Respiratory Tract Dysbiosis Is Associated with Worse Outcomes in Mechanically Ventilated Patients/Experiment 2
From BugSigDB
Reviewed Marked as Reviewed by Folakunmi on 2024-3-4
Subjects
- Location of subjects
- United States of America
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Homo sapiens
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Epithelium of oropharynx Oropharyngeal epithelium,Oropharynx epithelial tissue,Oropharynx epithelium,Epithelium of oropharynx,epithelium of oropharynx
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Acute respiratory failure acute respiratory failure,respiratory failure, acute,Acute respiratory failure
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Hyper-inflammatory subphenotype and mortality
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- VFD (Ventilator free days)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Clinical outcome stratification by numbers of ventilator-free days (VFDs) at 30 days in patients for whom respiratory specimen cultures were reported as negative (no growth or only normal respiratory flora detected, n=152) as well as those for whom no cultures were obtained (n=76)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 228
- Group 1 sample size Number of subjects in the case (exposed) group
- 228
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- none
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V4
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- Logistic Regression
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, chronic obstructive pulmonary disease, antibiotic exposure
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2024-3-2
Source: Supplementary figure E8
Description: Relative abundance of individual genera in Endotracheal aspirate (ETA) genera is associated with clinical outcomes and host-response subphenotypes in patients without positive respiratory cultures.
Abundance in Group 1: increased abundance in VFD (Ventilator free days)
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotella | ||
| Streptococcus | ||
| Veillonella | ||
| Rothia | ||
| Granulicatella | ||
| unclassified Pasteurellaceae |
Signature 2
Reviewed Marked as Reviewed by Folakunmi on 2024-3-2
Source: Supplementary figure E8
Description: Relative abundance of individual genera in Endotracheal aspirate (ETA) genera is associated with clinical outcomes and host-response subphenotypes in patients without positive respiratory cultures.
Abundance in Group 1: decreased abundance in VFD (Ventilator free days)
| NCBI | Quality Control | Links |
|---|---|---|
| Staphylococcus |
