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Nutrients 2017, 9(12), 1342; https://doi.org/10.3390/nu9121342

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

1
Unit of Human Microbiome, Bambino Gesù Children’s Hospital, IRCCS, Viale San Paolo 15, 00146 Rome, Italy
2
Department of Agricultural Sciences, Division of Microbiology, University of Naples Federico II, Via Università 100, Portici, 80055 Napoli, Italy
3
Cystic Fibrosis Unit, Bambino Gesù Children’s Hospital, IRCCS, Piazza Sant’ Onofrio 4, Rome 00165, Italy
4
Unit of Parasitology Bambino Gesù Children’s Hospital, IRCCS, Piazza Sant’ Onofrio 4, Rome 00165, Italy
These authors contributed equally to this work.
*
Author to whom correspondence should be addressed.
Received: 16 October 2017 / Revised: 4 December 2017 / Accepted: 5 December 2017 / Published: 9 December 2017
(This article belongs to the Special Issue Prebiotics and Probiotics)
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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. View Full-Text
Keywords: cystic fibrosis; gut microbiota profiling; KEGG prediction-tailored probiotic design cystic fibrosis; gut microbiota profiling; KEGG prediction-tailored probiotic design
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Vernocchi, P.; Del Chierico, F.; Quagliariello, A.; Ercolini, D.; Lucidi, V.; Putignani, L. A Metagenomic and in Silico Functional Prediction of Gut Microbiota Profiles May Concur in Discovering New Cystic Fibrosis Patient-Targeted Probiotics. Nutrients 2017, 9, 1342.

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