A Metagenomic and in Silico Functional Prediction of Gut Microbiota Profiles May Concur in Discovering New Cystic Fibrosis Patient-Targeted Probiotics
Abstract
:1. Introduction
2. Material and Methods
2.1. Patients
2.2. Anamnestic and Laboratory Features
2.3. DNA Extraction and Next Generation Sequencing (NGS) Analysis
2.4. Statistical Analysis
3. Results
3.1. Putative Probiotic Distribution in the GM Profiles
3.2. Metabolic Pathways of Probiotics
4. Discussion
4.1. Putative Probiotic Distribution in the GM Profiles
4.2. Metabolic Pathways of Probiotics
5. Conclusions
Acknowledgments
Author Contributions
Conflicts of Interest
References
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Subjects | Males | Mean Age | Mean W/L or BMI Z-Score * | Pancreatic Insufficiency: Yes/Not | Mean Value of Sweat Test | Chronic Use of Antibiotic: Yes/No | Disease Severity: Mild/Severe |
---|---|---|---|---|---|---|---|
CF | 11/28 (39%) | 3.5 | ±0.9 | 22/6 79/21 (%) | 93 | 12/16 43/57 (%) | 4/24 14/86 (%) |
HC | 20/31 (64.5%) | 3.06 | ±0.51 | nda ** | nda | nda | nda |
Bacteria | Group of Subjects |
---|---|
Bifidobacterium bifidum | HC |
Bifidobacterium longum | |
Bifidobacterium pseudocatenulatum | |
Faecalibacterium prausnitzii | |
Lactobacillus fermentum | |
Lactobacillus sanfranciscensis | |
Eubacterium siraeum | |
Eubacterium rectale | |
Eubacterium limosum | |
Bifidobacterium breve | CF |
Bifidobacterium dentium | |
Lactobacillus crispatus | |
Lactobacillus mucosae | |
Lactobacillus pentosus | |
Lactobacillus pontis | |
Lactobacillus reuteri | |
Lactobacillus vaginalis | |
Lactobacillus zeae | |
Eubacterium biforme | |
Eubacterium dolichum |
KEGG Pathways | Class * | Subclass | Group | KEGG Pathways | Class | Subclass | Group |
---|---|---|---|---|---|---|---|
Carbon fixation in photosynthetic organisms | 1 | Energy metabolism | HC | Lysine degradation | 1 | Amino acid metabolism | CF |
Alanine aspartate and glutamate metabolism | Amino acid metabolism | Phenylalanine metabolism | |||||
Arginine and proline metabolism | Tryptophan metabolism | ||||||
Histidine metabolism | Tyrosine metabolism | ||||||
Lysine biosynthesis | Valine leucine and isoleucine degradation | ||||||
Phenylalanine tyrosine and tryptophan biosynthesis | Ascorbate and aldarate metabolism | Carbohydrate metabolism | |||||
Valine leucine and isoleucine biosynthesis | Butanoate metabolism | ||||||
Flavonoid biosynthesis | Biosynthesis of other secondary metabolites | Citrate cycle TCA cycle | |||||
Streptomycin biosynthesis | Carbon fixation pathways in prokaryotes | Energy metabolism | |||||
C5 Branched dibasic acid metabolism | Carbohydrate metabolism | Sulfur metabolism | |||||
Pentose phosphate pathway | |||||||
Propanoate metabolism | Fatty acid metabolism | Lipid metabolism | |||||
Starch and sucrose metabolism | |||||||
Methane metabolism | Energy metabolism | Synthesis and degradation of ketone bodies | |||||
Photosynthesis | |||||||
N Glycan biosynthesis | Glycan biosynthesis and metabolism | Folate biosynthesis | Metabolism of cofactors and vitamins | ||||
Other glycan degradation | Lipoic acid metabolism | ||||||
Primary bile acid biosynthesis | Lipid metabolism | ||||||
Secondary bile acid biosynthesis | Ubiquinone and other terpenoid quinone biosynthesis | ||||||
Sphingolipid metabolism | |||||||
Biotin metabolism | Metabolism of cofactors and vitamins | Glutathione metabolism | Metabolism of other amino acids | ||||
Pantothenate and CoA biosynthesis | |||||||
Riboflavin metabolism | Taurine and hypotaurine metabolism | ||||||
Vitamin B6 metabolism | |||||||
Cyanoamino acid metabolism | Metabolism of other amino acids | Biosynthesis of siderophore group nonribosomal peptides | Metabolism of terpenoids and polyketides | ||||
D Alanine metabolism | |||||||
Biosynthesis of vancomycin group antibiotics | Metabolism of terpenoids and polyketides | Aminobenzoate degradation | Xenobiotics biodegradation and metabolism | ||||
Polyketide sugar unit biosynthesis | Benzoate degradation | ||||||
Atrazine degradation | Xenobiotics biodegradation and metabolism | Dioxin degradation | |||||
Protein processing in endoplasmic reticulum | 2 | Folding, sorting and degradation | Ethylbenzene degradation | ||||
RNA degradation | Fluorobenzoate degradation | ||||||
Base excision repair | Replication and repair | Xylene degradation | |||||
Non homologous end joining | Sulfur relay system | 2 | Folding, sorting and degradation | ||||
Basal transcription factors | Transcription | ||||||
Aminoacyl tRNA biosynthesis | Translation | Two component system | 3 | Signal transduction | |||
Insulin signaling pathway | 5 | Endocrine system | Flagellar assembly | 4 | Cell motility | ||
Nucleotide oligomerization domain (NOD) like receptor signaling pathway | Immune system | Peroxisome | Transport and catabolism | ||||
Amoebiasis | 6 | Infectious diseases | Chagas disease American trypanosomiasis | 6 | Infectious diseases | ||
Epithelial cell signaling in Helicobacter pylori infection |
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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. https://doi.org/10.3390/nu9121342
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(12):1342. https://doi.org/10.3390/nu9121342
Chicago/Turabian StyleVernocchi, Pamela, Federica Del Chierico, Andrea Quagliariello, Danilo Ercolini, Vincenzina Lucidi, and Lorenza Putignani. 2017. "A Metagenomic and in Silico Functional Prediction of Gut Microbiota Profiles May Concur in Discovering New Cystic Fibrosis Patient-Targeted Probiotics" Nutrients 9, no. 12: 1342. https://doi.org/10.3390/nu9121342