Respiratory Tract Dysbiosis Is Associated with Worse Outcomes in Mechanically Ventilated Patients/Experiment 7

EditHistoryDelete

Flag for review

Your review change was submittedDuplicate this ExperimentAdd a new Signature

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

Curated date: 2023/06/23

Curator: Atrayees

Revision editor(s): Atrayees, 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

Endothelium of trachea Endothelium of windpipe,Trachea endothelium,Windpipe endothelium,Endothelium of trachea,endothelium of trachea

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 stratifications by the number of days patients were ventilator-free

Group 0 sample size Number of subjects in the control (unexposed) group

103

Group 1 sample size Number of subjects in the case (exposed) group

60

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

EditHistoryDelete

Flag for review

Your review change was submitted

Reviewed Marked as Reviewed by Folakunmi on 2024-3-1

Curated date: 2023/06/23

Curator: Atrayees

Revision editor(s): Atrayees, Folakunmi

Source: Figure 4

Description: The relative abundance of individual genera is associated with clinical outcomes and host-response subphenotypes.

Abundance in Group 1: increased abundance in VFD (Ventilator free days)

NCBI	Quality Control	Links
Staphylococcus

Revision editor(s): Atrayees, Folakunmi

Signature 2

EditHistoryDelete

Flag for review

Your review change was submitted

Reviewed Marked as Reviewed by Folakunmi on 2024-3-1

Curated date: 2023/06/23

Curator: Atrayees

Revision editor(s): Atrayees, Folakunmi

Source: Figure 4

Description: The relative abundance of individual genera is associated with clinical outcomes and host-response subphenotypes.

Abundance in Group 1: decreased abundance in VFD (Ventilator free days)

NCBI	Quality Control	Links
Haemophilus
Rothia
Gemella
Streptococcus
Prevotella

Revision editor(s): Atrayees, Folakunmi