Twenty-two subjects with CF, with a severe/moderate pulmonary disease, were followed over a 15-month period. Functional and taxonomic features of bacterial airway microbiome of CF patients were inferred from shotgun metagenomic data obtained from sputum samples. Also, male CFTR tm1UNCTgN (FABPCFTR) and their WT congenic mice were studied at seven days post-infection to track changes of the gut and lung microbiome during chronic infection.
The lung microbiome of CF patients showed an extraordinary resilience of the main CF pathogens with patient-specific colonization even at strain-level. Genes associated to metabolic pathways (including antibiotic-resistance genes) were less variable but highly patient-specific suggesting the need for future development of personalized therapeutic approaches based on patient-specific airways microbiome. CFTR-deficient and WT congenic mice do not cluster separately for lung following Pseudomonas aeruginosa chronic infection, while a separation of the gut microbiota with respect to the mutation was found, suggesting that the CFTR genotype has more influence in our animal model for the gut microbiota than for lung microbiota. Animal studies will also assist in the development of microbiome manipulation of lung microbiome aimed to restore “healthy” microbial communities.

Congress abstracts

– Bevivino A, Bacci G, Taccetti G et al. “The personalised temporal dynamics of microbiome in the airways of cystic fibrosis patients” 42nd European Cystic Fibrosis Conference, 5-8 June 2019, Liverpool, UK
– Bevivino A “The airway microbiome in cystic fibrosis: where are we now “Microbiota” MI, Milan, 5-7 November 2018
– Bacci G, Taccetti G, Dolce D et al. “Environmental microbial signatures revealed by metagenomic analysis of the airways of cystic fibrosis patients” XV FISV Congress, Sapienza University Rome, 18-21 September 2018