Pyrosequencing unveils cystic fibrosis lung microbiome differences associated with a severe lung function decline

Giovanni Bacci, Patrizia Paganin, Loredana Lopez, Chiara Vanni, Claudia Dalmastri, Cristina Cantale, Loretta Daddiego, Gaetano Perrotta, Daniela Dolce, Patrizia Morelli, Vanessa Tuccio, Alessandra De Alessandri, Ersilia Vita Fiscarelli, Giovanni Taccetti, Vincenzina Lucidi, Annamaria Bevivino, Alessio Mengoni

Research output: Contribution to journalArticle

Abstract

Chronic airway infection is a hallmark feature of cystic fibrosis (CF) disease. In the present study, sputum samples from CF patients were collected and characterized by 16S rRNA gene-targeted approach, to assess how lung microbiota composition changes following a severe decline in lung function. In particular, we compared the airway microbiota of two groups of patients with CF, i.e. patients with a substantial decline in their lung function (SD) and patients with a stable lung function (S). The two groups showed a different bacterial composition, with SD patients reporting a more heterogeneous community than the S ones. Pseudomonas was the dominant genus in both S and SD patients followed by Staphylococcus and Prevotella. Other than the classical CF pathogens and the most commonly identified non-classical genera in CF, we found the presence of the unusual anaerobic genus Sneathia. Moreover, the oligotyping analysis revealed the presence of other minor genera described in CF, highlighting the polymicrobial nature of CF infection. Finally, the analysis of correlation and anti-correlation networks showed the presence of antagonism and ecological independence between members of Pseudomonas genus and the rest of CF airways microbiota, with S patients showing a more interconnected community in S patients than in SD ones. This population structure suggests a higher resilience of S microbiota with respect to SD, which in turn may hinder the potential adverse impact of aggressive pathogens (e.g. Pseudomonas). In conclusion, our findings shed a new light on CF airway microbiota ecology, improving current knowledge about its composition and polymicrobial interactions in patients with CF.

Original languageEnglish
Article numbere0156807
JournalPLoS One
Volume11
Issue number6
DOIs
Publication statusPublished - Jun 1 2016

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ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Bacci, G., Paganin, P., Lopez, L., Vanni, C., Dalmastri, C., Cantale, C., Daddiego, L., Perrotta, G., Dolce, D., Morelli, P., Tuccio, V., De Alessandri, A., Fiscarelli, E. V., Taccetti, G., Lucidi, V., Bevivino, A., & Mengoni, A. (2016). Pyrosequencing unveils cystic fibrosis lung microbiome differences associated with a severe lung function decline. PLoS One, 11(6), [e0156807]. https://doi.org/10.1371/journal.pone.0156807