, Lydell CP, Jones KD, Wolters PJ, King TE Jr, Collard HR. Gastroesophageal reflux therapy is associated with longer survival in patients with idiopathic pulmonary fibrosis. Am J Respir Crit Care Med 2011;184:1390–1394. 8. Savarino E, Carbone R, Marabotto E, Furnari M, Sconfienza L, Ghio M, Zentilin P, Savarino V. Gastro-oesophageal reflux and gastric aspiration in idiopathic pulmonary fibrosis patients. Eur Respir J 2013; 42:1322–1331. 9. Peljto AL, Zhang Y, Fingerlin TE, Ma SF, Garcia JG, Richards TJ, Silveira LJ, Lindell KO, Steele MP, Loyd JE, et al. Association between the MUC5B promoter polymorphism and survival in patients with idiopathic pulmonary fibrosis. JAMA 2013;309:2232–2239. 10. Seibold MA, Wise AL, Speer MC, Steele MP, Brown KK, Loyd JE, Fingerlin TE, Zhang W, Gudmundsson G, Groshong SD, et al. A common MUC5B promoter polymorphism and pulmonary fibrosis. N Engl J Med 2011;364:1503–1512. 11. Fingerlin TE, Murphy E, Zhang W, Peljto AL, Brown KK, Steele MP, Loyd JE, Cosgrove GP, Lynch D, Groshong S, et al. Genome-wide association study identifies multiple susceptibility loci for pulmonary fibrosis. Nat Genet 2013;45:613–620. 12. Roy MG, Livraghi-Butrico A, Fletcher AA, McElwee MM, Evans SE, Boerner RM, Alexander SN, Bellinghausen LK, Song AS, Petrova YM, et al. Muc5b is required for airway defence. Nature 2014;505: 412–416. 13. Noth I, Zhang Y, Ma SF, Flores C, Barber M, Huang Y, Broderick SM, Wade MS, Hysi P, Scuirba J, et al. Genetic variants associated with idiopathic pulmonary fibrosis susceptibility and mortality: a genomewide association study. Lancet Respir Med 2013;1:309–317. 14. Huijsdens XW, Linskens RK, Mak M, Meuwissen SG, VandenbrouckeGrauls CM, Savelkoul PH. Quantification of bacteria adherent to gastrointestinal mucosa by real-time PCR. J Clin Microbiol 2002;40: 4423–4427.
Copyright © 2014 by the American Thoracic Society
American Journal of Respiratory and Critical Care Medicine Volume 190 Number 8 | October 15 2014
14. Bhavsar P, Hew M, Khorasani N, Torrego A, Barnes PJ, Adcock I, Chung KF. Relative corticosteroid insensitivity of alveolar macrophages in severe asthma compared with non-severe asthma. Thorax 2008;63:784–790. 15. Bhavsar PK, Levy BD, Hew MJ, Pfeffer MA, Kazani S, Israel E, Chung KF. Corticosteroid suppression of lipoxin A4 and leukotriene B4 from alveolar macrophages in severe asthma. Respir Res 2010; 11:71. 16. Wang L, Yang J, Guo L, Uyeminami D, Dong H, Hammock BD, Pinkerton KE. Use of a soluble epoxide hydrolase inhibitor in smokeinduced chronic obstructive pulmonary disease. Am J Respir Cell Mol Biol 2012;46:614–622. 17. Smith KR, Pinkerton KE, Watanabe T, Pedersen TL, Ma SJ, Hammock BD. Attenuation of tobacco smoke–induced lung inflammation by treatment with a soluble epoxide hydrolase inhibitor. Proc Natl Acad Sci USA 2005;102:2186–2191.
