Disordered microbial communities in asthmatic airways

Markus Hilty, Conor Burke, Helder Pedro, Paul Cardenas, Andy Bush, Cara Bossley, Jane Davies, Aaron Ervine, Len Poulter, Lior Pachter, Miriam F Moffatt, William O C Cookson, Markus Hilty, Conor Burke, Helder Pedro, Paul Cardenas, Andy Bush, Cara Bossley, Jane Davies, Aaron Ervine, Len Poulter, Lior Pachter, Miriam F Moffatt, William O C Cookson

Abstract

Background: A rich microbial environment in infancy protects against asthma [1], [2] and infections precipitate asthma exacerbations [3]. We compared the airway microbiota at three levels in adult patients with asthma, the related condition of COPD, and controls. We also studied bronchial lavage from asthmatic children and controls.

Principal findings: We identified 5,054 16S rRNA bacterial sequences from 43 subjects, detecting >70% of species present. The bronchial tree was not sterile, and contained a mean of 2,000 bacterial genomes per cm(2) surface sampled. Pathogenic Proteobacteria, particularly Haemophilus spp., were much more frequent in bronchi of adult asthmatics or patients with COPD than controls. We found similar highly significant increases in Proteobacteria in asthmatic children. Conversely, Bacteroidetes, particularly Prevotella spp., were more frequent in controls than adult or child asthmatics or COPD patients.

Significance: The results show the bronchial tree to contain a characteristic microbiota, and suggest that this microbiota is disturbed in asthmatic airways.

Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Figure 1. Phylogenetic analysis of bacterial 16S…
Figure 1. Phylogenetic analysis of bacterial 16S rRNA DNA from the nose, oropharynx (OP) and left upper lobe (LUL) in adult patients with COPD (C) or asthma (A) and healthy controls (N).
The numbers of 16S rRNA gene phylotypes (OTUs) were calculated at 97% sequence identity and single-sequence OTUs omitted. OTU designations are located at the termination of each branch and represent potential organism names. Abundance of OTUs in each subject is indicated by different coloured squares (Yellow = 1 single OTU, Orange = 3–10%, Red = 10–20% and Black≥20%).
Figure 2. Percentage distribution of common phyla…
Figure 2. Percentage distribution of common phyla and genera at different airway levels (nose, OP and LUL), subdivided into the seven most frequent genera (Croynebacterium, Prevotella, Staphylococcus, Streptococcus, Veilonella, Haemophilus and Neisseria) found in the samples.
Figure 3. Bacterial community comparisons from the…
Figure 3. Bacterial community comparisons from the nose (N), oropharynx (OP) and left upper lobe (LUL) in adult patients with COPD or asthma and healthy controls.
Figure 4. Distribution of common phyla and…
Figure 4. Distribution of common phyla and genera in diseased and normal bronchi.
a) Distribution of the phyla from sheathed bronchoscopic brushings of the LUL for patients with asthma and COPD and normal subjects, subdivided into the seven most frequent genera (Croynebacterium, Prevotella, Staphylococcus, Streptococcus, Veilonella, Haemophilus and Neisseria). b) Distribution of the phyla from bronhco-alveolar lavage (BAL) in children with difficult asthma and controls.

