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Int. J. Mol. Sci. 2017, 18(8), 1654; doi:10.3390/ijms18081654

A Different Microbiome Gene Repertoire in the Airways of Cystic Fibrosis Patients with Severe Lung Disease

1
Department of Biology, University of Florence, Florence 50019, Italy
2
Cystic Fibrosis Microbiology and Cystic Fibrosis Center, “Bambino Gesù” Children’s Hospital and Research Institute, Rome 00165, Italy
3
Centre for Integrative Biology, University of Trento, Trento 38123, Italy
4
Department of Pediatric Medicine, Cystic Fibrosis Center, Anna Meyer Children’s University Hospital, Florence 50139, Italy
5
Territorial and Production Systems Sustainability Department, ENEA, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Casaccia Research Center, Rome 00123, Italy
6
Cystic Fibrosis Center, IRCCS G. Gaslini Institute, Genoa 16146, Italy
*
Author to whom correspondence should be addressed.
Received: 5 July 2017 / Revised: 24 July 2017 / Accepted: 25 July 2017 / Published: 29 July 2017
(This article belongs to the Special Issue Lung Diseases: Chronic Respiratory Infections)
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Abstract

In recent years, next-generation sequencing (NGS) was employed to decipher the structure and composition of the microbiota of the airways in cystic fibrosis (CF) patients. However, little is still known about the overall gene functions harbored by the resident microbial populations and which specific genes are associated with various stages of CF lung disease. In the present study, we aimed to identify the microbial gene repertoire of CF microbiota in twelve patients with severe and normal/mild lung disease by performing sputum shotgun metagenome sequencing. The abundance of metabolic pathways encoded by microbes inhabiting CF airways was reconstructed from the metagenome. We identified a set of metabolic pathways differently distributed in patients with different pulmonary function; namely, pathways related to bacterial chemotaxis and flagellar assembly, as well as genes encoding efflux-mediated antibiotic resistance mechanisms and virulence-related genes. The results indicated that the microbiome of CF patients with low pulmonary function is enriched in virulence-related genes and in genes encoding efflux-mediated antibiotic resistance mechanisms. Overall, the microbiome of severely affected adults with CF seems to encode different mechanisms for the facilitation of microbial colonization and persistence in the lung, consistent with the characteristics of multidrug-resistant microbial communities that are commonly observed in patients with severe lung disease. View Full-Text
Keywords: cystic fibrosis; lung disease; lung microbiome; shotgun metagenomics; bioinformatics; metabolic pathways; virulence genes cystic fibrosis; lung disease; lung microbiome; shotgun metagenomics; bioinformatics; metabolic pathways; virulence genes
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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Bacci, G.; Mengoni, A.; Fiscarelli, E.; Segata, N.; Taccetti, G.; Dolce, D.; Paganin, P.; Morelli, P.; Tuccio, V.; De Alessandri, A.; Lucidi, V.; Bevivino, A. A Different Microbiome Gene Repertoire in the Airways of Cystic Fibrosis Patients with Severe Lung Disease. Int. J. Mol. Sci. 2017, 18, 1654.

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