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Dataset results
30 results for “Respiratory microbiome”
Lung microbiome in children with hematological malignancies and lower respiratory tract infections
<p><strong>Background</strong>: Respiratory infectious complications remain a major cause of morbidity and mortality in children with hematological malignancies. Knowledge regarding the lung microbiome in the aforementioned children is limited.</p> <p><strong>Methods</strong>: A prospective cohort was conducted, enrolling 16 children with hematological malignancies complicated with moderate to severe lower respiratory tract infections(LRTIs), versus 21 LRTIs children with age, gender, weight, infection severity matched, with no underlying malignancies, to evaluate the lung microbiome from bronchoalveolar lavage fluid samples in different groups.</p> <p><strong>Results</strong>: Lung microbiome from children with hematological malignancies and LRTIs showed obviously decreased α and β diversity, increased microbial function in infectious disease:bacteria/parasite, drug resistance:antimicrobial and human pathogenesis than the control group, and significantly reduced proportion of <em>Firmicutes</em>, <em>Bacteroidota</em>, <em>Actinobacteriota</em> , increased <em>Proteobacteria</em> at the phylum level, distinctly elevated <em>Parabacteroides</em>, <em>Klebsiella</em>, <em>Grimontia</em>, <em>Escherichia_Shigella</em>, <em>unclassified_Enterobacteriaceae</em> at the genus level than the control group. Besides, it was revealed that α diversity (Shannon), β diversity (Bray Curtis dissimilarity), Proteobacteria at the phylum level, and <em>unclassified_Enterobacteriaceae</em> and <em>Escherichia_Shigella</em> at the genus level were significantly negatively associated with hospitalization course, whereas <em>Firmicutes</em> at the phylum level was established positively correlated with hospitalization course.</p> <p><strong>Conclusions</strong>: Children with hematological malignancies and LRTIs showed obviously decreased α and β diversity, significantly increased function in infectious disease pathogenesis, antimicrobial drug resistance, and unfavorable environment tolerance. Besides, α diversity (Shannon), β diversity (Bray Curtis dissimilarity), <em>Proteobacteria</em> may be used as negatively correlated predictors for hospitalization course in these children whereas <em>Firmicutes</em> is a positively correlated predictor. </p>
Meta-analysis of the human upper respiratory tract microbiome reveals robust taxonomic associations with health and disease.
<p>Contains all intermediate data files for the article <strong>Meta-analysis of the human upper respiratory tract microbiome reveals robust taxonomic associations with health and disease, </strong>Quinn-Bohmann et al. 2024. </p> <p>NP and OP refers to nasopharyngeal or oropharyngeal samples, respectively. As some study identifiers are duplicated across these groups, qiime_NP and qiime_OP should be unzipped in distinct directories. The same applies for metadata data files. </p> <p>Analyses of these data can be found at https://github.com/Gibbons-Lab/2023_URTmetaanalysis/tree/main. </p>
Antibiotic resistance alters the ability of Pseudomonas aeruginosa to invade the respiratory microbiome
<p>Sequencing data for spontaneous resistant mutants of <em>Pseudomonas aeruginosa </em>PAO1-GFP generated for the preprinted project "Antibiotic resistance alters the ability of Pseudomonas aeruginosa to invade the respiratory microbiome". A total of nine resistant mutants selected on the clinical breakpoint concentrations for meropenem, ciprofloxacin and ceftazidime were sequenced, along with the ancestral GFP-tagged PAO1 background strain (PAO1-GFP). Libraries were sequenced using the Illumina NovaSeq6000 platform using a 250bp paired-end protocol (via microbesNG), submitted for x60 depth sequencing.<br>Preprint for this project found here: https://www.biorxiv.org/content/10.1101/2023.11.14.567137v1</p>
Lung microbiome in children with hematological malignancies and lower respiratory tract infections
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Data from: Nasopharyngeal microbiome profiles in rural Venezuelan children are associated with respiratory and gastrointestinal infections
<p>Background: Recent research suggests that the microbiota affects susceptibility to both respiratory tract infections (RTIs) and gastrointestinal infections (GIIs). In order to optimize global treatment options, it is important to characterize microbiota profiles across different niches and geographic/socioeconomic areas where RTI and GII prevalences are high.</p> <p>Methods: We performed 16S sequencing of nasopharyngeal swabs from 209 Venezuelan Amerindian children aged 6 weeks–59 months who were participating in a 13-valent pneumococcal conjugate vaccine (PCV13) study. Using random forest models, differential abundance testing, and regression analysis, we determined whether specific bacteria were associated with RTIs or GIIs and variation in PCV13 response.</p> <p>Results: Microbiota compositions differed between children with or without RTIs (P = .018) or GIIs (P = .001). Several species were associated with the absence of infections. Some of these health-associated bacteria are also observed in developed regions, such as Corynebacterium (log2(fold change [FC]) = 3.30 for RTIs and log2(FC) = 1.71 for GIIs), while others are not commonly observed in developed regions, such as Acinetobacter (log2(FC) = 2.82 and log2(FC) = 5.06, respectively). Klebsiella spp. presence was associ- ated with both RTIs (log2(FC) = 5.48) and GIIs (log2(FC) = 7.20).</p> <p>Conclusions: The nasopharyngeal microbiota of rural Venezuelan children included several bacteria that thrive in tropical humid climates. Interestingly, nasopharyngeal microbiota composition not only differed in children with an RTI but also in those with a GII, which suggests a reciprocal interplay between the 2 environments. Knowledge of region-specific microbiota patterns enables tailoring of preventive and therapeutic approaches.</p>
Respiratory Microbiome in COPD and Associated Inmune Response.
