Skip to main content
Top
Published in:

Open Access 01-12-2017 | Review

Acquisition and adaptation of the airway microbiota in the early life of cystic fibrosis patients

Authors: Sébastien Boutin, Alexander H. Dalpke

Published in: Molecular and Cellular Pediatrics | Issue 1/2017

Login to get access

Abstract

Cystic fibrosis (CF) is a genetic disease in which bacterial infections of the airways play a major role in the long-term clinical outcome. In recent years, a number of next-generation sequencing (NGS)-based studies aimed at deciphering the structure and composition of the airways’ microbiota. It was shown that the nasal cavity of CF patients displays dysbiosis early in life indicating a failure in the first establishment of a healthy microbiota. In contrast, within the conducting and lower airways, the establishment occurs normally first, but is sensitive to future dysbiosis including chronic infections with classical pathogens in later life. The objective of this mini-review is to give an update on the current knowledge about the development of the microbiota in the early life of CF patients. Microbial acquisition in the human airways can be described by the island model: Microbes found in the lower airways of CF patients represent “islands” that are at first populated from the upper airways reflecting the “mainland.” Colonization can be modeled following the neutral theory in which the most abundant bacteria in the mainland are also frequently found in the lower airways initially. At later times, however, the colonization process of the lower airways segregates by active selection of specific microbes. Future research should focus on those processes of microbial and host interactions to understand how microbial communities are shaped on short- and long-term scales. We point out what therapeutic consequences arise from the microbiome data obtained within ecological framework models.
Literature
4.
go back to reference Burns JL, Gibson RL, McNamara S et al (2001) Longitudinal assessment of Pseudomonas aeruginosa in young children with cystic fibrosis. J Infect Dis 183:444–452. doi:10.1086/318075 Burns JL, Gibson RL, McNamara S et al (2001) Longitudinal assessment of Pseudomonas aeruginosa in young children with cystic fibrosis. J Infect Dis 183:444–452. doi:10.​1086/​318075
5.
go back to reference Marchandin H, Michon AL and Jumas-Bilak E (2012). Atypical Bacteria in the CF Airways: Diversity, Clinical Consequences, Emergence and Adaptation, Cystic Fibrosis - Renewed Hopes Through Research, D Sriramulu (Ed.), InTech, doi:10.5772/30253 Marchandin H, Michon AL and Jumas-Bilak E (2012). Atypical Bacteria in the CF Airways: Diversity, Clinical Consequences, Emergence and Adaptation, Cystic Fibrosis - Renewed Hopes Through Research, D Sriramulu (Ed.), InTech, doi:10.​5772/​30253
8.
go back to reference Beringer PM, Appleman MD (2000) Unusual respiratory bacterial flora in cystic fibrosis: microbiologic and clinical features. Curr Opin Pulm Med 6:545–550CrossRefPubMed Beringer PM, Appleman MD (2000) Unusual respiratory bacterial flora in cystic fibrosis: microbiologic and clinical features. Curr Opin Pulm Med 6:545–550CrossRefPubMed
14.
go back to reference Madan JC, Koestler DC, Stanton BA, et al (2012) Serial analysis of the gut and respiratory microbiome in cystic fibrosis in infancy: interaction between intestinal and respiratory tracts and impact of nutritional exposures. mBio. 3: e00251-12. doi:10.1128/mBio.00251-12 Madan JC, Koestler DC, Stanton BA, et al (2012) Serial analysis of the gut and respiratory microbiome in cystic fibrosis in infancy: interaction between intestinal and respiratory tracts and impact of nutritional exposures. mBio. 3: e00251-12. doi:10.​1128/​mBio.​00251-12