References

    1. Eder W, Ege MJ, von Mutius E. The asthma epidemic. N Engl J Med. 2006;355:2226–2235.
    1. Cookson WO, Moffatt MF. Asthma: an epidemic in the absence of infection? [comment]. Science. 1997;275:41–42.
    1. Sykes A, Johnston SL. Etiology of asthma exacerbations. J Allergy Clin Immunol. 2008;122:685–688.
    1. Cookson W. The immunogenetics of asthma and eczema: a new focus on the epithelium. Nat Rev Immunol. 2004;4:978–988.
    1. Johnston S, Pattemore P, Sanderson G, Smith S, Lampe F, et al. Community study of role of viral infections in exacerbations of asthma in 9–11 year old children. BMJ. 1995;310:p1225–1229.
    1. Bisgaard H, Hermansen MN, Buchvald F, Loland L, Halkjaer LB, et al. Childhood asthma after bacterial colonization of the airway in neonates. N Engl J Med. 2007;357:1487–1495.
    1. Kraft M. The role of bacterial infections in asthma. Clin Chest Med. 2000;21:301–313.
    1. Sethi S, Evans N, Grant BJ, Murphy TF. New strains of bacteria and exacerbations of chronic obstructive pulmonary disease. N Engl J Med. 2002;347:465–471.
    1. Blasi F, Johnston SL. The role of antibiotics in asthma. Int J Antimicrob Agents. 2007;29:485–493.
    1. Morens DM, Taubenberger JK, Fauci AS. Predominant role of bacterial pneumonia as a cause of death in pandemic influenza: implications for pandemic influenza preparedness. J Infect Dis. 2008;198:962–970.
    1. Hussell T, Wissinger E, Goulding J. Bacterial complications during pandemic influenza infection. Future Microbiol. 2009;4:269–272.
    1. Sethi S, Murphy TF. Bacterial infection in chronic obstructive pulmonary disease in 2000: a state-of-the-art review. Clin Microbiol Rev. 2001;14:336–363.
    1. Staley JT, Konopka A. Measurement of in situ activities of nonphotosynthetic microorganisms in aquatic and terrestrial habitats. Annu Rev Microbiol. 1985;39:321–346.
    1. Turnbaugh PJ, Ley RE, Hamady M, Fraser-Liggett CM, Knight R, et al. The human microbiome project. Nature. 2007;449:804–810.
    1. Ahmed S, Macfarlane GT, Fite A, McBain AJ, Gilbert P, et al. Mucosa-associated bacterial diversity in relation to human terminal ileum and colonic biopsy samples. Appl Environ Microbiol. 2007;73:7435–7442.
    1. Grice EA, Kong HH, Renaud G, Young AC, Bouffard GG, et al. A diversity profile of the human skin microbiota. Genome Res. 2008;18:1043–1050.
    1. Dethlefsen L, McFall-Ngai M, Relman DA. An ecological and evolutionary perspective on human-microbe mutualism and disease. Nature. 2007;449:811–818.
    1. Pei Z, Bini EJ, Yang L, Zhou M, Francois F, et al. Bacterial biota in the human distal esophagus. Proc Natl Acad Sci U S A. 2004;101:4250–4255.
    1. Gao Z, Tseng CH, Pei Z, Blaser MJ. Molecular analysis of human forearm superficial skin bacterial biota. Proc Natl Acad Sci U S A. 2007;104:2927–2932.
    1. Wang M, Ahrne S, Jeppsson B, Molin G. Comparison of bacterial diversity along the human intestinal tract by direct cloning and sequencing of 16S rRNA genes. FEMS Microbiol Ecol. 2005;54:219–231.
    1. Frank DN, St Amand AL, Feldman RA, Boedeker EC, Harpaz N, et al. Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proc Natl Acad Sci U S A. 2007;104:13780–13785.
    1. Didierlaurent A, Goulding J, Hussell T. The impact of successive infections on the lung microenvironment. Immunology. 2007;122:457–465.
    1. Donnelly D, Critchlow A, Everard ML. Outcomes in children treated for persistent bacterial bronchitis. Thorax. 2007;62:80–84.
    1. Sutherland ER, Martin RJ. Asthma and atypical bacterial infection. Chest. 2007;132:1962–1966.
    1. Aas JA, Paster BJ, Stokes LN, Olsen I, Dewhirst FE. Defining the normal bacterial flora of the oral cavity. J Clin Microbiol. 2005;43:5721–5732.
    1. Tunney MM, Field TR, Moriarty TF, Patrick S, Doering G, et al. Detection of anaerobic bacteria in high numbers in sputum from patients with cystic fibrosis. Am J Respir Crit Care Med. 2008;177:995–1001.
    1. Murray PR, Rosenblatt JE. Bacterial interference by oropharynegeal and clinical isolates of anaerobic bacteria. J Infect Dis. 1976;134:281–285.
    1. Artis D. Epithelial-cell recognition of commensal bacteria and maintenance of immune homeostasis in the gut. Nat Rev Immunol. 2008;8:411–420.
    1. Macpherson AJ, Harris NL. Interactions between commensal intestinal bacteria and the immune system. Nat Rev Immunol. 2004;4:478–485.
    1. Henriksson G, Helgeland L, Midtvedt T, Stierna P, Brandtzaeg P. Immune response to Mycoplasma pulmonis in nasal mucosa is modulated by the normal microbiota. Am J Respir Cell Mol Biol. 2004;31:657–662.
    1. Payne D, McKenzie SA, Stacey S, Misra D, Haxby E, et al. Safety and ethics of bronchoscopy and endobronchial biopsy in difficult asthma. Arch Dis Child. 2001;84:423–426.
    1. Green SJ, Michel FC, Jr, Hadar Y, Minz D. Similarity of bacterial communities in sawdust- and straw-amended cow manure composts. FEMS Microbiol Lett. 2004;233:115–123.
    1. DeSantis TZ, Jr, Hugenholtz P, Keller K, Brodie EL, Larsen N, et al. NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes. Nucleic Acids Res. 2006;34:W394–399.
    1. Huber T, Faulkner G, Hugenholtz P. Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics. 2004;20:2317–2319.
    1. Schloss PD, Handelsman J. Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl Environ Microbiol. 2005;71:1501–1506.
    1. Kittles RA, Long JC, Bergen AW, Eggert M, Virkkunen M, et al. Cladistic association analysis of Y chromosome effects on alcohol dependence and related personality traits. Proc Natl Acad Sci U S A. 1999;96:4204–4209.
    1. Durrant C, Zondervan KT, Cardon LR, Hunt S, Deloukas P, et al. Linkage disequilibrium mapping via cladistic analysis of single-nucleotide polymorphism haplotypes. Am J Hum Genet. 2004;75:35–43.
    1. Lozupone C, Hamady M, Knight R. UniFrac–an online tool for comparing microbial community diversity in a phylogenetic context. BMC Bioinformatics. 2006;7:371.
    1. Paster BJ, Boches SK, Galvin JL, Ericson RE, Lau CN, et al. Bacterial diversity in human subgingival plaque. J Bacteriol. 2001;183:3770–3783.
    1. Smith NH, Holmes EC, Donovan GM, Carpenter GA, Spratt BG. Networks and groups within the genus Neisseria: analysis of argF, recA, rho, and 16S rRNA sequences from human Neisseria species. Mol Biol Evol. 1999;16:773–783.

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