Untargeted Metagenomic Investigation of the Airway Microbiome of Cystic Fibrosis Patients with Moderate-Severe Lung Disease.

Giovanni Bacci,Anna Negroni,Vincenzina Lucidi,Ersilia Fiscarelli,Daniela Dolce,Federica Armanini,Annamaria Bevivino,Giovanni Taccetti,Rosaria Casciaro,Patrizia Morelli,Francesca Di Cesare,Nicola Segata,Alessio Mengoni

doi:10.3390/microorganisms8071003

Abstract

Although the cystic fibrosis (CF) lung microbiota has been characterized in several studies, little is still known about the temporal changes occurring at the whole microbiome level using untargeted metagenomic analysis. The aim of this study was to investigate the taxonomic and functional temporal dynamics of the lower airway microbiome in a cohort of CF patients. Multiple sputum samples were collected over 15 months from 22 patients with advanced lung disease regularly attending three Italian CF Centers, given a total of 79 samples. DNA extracted from samples was subjected to shotgun metagenomic sequencing allowing both strain-level taxonomic profiling and assessment of the functional metagenomic repertoire. High inter-patient taxonomic heterogeneity was found with short-term compositional changes across clinical status. Each patient exhibited distinct sputum microbial communities at the taxonomic level, and strain-specific colonization of both traditional and atypical CF pathogens. A large core set of genes, including antibiotic resistance genes, were shared across patients despite observed differences in clinical status, and consistently detected in the lung microbiome of all subjects independently from known antibiotic exposure. In conclusion, an overall stability in the microbiome-associated genes was found despite taxonomic fluctuations of the communities.

Highlights

The respiratory microbial composition is relevant for cystic fibrosis (CF) patients
The patients were chosen from a larger cohort of patients with moderate-severe lung disease (30 < %FEV1 < 70) and chronically infected by Pseudomonas aeruginosa
Our results describe a unique examination of the dynamic of the lung microbiome in patients with moderate-severe lung disease carrying the ∆F508 mutation of cystic fibrosis transmembrane regulator (CFTR) gene and containing clinical measurements over a 15-month period

Summary

Introduction

The respiratory microbial composition is relevant for CF patients. bacterial lung infections reduce life expectancy in most individuals with cystic fibrosis (CF) [1]. Many analyses of CF microbiota have been done (see for instance [2,3]) Most of these studies used 16S rRNA gene sequencing, yielding the identities and relative abundances of the taxa present (i.e., the microbiota). Longitudinal studies that analyze serial samples obtained from individual patients over time allow a better assessment of the impact of these potentially confounding variables (including patient’s age, sex, lung disease stage, and antibiotic use) in constructing tractable models of the relationship between the dynamics of the lung microbial community and the disease progression. The availability of microbiome data from longitudinal studies would allow to gain information for constructing systems-biology based models of microbiome evolution inside the CF patients, of potential relevance for patient’s treatment and prognosis [3]

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