Respiratory Tract Dysbiosis Is Associated with Worse Outcomes in Mechanically Ventilated Patients/Experiment 12

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Reviewed Marked as Reviewed by Folakunmi on 2024-3-5

Curated date: 2024/03/05

Curator: Folakunmi

Revision editor(s): Folakunmi

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

VFD (Ventilator free days) and mortality

Group 1 name Corresponds to the case (exposed) group for case-control studies

Hyper-inflammatory subphenotype

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

participants who were classified into a hyperinflammatory subphenotype of host responses, 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

increased