Resilience of the respiratory microbiome in controlled adult RSV challenge study/Experiment 1

EditHistoryDelete

Mark reviewed

Your review change was submittedDuplicate this ExperimentAdd a new Signature

Needs review

Curated date: 2024/03/10

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Subjects

Location of subjects

United Kingdom

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

Throat , Nasal cavity Gula,Throat,throat,Cavitas nasalis,Cavitas nasi,Cavity of nose,Cavity of olfactory apparatus,Cavum nasi,Nasal canal,Nasal conduit space,Nasal fossa,Nasal pit,Olfactory cavity,Olfactory chamber,Olfactory chamber cavity,Olfactory pit,Nasal cavity,nasal cavity

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology

Respiratory Syncytial Virus Infection Human respiratory syncytial virus infection,infections, Human respiratory syncytial virus,respiratory syncytial virus infection,respiratory syncytial virus infectious disease,Respiratory Syncytial Virus Infection,respiratory Syncytial Virus Infection

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

Healthy non-smoking adults

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

Healthy non-smoking adults between 18 and 50 years of age.

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

37

Lab analysis

Sequencing type

16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene

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

DESeq2

Mann-Whitney (Wilcoxon)

PERMANOVA

ANOVA

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

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness

unchanged

Simpson Estimator of species richness and species evenness: more weight on species evenness

unchanged

Richness Number of species

unchanged