A Metagenomic and in Silico Functional Prediction of Gut Microbiota Profiles May Concur in Discovering New Cystic Fibrosis Patient-Targeted Probiotics.

Pamela Vernocchi,Lorenza Putignani,Federica Del Chierico,Andrea Quagliariello,Danilo Ercolini,Vincenzina Lucidi

doi:10.3390/nu9121342

Abstract

Cystic fibrosis (CF) is a life-limiting hereditary disorder that results in aberrant mucosa in the lungs and digestive tract, chronic respiratory infections, chronic inflammation, and the need for repeated antibiotic treatments. Probiotics have been demonstrated to improve the quality of life of CF patients. We investigated the distribution of gut microbiota (GM) bacteria to identify new potential probiotics for CF patients on the basis of GM patterns. Fecal samples of 28 CF patients and 31 healthy controls (HC) were collected and analyzed by 16S rRNA-based pyrosequencing analysis of GM, to produce CF-HC paired maps of the distribution of operational taxonomic units (OTUs), and by Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) for Kyoto Encyclopedia of Genes and Genomes (KEGG) biomarker prediction. The maps were scanned to highlight the distribution of bacteria commonly claimed as probiotics, such as bifidobacteria and lactobacilli, and of butyrate-producing colon bacteria, such as Eubacterium spp. and Faecalibacterium prausnitzii. The analyses highlighted 24 OTUs eligible as putative probiotics. Eleven and nine species were prevalently associated with the GM of CF and HC subjects, respectively. Their KEGG prediction provided differential CF and HC pathways, indeed associated with health-promoting biochemical activities in the latter case. GM profiling and KEGG biomarkers concurred in the evaluation of nine bacterial species as novel putative probiotics that could be investigated for the nutritional management of CF patients.

Highlights

Cystic fibrosis (CF) is an autosomal recessive condition occurring among people with European origins, which is caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene
Patients with CF usually have an abnormal intestinal microbiota and dysregulated immune mediators resulting from a massive exposure to antibiotics
The results reported in this study may point out new putative probiotic species on the basis of the gut microbiota (GM) differential profiles and predicted metabolic pathways of CF patients compared to healthy controls (HC)

Summary

Introduction

Cystic fibrosis (CF) is an autosomal recessive condition occurring among people with European origins, which is caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. The CFTR mutation leads to the failure or the absence of functional CFTR proteins at the apical membrane of epithelial cells in several body systems [1]. Nutrients 2017, 9, 1342 the lungs and digestive tract. This condition increases the risk of recurrent and chronic pulmonary infection and inflammation, pancreatic insufficiency (PI), CF-related liver disease, and diabetes [2]. The recurrent destructive airway infections, determined by the progressive inflammatory lung diseases, represent the principal cause of mortality, morbidity, and altered quality of life in CF patients, resulting in respiratory failure in 90% of patients with CF [3]

Objectives

Methods

Discussion

Conclusion