Abstract
Cystic fibrosis (CF) is a common fatal genetic disorder with mortality most often resulting from microbial infections of the lungs. Culture-independent studies of CF-associated microbial communities have indicated that microbial diversity in the CF airways is much higher than suggested by culturing alone. However, these studies have relied on indirect methods to sample the CF lung such as expectorated sputum and bronchoalveolar lavage (BAL). Here, we characterize the diversity of microbial communities in tissue sections from anatomically distinct regions of the CF lung using barcoded 16S amplicon pyrosequencing. Microbial communities differed significantly between different areas of the lungs, and few taxa were common to microbial communities in all anatomical regions surveyed. Our results indicate that CF lung infections are not only polymicrobial, but also spatially heterogeneous suggesting that treatment regimes tailored to dominant populations in sputum or BAL samples may be ineffective against infections in some areas of the lung.
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References
Armougom F, Bittar F, Stremler N, Rolain JM, Robert C, Dubus JC et al. (2009). Microbial diversity in the sputum of a cystic fibrosis patient studied with 16S rDNA pyrosequencing. Eur J Clin Microbiol Infect Dis 28: 1151–1154.
Bittar EE . (2002). Pulmonary Biol health Dis. Springer.
Bousbia S, Papazian L, La Scola B, Raoult D . (2010). Detection of plant DNA in the bronchoalveolar lavage of patients with ventilator-associated pneumonia. PLoS One 5: e11298.
Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK et al. (2010). QIIME allows analysis of high-throughput community sequencing data. Nat Meth 7: 335–336.
Coenye T, Goris J, Spilker T, Vandamme P, LiPuma JJ . (2002). Characterization of unusual bacteria isolated from respiratory secretions of cystic fibrosis patients and description of inquilinus limosus gen. nov., sp. nov. J Clin Microbiol 40: 2062–2069.
Cox MJ, Cox MJ, Allgaier M, Taylor B, Baek MS, Huang YJ et al. (2010). Airway microbiota and pathogen abundance in age-stratified cystic fibrosis patients. PLoS One 5: e11044.
Cystic Fibrosis Foundation Patient Registry 2008 Annual Report (2008).
Cystic Fibrosis Foundation (2011) Available at: http://www.cff.org (accessed 20 February 2011).
Erb-Downward JR, Thompson DL, Han MK, Freeman CM, McCloskey L, Schmidt LA et al. (2011). Analysis of the lung microbiome in the ‘Healthy’ smoker and in COPD. PLoS One 6: e16384.
Gilchrist FJ, Salamat S, Clayton S, Peach J, Alexander J, Lenney W et al. (2011). Bronchoalveolar lavage in children with cystic fibrosis: how many lobes should be sampled? Arch Dis Child 96: 215–217. Available at: http://www.ncbi.nlm.nih.gov/pubmed/20930010 (accessed 7 December 2010).
Guss AM, Roeselers G, Newton IL, Young CR, Klepac-Ceraj V, Lory S et al. (2011). Phylogenetic and metabolic diversity of bacteria associated with cystic fibrosis. ISME J 5: 20–29. Available at: http://www.ncbi.nlm.nih.gov/pubmed/20631810 (accessed 19 September 2010).
Gutierrez JP, Grimwood K, Armstrong DS, Carlin JB, Carzino R, Olinsky A et al. (2001). Interlobar differences in bronchoalveolar lavage fluid from children with cystic fibrosis. Eur Respir J 17: 281–286.
Harrison F . (2007). Microbial ecology of the cystic fibrosis lung. Microbiology (Reading, Engl) 153: 917–923.
LiPuma JJ . (2010). The changing microbial epidemiology in cystic fibrosis. Clin Microbiol Rev 23: 299–323.
Rodriguez-Brito B, Rohwer F, Edwards RA . (2006). An application of statistics to comparative metagenomics. BMC Bioinformatics 7: 162.
Rogers GB, Carroll MP, Bruce KD . (2009). Studying bacterial infections through culture-independent approaches. J Med Microbiol 58: 1401–1418.
Smith D, Smith E, Pitt T, Stableforth D . (1998). Regional microbiology of the cystic fibrosis lung: a post-mortem study in adults. J Infect 37: 41–43.
van der Gast CJ, Walker AW, Stressmann FA, Rogers GB, Scott P, Daniels TW et al. (2011). Partitioning core and satellite taxa from within cystic fibrosis lung bacterial communities. ISME J 5: 780–791.
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Willner, D., Haynes, M., Furlan, M. et al. Spatial distribution of microbial communities in the cystic fibrosis lung. ISME J 6, 471–474 (2012). https://doi.org/10.1038/ismej.2011.104
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DOI: https://doi.org/10.1038/ismej.2011.104
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