Copyright © 2014 by the American Thoracic Society
The Lung Microbiome in Idiopathic Pulmonary Fibrosis What Does It Mean and What Should We Do about It? Idiopathic pulmonary fibrosis (IPF) is a devastating, progressive lung disease. Despite years of investigation, the cause of IPF remains enigmatic. The disease is likely multifactorial, with contributions of genetics and environment that determine both the development and the trajectory of the disease. A potential role for infections as a cofactor in fibrosis initiation and progression or as a trigger in exacerbations has been postulated, but in most cases, traditional culture methods in IPF patients are unrevealing. High-throughput DNA sequencing technologies now allow examination of complex microbial communities, including organisms that cannot be cultured. The microbiome refers to the entire set of microbes and microbial genes contained in an environment (1). Metagenomic tools (i.e., approaches that comprehensively analyze microbes as they exist in their natural environmental niche, rather than after isolation or culture in vitro) have been extensively applied to understanding microbial communities in gut, skin, genital tract, the oropharyngeal cavity, and other easily accessible sites. Only recently have studies begun to address bacterial communities in the lung. These studies show extensive alterations in cystic fibrosis and lung transplantation, with evidence supporting an emerging concept that more subtle changes are present in chronic obstructive pulmonary disease, but little is known about the lung microbiome in other lung diseases. In this issue of the Journal, Molyneaux and colleagues (pp. 906–913) applied these metagenomic techniques to investigating the bacterial burden and composition in bronchoalveolar lavage (BAL) of individuals with IPF (2). The BAL microbiome in IPF was compared with that in healthy subjects and among individuals with stable or progressive IPF. Using 16S ribosomal RNA gene quantitative polymerase chain reaction, the authors found a statistically significant twofold higher bacterial burden in BAL of individuals with IPF compared with that of healthy control patients or individuals with chronic obstructive pulmonary disease. Furthermore, although there was no 850
relationship between 16S levels and disease severity at baseline, 16S levels were significantly higher in participants with progressive IPF compared with those with stable disease. Using high-density pyrosequencing, the authors also reported modest differences in microbiome composition in individuals with IPF compared with control patients. This study complements another very recent report that identified higher abundances of Staphylococcus and Streptococcus sequences in progressive compared with stable IPF (3). To put the current study in context, it is worth reviewing what is known about lung bacteria in healthy individuals. In individuals without lung disease, bacteria found in the lung closely match those in the upper respiratory tract, with similar composition and relative abundances of individual taxa, but at overall much lower bacterial quantities (4, 5). Several taxa have been found at somewhat higher relative abundances in lung compared with the upper respiratory tract. Although these findings suggest that limited local replication and enrichment in the lung may occur, the close relationship in composition, but difference in quantities of microbial communities in the upper respiratory tract and the lung, suggest the majority of the lung microbiome may be derived from the upper respiratory tract, largely by microaspiration, which occurs even in healthy people. Thus, one potential explanation for the study’s findings of a higher bacterial burden in patients with IPF than in control patients, and in patients with progressive rather than stable disease, could be increased microaspiration (or decreased clearance) of normally aspirated upper respiratory tract bacteria. IPF has previously been associated with gastroesophageal reflux and aspiration (6–8), so this is a plausible explanation for why bacterial quantities may be higher in IPF (Figure 1). Alternatively, the higher relative abundance of Haemophilus, Streptococcus, Neisseria, and Veillonella species in IPF compared with control patients reported here could reflect local replication within the lower respiratory tract, but the absence of matched upper respiratory tract samples
American Journal of Respiratory and Critical Care Medicine Volume 190 Number 8 | October 15 2014
EDITORIALS
B
4C/FPO
A
C
Figure 1. Schematic of possible mechanisms by which lung bacteria may contribute to idiopathic pulmonary fibrosis (IPF) pathogenesis and progression. (A) Increased lung bacterial burden resulting from chronic microaspiration of oropharyngeal contents or limited local replication within the lower respiratory tract results in chronically increased exposure of distal lung to bacterial stimuli. (B) Alternatively, genetic polymorphisms of genes that regulate local management of or responses to bacteria such as MUC5B or TOLLIP result in increased local exposure at the alveolar region or aberrant cellular responses to bacterial stimuli. (C) Resulting chronic low-level inflammation and damage contribute to progressive fibrosis and lung injury.
