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Microbiome analysis in cystic fibrosis

Interactions between bacteria and their host represent a full continuum from pathogenicity to mutualism. From an evolutionary perspective, host-bacteria relationships are no longer considered a two-component ecological system but rather a complex interactive network. Cystic fibrosis (CF) is characterized by defective mucociliary clearance associated with polymicrobial chronic airway infections. Those infections, leading to persistent inflammation and periodic episodes of acute pulmonary exacerbation, contribute to an irreversible decline in CF lung function. However, the link between bacterial infections and decline in CF lung function is not yet understood but it seems that antibiotic treatment can restore the homeostasis of the system. We study CF lung microbiome aiming to answer different questions about CF microbiome resilience, antibiotic treatment effect and possible dysbiosis induced by exacerbation.

Selected publications

  1. Boutin S, Dalpke AH (2017): Acquisition and Adaptation of the airway microbiota in the early life of cystic fibrosis patients. Mol Cell Pediatr 4(1): 1-9. doi: 10.1186/s40348-016-0067-1.
  2. Boutin S, Graeber SY, Stahl M, Dittrich SA, Mall MA and Dalpke AH (2017): Chronic but not intermittent infection with Pseudomonas aeruginosa is associated with global changes of the lung microbiome in cystic fibrosis. Eur Respir J 50 (4): 1701086, doi: 10.1183/13993003.01086-2017
  3. Boutin S, Graeber SY, Weitnauer M, Panitz J, Stahl M, Clausznitzer D, Kaderali L, Einarsson G, Tunney MM, Elborn JS, Mall MA and Dalpke AH (2015): Comparison of microbiomes from different niches of upper and lower airways in children and adolescents with cystic fibrosis. PLOS One 10(1):e0116029
  4. Boutin S, Hagenfeld D, Zimmermann H, El Sayed N, Höpker T, Greiser HK, Becher H, Kim TS, Dalpke AH (2017): Clustering of subgingival microbiota reveals microbial disease ecotypes associated with clinical stages of periodontitis in a cross-sectional study. Front Microbiol. 8: 340. doi: 10.3389/fmicb.2017.00340
  5. Gehrig S, Duer J, Weitnauer M, Wagner CJ, Graeber SY, Schatterny J, Hirtz S, Belaaouai A, Dalpke AH, Schultz C, Mall MA (2014): Lack of neutrophil elastase reduces inflammation, mucus hypersecretion and emphysema, but not mucus obstruction, in mice with CF-like lung disease. AJRCCM doi10.1164/rccm.201311-1932OC, in press
  6. Zhou Z, Duerr J, Johannesson B, Schubert SC, Treis D, Harm M, Gräber S, Dalpke A, Schultz C, Mall MA (2011): The ENaC-overexpressing mouse as a model of cystic fibrosis lung disease. Journal of Cystic Fibrosis 10(Suppl. 2): S172-182