ClinicalTrials.gov study NCT03321708. IPD Sharing: UNDECIDED. Countries: 1. Publications: 10.
Dynamics of the Upper and Lower Airway Respiratory Microbiomes Associated With Severe Infant Asthma
ClinicalTrials.gov study NCT06044051. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Clinical Significance of Community-acquired Respiratory Virus Infection and Longitudinal Analysis of the Lung Microbiome in Lung Transplantation
ClinicalTrials.gov study NCT03545919. IPD Sharing: UNDECIDED. Countries: 1. Publications: 8.
Data from: Nasopharyngeal microbiome profiles in rural Venezuelan children are associated with respiratory and gastrointestinal infections
Open the record for dataset details and reuse information.
Effects of Interleukin (IL)- 4R-alpha Inhibition on Respiratory Microbiome and Immunologic Correlates in Severe Asthma
ClinicalTrials.gov study NCT05036733. IPD Sharing: NO. Countries: 1. Publications: 0.
Evaluation the Association of Microbiome Between Respiratory Tract Samples and Stool Samples in Pneumonic Patients Accompanied by Respiratory Failure
ClinicalTrials.gov study NCT03379779. IPD Sharing: YES. Countries: 1. Publications: 0.
MOdification Of THe Early-Life Respiratory Microbiome Through Vaginal SEEDing
ClinicalTrials.gov study NCT05505110. IPD Sharing: YES. Countries: 1. Publications: 0.
Leveraging the pulmonary immune response and microbiome for improved lower respiratory tract infection diagnosis in critically ill children
GEO Series GSE212532. Homo sapiens. 261 samples. Type: Expression profiling by high throughput sequencing; Other.
Characterization of antibiotic resistance and host-microbiome interactions in the human upper respiratory tract during influenza infection [16s rRNA gene V4 region]
GEO Series GSE126900. human metagenome. 34 samples. Type: Other.
Characterization of antibiotic resistance and host-microbiome interactions in the human upper respiratory tract during influenza infection [human host RNA-seq]
GEO Series GSE114588. Homo sapiens. 56 samples. Type: Expression profiling by high throughput sequencing.
Characterization of antibiotic resistance and host-microbiome interactions in the human upper respiratory tract during influenza infection [RNA-Seq]
GEO Series GSE126901. human metagenome. 35 samples. Type: Expression profiling by high throughput sequencing.
Probiotics, Respiratory and Intestinal Microbiome and Respiratory Tract Infections in Children
ClinicalTrials.gov study NCT03683927. IPD Sharing: NO. Countries: 1. Publications: 0.
Respiratory Microbiome and COPD Exacerbations (RESMECOPD)
ClinicalTrials.gov study NCT03432234. IPD Sharing: UNDECIDED. Countries: 1. Publications: 0.
Shifts in the Respiratory Microbiome and Clinical Outcomes of SARS-CoV-2
ClinicalTrials.gov study NCT04815018. IPD Sharing: NO. Countries: 1. Publications: 0.
Definition of Sub-phenotypes of Pneumonia Based on the Respiratory Microbiome Composition to Predict Microbial and Clinical Treatment Failures
ClinicalTrials.gov study NCT06916481. IPD Sharing: Not stated. Countries: 1. Publications: 0.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.