limits the ability to distinguish this possibility from passive aspiration. This point is significant, as even if higher bacterial loads in IPF were found to be causal in disease progression, any therapeutic approach to bacterial aspiration from the upper respiratory tract versus endogenous replication within the lung would necessarily be different. The association with higher bacterial burden was seen only in patients with IPF who lacked the MUC5B promoter polymorphism, which suggests another mechanism for bacteria in IPF pathogenesis (Figure 1). This polymorphism has been linked to higher IPF risk but, paradoxically, slower disease progression (9, 10). Patients with IPF without the MUC5B polymorphisms had a significantly higher 16S bacterial burden in BAL and more rapid progression than those with the polymorphism. MUC5B is a protein that is more highly expressed in the lung of patients with IPF compared with control patients, and the polymorphism is associated with higher levels of MUC5B expression (10, 11). In addition to mucus production, MUC5B plays an important role in airway defense. Editorials
Curiously, given the current findings, it is the absence of MUC5B that has been associated with increased bacteria in the lungs and defective airway defense (12). The findings of this study raise the possibility that there may be two distinct pathways that lead to bacterially induced tissue injury: one involving higher bacterial overall burden in those without the MUC5B polymorphism and another in which bacterial burden is not increased overall, but MUC5B overexpression at the distal airway/alveolar junction results in, perhaps, adequate airway clearance, but aberrant entry into the alveolar region (Figure 1). IPF risk or progression has also been associated with single nucleotide polymorphisms in microbially linked genes such as TOLLIP, which serves as an adaptor protein for Toll-like receptors that mediate microbe–host interactions (13). Whatever the mechanisms responsible for altered abundance and composition of bacteria in lungs in IPF, the key question is whether this serves as a marker for disease or disease progression, is a covariant of other pathogenic factors (such as aspiration, which 851
EDITORIALS may cause injury through various factors), or plays a direct causative role in tissue injury. It is not difficult to envision how increased exposure of distal lung tissue to bacterial products could augment tissue injury in the context of a susceptible host. Indeed, a central role for microbial agents as a driver of tissue injury could be part of the reason for the remarkable failure of immunosuppressive therapies to benefit IPF. Alternatively, more profound physiological derangement from other underlying processes in IPF could increase susceptibility to bacterial colonization that would then be a marker of other causative underlying processes. This study had many strengths. It reflects a relatively large group of patients with clearly defined IPF, had appropriate control patients, and paid attention to both the quantification and composition of the lung microbiome; however, several caveats are worth noting. First, the differences in bacterial burden are modest (approximately twofold) in measurements that can be substantially affected by sample collection technical factors. As noted earlier, the lack of upper respiratory tract samples makes it difficult to distinguish between lung-specific versus aspirationderived differences in microbiome composition. The overall BAL bacterial burden reported here (approximately 108 16S copies per microliter of BAL) is remarkably high, especially given the traditional estimate of 30-fold dilution of lung lining fluid in BAL. Although individual bacteria can have multiple 16S copies, the BAL quantities reported reflect numbers that exceed the 16S copy number associated with the small intestinal mucosa (14). As the authors correctly point out, laboratory-specific factors can affect absolute quantification levels in quantitative polymerase chain reaction. Thus, relative differences between groups identified here, rather than absolute quantities, are the principal relevant observation. Finally, bacteria are not the only constituents of the human microbiome, and further studies would be needed to investigate fungi and viruses. IPF is an intractable disease with a dismal prognosis that has so far eluded effective therapy. Thus, the identification of a mechanism by which respiratory tract bacteria contribute to