title: Pyrosequencing Unveils Cystic Fibrosis Lung Microbiome Differences Associated with a Severe Lung Function Decline.
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.
authors.affiliation: Department of Biology, University of Florence, Florence, Italy.
authors.forename: Giovanni
authors.initials: G
authors.lastname: Bacci
authors.affiliation: Department for Sustainability of Production and Territorial Systems, Biotechnologies and Agro-Industry Division, ENEA Casaccia Research Center, Rome, Italy.
authors.forename: Patrizia
authors.initials: P
authors.lastname: Paganin
authors.affiliation: Department of Energy Technologies, Bioenergy, Biorefinery and Green Chemistry Division, ENEA Trisaia Research Center, Rotondella (MT), Italy.
authors.forename: Loredana
authors.initials: L
authors.lastname: Lopez
authors.affiliation: Department of Biology, University of Florence, Florence, Italy.
authors.forename: Chiara
authors.initials: C
authors.lastname: Vanni
authors.affiliation: Department for Sustainability of Production and Territorial Systems, Biotechnologies and Agro-Industry Division, ENEA Casaccia Research Center, Rome, Italy.
authors.forename: Claudia
authors.initials: C
authors.lastname: Dalmastri
authors.affiliation: Department for Sustainability of Production and Territorial Systems, Biotechnologies and Agro-Industry Division, ENEA Casaccia Research Center, Rome, Italy.
authors.forename: Cristina
authors.initials: C
authors.lastname: Cantale
authors.affiliation: Department of Energy Technologies, Bioenergy, Biorefinery and Green Chemistry Division, ENEA Trisaia Research Center, Rotondella (MT), Italy.
authors.forename: Loretta
authors.initials: L
authors.lastname: Daddiego
authors.affiliation: Department of Energy Technologies, Bioenergy, Biorefinery and Green Chemistry Division, ENEA Trisaia Research Center, Rotondella (MT), Italy.
authors.forename: Gaetano
authors.initials: G
authors.lastname: Perrotta
authors.affiliation: Department of Pediatrics, Cystic Fibrosis Center, Meyer Hospital, Florence, Italy.
authors.forename: Daniela
authors.initials: D
authors.lastname: Dolce
authors.affiliation: Department of Pediatrics, Cystic Fibrosis Center, G. Gaslini Institute, Genoa, Italy.
authors.forename: Patrizia
authors.initials: P
authors.lastname: Morelli
authors.affiliation: Cystic Fibrosis Microbiology and Cystic Fibrosis Center, Children's Hospital and Research Institute Bambino Gesù, Rome, Italy.
authors.forename: Vanessa
authors.initials: V
authors.lastname: Tuccio
authors.affiliation: Department of Pediatrics, Cystic Fibrosis Center, G. Gaslini Institute, Genoa, Italy.
authors.forename: Alessandra
authors.initials: A
authors.lastname: De Alessandri
authors.affiliation: Cystic Fibrosis Microbiology and Cystic Fibrosis Center, Children's Hospital and Research Institute Bambino Gesù, Rome, Italy.
authors.forename: Ersilia Vita
authors.initials: EV
authors.lastname: Fiscarelli
authors.affiliation: Department of Pediatrics, Cystic Fibrosis Center, Meyer Hospital, Florence, Italy.
authors.forename: Giovanni
authors.initials: G
authors.lastname: Taccetti
authors.affiliation: Cystic Fibrosis Microbiology and Cystic Fibrosis Center, Children's Hospital and Research Institute Bambino Gesù, Rome, Italy.
authors.forename: Vincenzina
authors.initials: V
authors.lastname: Lucidi
authors.affiliation: Department of Biology, University of Florence, Florence, Italy.
authors.forename: Annamaria
authors.identifier: http://orcid.org/0000-0003-4277-7048
authors.initials: A
authors.lastname: Bevivino
authors.affiliation: Department of Biology, University of Florence, Florence, Italy.
authors.forename: Alessio
authors.initials: A
authors.lastname: Mengoni
mesh_terms: D000293:Adolescent; D000328:Adult; D002648:Child; D003550:Cystic Fibrosis / Q000382:microbiology*; D004463:Ecology; D005260:Female; D006801:Humans; D007558:Italy; D008168:Lung / Q000382:microbiology* / Q000503:physiopathology; D008297:Male; D064307:Microbiota; D008875:Middle Aged; D010802:Phylogeny; D018720:Prevotella; D011549:Pseudomonas; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012129:Respiratory Function Tests; D012143:Respiratory Physiological Phenomena; D017422:Sequence Analysis, DNA; D013183:Sputum / Q000382:microbiology*; D013210:Staphylococcus; D055815:Young Adult
chemical_list: D012336:RNA, Ribosomal, 16S