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16 results for “respiratory microbiota”
Uncover a microbiota signature of upper respiratory tract in patients with SARS-CoV-2+
<p>This is the repository containing the code used to obtain the results shown in <a href="https://doi.org/10.1038/s41598-023-43040-x"><i><strong>Bellato M, Cappellato M, Longhin F, Del Vecchio C, Brancaccio G, Cattelan AM, Brun P, Salaris C, Castagliuolo I, Di Camillo B. "Uncover a microbiota signature of upper respiratory tract in patients with SARS-CoV-2+" Sci Rep 13, 16867 (2023)</strong></i></a>.</p><p>We characterized through 16S rDNA-seq the microbiota in the upper airways of 192 subjects with a positive nasopharyngeal swab for SARS-CoV-2 to identify a microbial signature predictive of disease progression. Patients were divided in groups based on the presence of symptoms, the level of pneumonia, and whether or not they needed oxygen therapy or intubation. </p><p>In the GitLab repository <a href="https://gitlab.com/sysbiobig/microbiomecovid/-/tree/v1.0">here</a> there are all the scripts used to perform the preprocessing step and the downstream analysis. The GitLab repository (version 1.0) contains also the Docker image <strong>microbiomecovid:1.0.0</strong> that can be used to reproduce the results shown in the paper (see the instruction <a href="https://gitlab.com/sysbiobig/microbiomecovid/-/tree/v1.0#reproduce-the-results-%EF%B8%8F">here</a>).</p><p>Here in Zenodo you can find the <strong>microbiomecovid_data.zip </strong>file containing two folders that need to be unzipped and put in the <i>microbiomecovid</i> local repository, downloaded from GitLab.</p><p>In particular, the <i><strong>original_data</strong></i> folder contains:</p><ul><li><i><strong>Raw_data</strong></i><strong>: </strong>a folder with two FASTQ files for each sample, i.e., forward (R1) and reverse (R2) reads.</li><li><strong>Metadata.xlsx: </strong>the table containing information on the - anonymized - subjects involved in the study.</li><li><strong>QC Report.pdf: </strong>The report provided by the sequencing center.</li></ul><p>Additionally, in the <i><strong>output</strong></i><strong> </strong>folder, the following items can be found:</p><ul><li><i><strong>Preprocessing</strong></i><strong>: </strong>a folder containing all the output file from step1 to step7, namely:<ul><li>create input data for QIIME2;</li><li>import data in QIIME2;</li><li>remove primers;</li><li>denoising and imputation;</li><li>taxonomy classification;</li><li>phylogenetic tree reconstruction;</li><li>collapse at specific taxonomic level and normalize data.</li></ul></li><li><i><strong>Analysis</strong></i><strong>: </strong>a folder containing all the output files form step8 to step10 namely:<ul><li>alpha and beta diversity results;</li><li><i><strong>DA_output</strong></i><strong>:</strong> a folder containing the differential abundance analysis performed for each taxonomic level and for each covariate;</li><li><i><strong>Network_output:</strong></i> a folder containing the sparCC and Cytoscape networks and results.</li></ul></li></ul><p>For more info about all the bioinformatic pipeline see the <a href="https://gitlab.com/sysbiobig/microbiomecovid/-/tree/v1.0#pipeline">GitLab repository</a><strong>.</strong></p><p>Remember to set the path as <i>ABSOLUTE_PATH_MICROBIOMECOVID.</i></p>
Microbiota Upper Respiratory Tract
ClinicalTrials.gov study NCT02933983. IPD Sharing: NO. Countries: 1. Publications: 1.
Lum-Iva-biota: Exploring the Respiratory Mycobiota and Microbiota Profile in French CF Patients Taking Lumacaftor-Ivacaftor
ClinicalTrials.gov study NCT03565692. IPD Sharing: NO. Countries: 1. Publications: 1.
Modulation of Gut Microbiota by Probiotic in Children With Respiratory Symptoms
ClinicalTrials.gov study NCT05794815. IPD Sharing: NO. Countries: 1. Publications: 2.
Nasopharyngeal microbiota, host transcriptome and disease severity in children with respiratory syncytial virus infection
GEO Series GSE77087. Homo sapiens. 104 samples. Type: Expression profiling by array.
Respiratory Microbiota and Immune Response in CVID
ClinicalTrials.gov study NCT06173128. IPD Sharing: UNDECIDED. Countries: 1. Publications: 0.
Clinical Course and Changes in the Respiratory Microbiota Based on Antibiotic Treatment in Patients With Cystic Fibrosis
ClinicalTrials.gov study NCT01693965. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Microbiota of the Respiratory Flora in Children With Cystic Fibrosis During the First Year of Life
ClinicalTrials.gov study NCT00977158. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Integrated Study on Gut Microbiota, Immune Indicators, and Trace Elements in Children With Respiratory Tract Infections
ClinicalTrials.gov study NCT07378852. IPD Sharing: NO. Countries: 2. Publications: 0.
Variations in the Composition of Respiratory Microbiota
ClinicalTrials.gov study NCT04747184. IPD Sharing: UNDECIDED. Countries: 1. Publications: 0.
Characterization of Respiratory Microbiota in Susceptibility to Viral Respiratory Infections
ClinicalTrials.gov study NCT03600753. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Airway microbiota in patients with synchronous multiple primary lung cancer: the bacterial topography of the respiratory tract
GEO Series GSE200111. human lung metagenome. 39 samples. Type: Other.
Respiratory Microbiota, Infection Characteristics and Imaging Manifestations in Patients With Chronic Airway Inflammation
ClinicalTrials.gov study NCT06938022. IPD Sharing: NO. Countries: 0. Publications: 0.
Effects of rTMS on Respiratory Function and Gut Microbiota in Patients With Brain Injury
ClinicalTrials.gov study NCT06288984. IPD Sharing: NO. Countries: 0. Publications: 0.
Analysis of Nasopharyngeal Microbiota in Patients With Respiratory Infections
ClinicalTrials.gov study NCT06556420. IPD Sharing: Not stated. Countries: 0. Publications: 0.
Distinct patterns of metagenomic surveillance and respiratory microbiota between two P1 genotypes of Mycoplasma pneumoniae
GEO Series GSE274269. Homo sapiens. 174 samples. Type: Expression profiling by high throughput sequencing.
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