IPF pathogenesis would be a welcome step forward in selecting avenues for further study. A previous trial of IPF treatment with the antibacterial co-trimoxazole failed to show an effect on disease progression, even though discrete infectious complications were reduced (14). Such a result would be consistent with upper respiratory tract aspiration-derived lung bacteria in IPF, which would not likely be globally reduced by antibiotic treatment, even if the bacteria themselves were playing a causal role in injury. Nevertheless, this study supports the need for future work examining the relationship of bacteria with IPF progression and suggests antibacterial therapy may be a promising avenue for treatment of this currently untreatable disease. n Author disclosures are available with the text of this article at www.atsjournals.org. Alison Morris, M.D., M.S. Kevin Gibson, M.D. Department of Medicine University of Pittsburgh School of Medicine Pittsburgh, Pennsylvania
852
Ronald G. Collman, M.D. Department of Medicine University of Pennsylvania School of Medicine Philadelphia, Pennsylvania
References 1. Ley RE, Lozupone CA, Hamady M, Knight R, Gordon JI. Worlds within worlds: evolution of the vertebrate gut microbiota. Nat Rev Microbiol 2008;6:776–788. 2. Molyneaux PL, Cox MJ, Willis-Owen SAG, Mallia P, Russell KE, Russell A-M, Murphy E, Johnston SL, Schwartz DA, Wells AU, et al. The role of bacteria in the pathogenesis and progression of idiopathic pulmonary fibrosis. Am J Respir Crit Care Med 2014;190:906–913. 3. Han MK, Zhou Y, Murray S, Tayob N, Noth I, Lama VN, Moore BB, White ES, Flaherty KR, Huffnagle GB, et al.; COMET Investigators. Lung microbiome and disease progression in idiopathic pulmonary fibrosis: an analysis of the COMET study. Lancet Respir Med 2014;2:548–556. 4. Charlson ES, Bittinger K, Haas AR, Fitzgerald AS, Frank I, Yadav A, Bushman FD, Collman RG. Topographical continuity of bacterial populations in the healthy human respiratory tract. Am J Respir Crit Care Med 2011;184:957–963. 5. Morris A, Beck JM, Schloss PD, Campbell TB, Crothers K, Curtis JL, Flores SC, Fontenot AP, Ghedin E, Huang L, et al.; Lung HIV Microbiome Project. Comparison of the respiratory microbiome in healthy nonsmokers and smokers. Am J Respir Crit Care Med 2013; 187:1067–1075. 6. Tobin RW, Pope CE II, Pellegrini CA, Emond MJ, Sillery J, Raghu G. Increased prevalence of gastroesophageal reflux in patients with idiopathic pulmonary fibrosis. Am J Respir Crit Care Med 1998;158: 1804–1808. 7. Lee JS, Ryu JH, Elicker BM, Lydell CP, Jones KD, Wolters PJ, King TE Jr, Collard HR. Gastroesophageal reflux therapy is associated with longer survival in patients with idiopathic pulmonary fibrosis. Am J Respir Crit Care Med 2011;184:1390–1394. 8. Savarino E, Carbone R, Marabotto E, Furnari M, Sconfienza L, Ghio M, Zentilin P, Savarino V. Gastro-oesophageal reflux and gastric aspiration in idiopathic pulmonary fibrosis patients. Eur Respir J 2013; 42:1322–1331. 9. Peljto AL, Zhang Y, Fingerlin TE, Ma SF, Garcia JG, Richards TJ, Silveira LJ, Lindell KO, Steele MP, Loyd JE, et al. Association between the MUC5B promoter polymorphism and survival in patients with idiopathic pulmonary fibrosis. JAMA 2013;309:2232–2239. 10. Seibold MA, Wise AL, Speer MC, Steele MP, Brown KK, Loyd JE, Fingerlin TE, Zhang W, Gudmundsson G, Groshong SD, et al. A common MUC5B promoter polymorphism and pulmonary fibrosis. N Engl J Med 2011;364:1503–1512. 11. Fingerlin TE, Murphy E, Zhang W, Peljto AL, Brown KK, Steele MP, Loyd JE, Cosgrove GP, Lynch D, Groshong S, et al. Genome-wide association study identifies multiple susceptibility loci for pulmonary fibrosis. Nat Genet 2013;45:613–620. 12. Roy MG, Livraghi-Butrico A, Fletcher AA, McElwee MM, Evans SE, Boerner RM, Alexander SN, Bellinghausen LK, Song AS, Petrova YM, et al. Muc5b is required for airway defence. Nature 2014;505: 412–416. 13. Noth I, Zhang Y, Ma SF, Flores C, Barber M, Huang Y, Broderick SM, Wade MS, Hysi P, Scuirba J, et al. Genetic variants associated with idiopathic pulmonary fibrosis susceptibility and mortality: a genomewide association study. Lancet Respir Med 2013;1:309–317. 14. Huijsdens XW, Linskens RK, Mak M, Meuwissen SG, VandenbrouckeGrauls CM, Savelkoul PH. Quantification of bacteria adherent to gastrointestinal mucosa by real-time PCR. J Clin Microbiol 2002;40: 4423–4427.
Copyright © 2014 by the American Thoracic Society
American Journal of Respiratory and Critical Care Medicine Volume 190 Number 8 | October 15 2014
