signature=9ffc903949b460c0a6fb77a1db06d303,TAXONOMIC AND FUNCTIONAL METAGENOMIC ANALYSIS OF SPUTUM S...

摘要：

Introduction: In a preliminary study (Paganin P, et al. PLoS ONE 2015;10:e0124348), we revealed changes in the airway microbial communities of cystic fibrosis (CF) patients associated with a severe decline in lung function. Our findings suggest that the microbiome composition of patients with moderate lung deficiencies might be slightly different from that of patients with severe lung disease. Indeed, an in-depth analysis of the lung microbiota is needed to understand fully these modifications from both a taxonomical and a functional perspective. Objectives: To gain insight into the underlying causes of severe lung diseases, we compared the airway microbiome from CF patients with and without a substantial decline in lung function, by means of deep-sequencing 16S rRNA metabarcoding and shotgun metagenomics of airway samples of CF patients. Methods: This study included 52 patients with a severe decline (SD) in lung function (loss of FEV1% higher than 5% in the previous year) or in stable (S) lung function (loss of FEV1% lower than 1.44% in the previous year). DNA was extracted from sputum samples; then, a 16S rRNA metabarcoding analysis was performed using the Roche 454 platform. Moreover, a full-genome shotgun metagenomics analysis was executed using the Illumina HiSeq 2000 platform, on a subset of 12 patients. Data were analysed with ad-hoc pipelines including MetaPhlAn (Segata N, et al. Nature methods 2012;9:811-814), HUMAnN (Abubucker S, et al. PLoS Comput. Biol. 2012;8:e1002358) and StreamingTrim 1.0 (Bacci G, et al. Mol. Ecol. Resour. 2014;14:426-434) software. Results: SD patients displayed differential occurrences of Haemophilus, Pseudomonas, Stenotrophomonas and Burkholderia representatives. In particular, co-occurrence network analysis highlighted that the presence of Pseudomonas is uncorrelated with that of any other taxon, suggesting that its colonization did not depend on the presence of other bacterial species. In addition, S patients (with intermediate FEV1 values) displayed the highest drop in microbiota diversity along with a decreasing lung function. Moreover, the metagenomic analysis revealed a more conservative pattern of metabolic pathways in S patients with a lower presence of antibiotic resistance genes than the SD group. Conclusion: We can make out that both taxonomical signatures and functional genes related to metabolism and antibiotic resistance changed along with a substantial decline in lung function. A relatively complex bacterial community is present only in S patients with a normal/mild lung function whereas higher levels of lung decline (in patients within the S group, i.e. not under exacerbation) can lead to a decrement of this bacterial complexity leaving the way clear for the proliferation of pathogens bacteria (like representatives of Pseudomonas genus). Supported by Grants FFC#8/2012 and FFC #10/2014.

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