The adult microbiome of healthy and otitis patients: Definition of the core healthy and diseased ear microbiomes/Experiment 2

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Curated date: 2024/03/31

Curator: Alcantara.m

Revision editor(s): Alcantara.m

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

Inner ear canal Inner ear canal,inner ear canal

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

Otitis externa external Ear infection,infectious otitis externa,otitis externa,outer Ear infection,swimmer's Ear,swimmer's ear,Otitis externa

Group 0 name Corresponds to the control (unexposed) group for case-control studies

healthy group

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

patients with otitis externa

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

patients suffering from otitis externa (OE)

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

92

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

44

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)

N/A

Lab analysis

Sequencing type

ITS / ITS2

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

Not specified

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

LEfSe

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)?

No

LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool

2

Alpha Diversity

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

unchanged

Richness Number of species

unchanged