21.
go back to reference Venkataraman A, Bassis CM, Beck JM, et al (2015) Application of a neutral community model to assess structuring of the human lung microbiome. mBio 6:e02284-14. doi: 10.1128/mBio.02284-14 Venkataraman A, Bassis CM, Beck JM, et al (2015) Application of a neutral community model to assess structuring of the human lung microbiome. mBio 6:e02284-14. doi: 10.​1128/​mBio.​02284-14
23.
24.
go back to reference Cohen NA (2006) Sinonasal mucociliary clearance in health and disease. Ann Otol Rhinol Laryngol Suppl 196:20–26CrossRefPubMed Cohen NA (2006) Sinonasal mucociliary clearance in health and disease. Ann Otol Rhinol Laryngol Suppl 196:20–26CrossRefPubMed
26.
go back to reference Mika M, Korten I, Qi W et al (2016) The nasal microbiota in infants with cystic fibrosis in the first year of life: a prospective cohort study. Lancet Respir Med. 4:627-35. doi:10.1016/S2213-2600(16)30081-9 Mika M, Korten I, Qi W et al (2016) The nasal microbiota in infants with cystic fibrosis in the first year of life: a prospective cohort study. Lancet Respir Med. 4:627-35. doi:10.​1016/​S2213-2600(16)30081-9
27.
31.
35.
go back to reference Kosorok MR, Jalaluddin M, Farrell PM et al (1998) Comprehensive analysis of risk factors for acquisition of Pseudomonas aeruginosa in young children with cystic fibrosis. Pediatr Pulmonol 26:81–88. Kosorok MR, Jalaluddin M, Farrell PM et al (1998) Comprehensive analysis of risk factors for acquisition of Pseudomonas aeruginosa in young children with cystic fibrosis. Pediatr Pulmonol 26:81–88.
37.
go back to reference Ciofu O, Johansen HK, Aanaes K et al (2013) P. aeruginosa in the paranasal sinuses and transplanted lungs have similar adaptive mutations as isolates from chronically infected CF lungs. J Cyst Fibros Off J Eur Cyst Fibros Soc 12:729–736. doi:10.1016/j.jcf.2013.02.004 CrossRef Ciofu O, Johansen HK, Aanaes K et al (2013) P. aeruginosa in the paranasal sinuses and transplanted lungs have similar adaptive mutations as isolates from chronically infected CF lungs. J Cyst Fibros Off J Eur Cyst Fibros Soc 12:729–736. doi:10.​1016/​j.​jcf.​2013.​02.​004 CrossRef
39.
go back to reference Venkataraman A, Rosenbaum MA, Perkins SD et al (2011) Metabolite-based mutualism between Pseudomonas aeruginosaPA14 and Enterobacter aerogenes enhances current generation in bioelectrochemical systems. Energy Environ Sci 4:4550–4559. doi:10.1039/C1EE01377G CrossRef Venkataraman A, Rosenbaum MA, Perkins SD et al (2011) Metabolite-based mutualism between Pseudomonas aeruginosaPA14 and Enterobacter aerogenes enhances current generation in bioelectrochemical systems. Energy Environ Sci 4:4550–4559. doi:10.​1039/​C1EE01377G CrossRef
42.
go back to reference Armbruster CR, Wolter DJ, Mishra M, et al (2016) Staphylococcus aureus Protein A mediates interspecies interactions at the cell surface of Pseudomonas aeruginosa. mBio 7:e00538-16. doi: 10.1128/mBio.00538-16 Armbruster CR, Wolter DJ, Mishra M, et al (2016) Staphylococcus aureus Protein A mediates interspecies interactions at the cell surface of Pseudomonas aeruginosa. mBio 7:e00538-16. doi: 10.​1128/​mBio.​00538-16
44.
45.
52.
go back to reference Whiley RA, Fleming EV, Makhija R, Waite RD (2015) Environment and colonisation sequence are key parameters driving cooperation and competition between Pseudomonas aeruginosa cystic fibrosis strains and oral commensal Streptococci. PLoS ONE 10:e0115513. doi:10.1371/journal.pone.0115513 Whiley RA, Fleming EV, Makhija R, Waite RD (2015) Environment and colonisation sequence are key parameters driving cooperation and competition between Pseudomonas aeruginosa cystic fibrosis strains and oral commensal Streptococci. PLoS ONE 10:e0115513. doi:10.​1371/​journal.​pone.​0115513
