The adult microbiome of healthy and otitis patients: Definition of the core healthy and diseased ear microbiomes/Experiment 3
From BugSigDB
Reviewed Marked as Reviewed by Svetlana up on 2024-7-15
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
- Ear Auditory apparatus,Auris,Ear,ear
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Otitis externa , Otitis media external Ear infection,infectious otitis externa,otitis externa,outer Ear infection,swimmer's Ear,swimmer's ear,Otitis externa,inflammation of middle ear,medial otitis,middle Ear Inflammation,middle ear inflammation,otitis Media,otitis media,otitis media (disease),Otitis media
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy and Otitis externa
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Otitis media
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Adults patients affected by otitis media (OM)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 114
- Group 1 sample size Number of subjects in the case (exposed) group
- 48
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Patients receiving any antimicrobial treatment at time of sample collection
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V1-V3
- 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)?
- Yes
- 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
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-7-15
Source: Fig. 3A
Description: Taxa significantly different in healthy and otitis externa (OE) versus otitis media (OM) groups at the phylum to genus level for bacteria.
Abundance in Group 1: increased abundance in Otitis media
| NCBI | Quality Control | Links |
|---|---|---|
| Enterococcaceae | ||
| Peptoniphilaceae | ||
| Tissierellales | ||
| Tissierellia | ||
| Alcaligenaceae | ||
| Campylobacteraceae | ||
| Campylobacterales | ||
| Epsilonproteobacteria | ||
| Yersiniaceae |
Revision editor(s): Scholastica