63.
65.
go back to reference O’Dwyer DN, Dickson RP, Moore BB (2016) The lung microbiome, immunity, and the pathogenesis of chronic lung disease. J Immunol Baltim Md 196:4839–4847. doi:10.4049/jimmunol.1600279, 1950 O’Dwyer DN, Dickson RP, Moore BB (2016) The lung microbiome, immunity, and the pathogenesis of chronic lung disease. J Immunol Baltim Md 196:4839–4847. doi:10.​4049/​jimmunol.​1600279, 1950
71.
go back to reference Sherrard LJ, Graham KA, McGrath SJ, et al (2013) Antibiotic resistance in Prevotella species isolated from patients with cystic fibrosis. J Antimicrob Chemother 68:2369–74. doi:10.1093/jac/dkt191 Sherrard LJ, Graham KA, McGrath SJ, et al (2013) Antibiotic resistance in Prevotella species isolated from patients with cystic fibrosis. J Antimicrob Chemother 68:2369–74. doi:10.​1093/​jac/​dkt191
73.
go back to reference Fouhy F, Stanton C, Cotter PD et al (2015) Proteomics as the final step in the functional metagenomics study of antimicrobial resistance. Antimicrob Resist Chemother 6:172. doi:10.3389/fmicb.2015.00172 Fouhy F, Stanton C, Cotter PD et al (2015) Proteomics as the final step in the functional metagenomics study of antimicrobial resistance. Antimicrob Resist Chemother 6:172. doi:10.​3389/​fmicb.​2015.​00172
74.
go back to reference Bronstein MN, Sokol RJ, Abman SH et al (1992) Pancreatic insufficiency, growth, and nutrition in infants identified by newborn screening as having cystic fibrosis. J Pediatr 120:533–540CrossRefPubMed Bronstein MN, Sokol RJ, Abman SH et al (1992) Pancreatic insufficiency, growth, and nutrition in infants identified by newborn screening as having cystic fibrosis. J Pediatr 120:533–540CrossRefPubMed
77.
go back to reference Li L, Somerset S (2014) Digestive system dysfunction in cystic fibrosis: challenges for nutrition therapy. Dig Liver Dis Off J Ital Soc Gastroenterol Ital Assoc Study Liver 46:865–874. doi:10.1016/j.dld.2014.06.011 Li L, Somerset S (2014) Digestive system dysfunction in cystic fibrosis: challenges for nutrition therapy. Dig Liver Dis Off J Ital Soc Gastroenterol Ital Assoc Study Liver 46:865–874. doi:10.​1016/​j.​dld.​2014.​06.​011
79.
82.
go back to reference Bazett M, Honeyman L, Stefanov AN et al (2015) Cystic fibrosis mouse model-dependent intestinal structure and gut microbiome. Mamm Genome 26:222–234. doi:10.1007/s00335-015-9560-4 Bazett M, Honeyman L, Stefanov AN et al (2015) Cystic fibrosis mouse model-dependent intestinal structure and gut microbiome. Mamm Genome  26:222–234. doi:10.​1007/​s00335-015-9560-4
83.
84.
Metadata
Title
Acquisition and adaptation of the airway microbiota in the early life of cystic fibrosis patients
Authors
Sébastien Boutin
Alexander H. Dalpke
Publication date
01-12-2017
Publisher
Springer Berlin Heidelberg
Published in
Molecular and Cellular Pediatrics / Issue 1/2017
Electronic ISSN: 2194-7791
DOI
https://doi.org/10.1186/s40348-016-0067-1

Keynote webinar | Spotlight on adolescent vaping

  • Live
  • Webinar | 29-01-2025 | 18:00 (CET)

Growing numbers of young people are using e-cigarettes, despite warnings of respiratory effects and addiction. How can doctors tackle the epidemic, and what health effects should you prepare to manage in your clinics?

Watch it live: Wednesday 29th January, 18:00-19:30 CET
 

Prof. Ann McNeill
Dr. Debbie Robson
Benji Horwell
Developed by: Springer Medicine
Join the webinar