The adult microbiome of healthy and otitis patients: Definition of the core healthy and diseased ear microbiomes
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Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Burton M, Krumbeck JA, Wu G, Tang S, Prem A, Gupta AK, Dawson TL
Journal
PloS one
Year
2022
Otitis media (OM) and externa (OE) are painful, recurrent ear conditions. As most otitis publications focus on the bacterial content of childhood ears, there remains a dearth of information regarding the adult ear microbiome including both bacteria and fungi. This study compares the outer ear microbiome of healthy adults to adults affected by OE and OM using both intergenic-transcribed-spacer (ITS) and 16S-rDNA sequencing. The adult ear core microbiome consists of the prokaryote Cutibacterium acnes and the eukaryotic Malassezia arunalokei, M. globosa, and M. restricta. The healthy ear mycobiome is dominated by Malassezia and can be divided into two groups, one dominated by M. arunalokei, the other by M. restricta. Microbiome diversity and biomass varied significantly between healthy and diseased ears, and analyses reveal the presence of a potential mutualistic, protective effect of Malassezia species and C. acnes. The healthy ear core microbiome includes the bacteria Staphylococcus capitis and S. capitis/caprae, while the diseased ear core is composed of known bacterial and fungal pathogens including Aspergillus sp., Candida sp., Pseudomonas aeruginosa, S. aureus, and Corynebacterium jeikeium. The data presented highlight the need for early detection of the cause of otitis to direct more appropriate, efficient treatments. This will improve patient outcomes and promote improved antimicrobial stewardship.
Experiment 1
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 media , Otitis externa inflammation of middle ear,medial otitis,middle Ear Inflammation,middle ear inflammation,otitis Media,otitis media,otitis media (disease),Otitis media,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
- Otitis media and otitis externa
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Adults patients affected by otitis externa (OE) and otitis media (OM)
- 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
- 70
- 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 versus otitis externa (OE) and otitis media (OM) groups at the phylum to genus level for bacteria.
Abundance in Group 1: decreased abundance in Otitis media and otitis externa
| NCBI | Quality Control | Links |
|---|---|---|
| Propionibacteriaceae | ||
| Propionibacteriales | ||
| Actinomycetota | ||
| Staphylococcaceae | ||
| Bacillales | ||
| Carnobacteriaceae | ||
| Bacilli |
Revision editor(s): Scholastica
Experiment 2
Reviewed Marked as Reviewed by Svetlana up on 2024-7-15
Differences from previous experiment shown
Subjects
- 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 media
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Otitis externa
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Adults patients affected by otitis externa (OE)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 140
- Group 1 sample size Number of subjects in the case (exposed) group
- 22
Lab analysis
Statistical Analysis
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 media (OM) versus otitis externa (OE) groups at the phylum to genus level for bacteria.
Abundance in Group 1: increased abundance in Otitis externa
| NCBI | Quality Control | Links |
|---|---|---|
| Chroococcidiopsidaceae | ||
| Chroococcidiopsidales | ||
| Enterobacteriaceae | ||
| Enterobacterales | ||
| Pseudomonadaceae | ||
| Pseudomonadales | ||
| Gammaproteobacteria | ||
| OtherOther |
Revision editor(s): Scholastica
Experiment 3
Reviewed Marked as Reviewed by Svetlana up on 2024-7-15
Differences from previous experiment shown
Subjects
- 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
Lab analysis
Statistical Analysis
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
Experiment 4
Reviewed Marked as Reviewed by Svetlana up on 2024-7-15
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Otitis media , Otitis externa inflammation of middle ear,medial otitis,middle Ear Inflammation,middle ear inflammation,otitis Media,otitis media,otitis media (disease),Otitis media,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
- Otitis media and otitis externa
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Adults patients affected by otitis externa (OE) and otitis media (OM)
- 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
- 70
Lab analysis
- Sequencing type
- ITS / ITS2
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Richness Number of species
- increased
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-7-15
Source: Fig. 3B
Description: Taxa significantly different in healthy versus otitis externa (OE) and otitis media (OM) groups at the phylum to genus level for fungi.
Abundance in Group 1: decreased abundance in Otitis media and otitis externa
| NCBI | Quality Control | Links |
|---|---|---|
| Malasseziales | ||
| Malasseziomycetes | ||
| Malasseziaceae |
Revision editor(s): Scholastica
Experiment 5
Reviewed Marked as Reviewed by Svetlana up on 2024-7-15
Differences from previous experiment shown
Subjects
- 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 media
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Otitis externa
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Adults patients affected by otitis externa (OE)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 140
- Group 1 sample size Number of subjects in the case (exposed) group
- 22
Lab analysis
Statistical Analysis
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-7-15
Source: Fig. 3B
Description: Taxa significantly different in healthy and otitis media (OM) versus otitis externa (OE) groups at the phylum to genus level for fungi.
Abundance in Group 1: increased abundance in Otitis externa
| NCBI | Quality Control | Links |
|---|---|---|
| Aspergillaceae | ||
| Eurotiales | ||
| Eurotiomycetes | ||
| Sordariomycetes | ||
| Hymenochaetales | ||
| Polyporales | ||
| Agaricomycetes | ||
| Tremellales | ||
| Tremellomycetes |
Revision editor(s): Scholastica
Experiment 6
Reviewed Marked as Reviewed by Svetlana up on 2024-7-15
Differences from previous experiment shown
Subjects
- 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
Lab analysis
Statistical Analysis
Alpha Diversity
- Richness Number of species
- increased
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-7-15
Source: Fig. 3B
Description: Taxa significantly different in healthy and otitis externa (OE) versus otitis media (OM) groups at the phylum to genus level for fungi.
Abundance in Group 1: increased abundance in Otitis media
| NCBI | Quality Control | Links |
|---|---|---|
| Dothideomycetes | ||
| Debaryomycetaceae | ||
| Saccharomycetales | ||
| Saccharomycetes | ||
| Stereaceae | ||
| Russulales | ||
| Cystofilobasidiales | ||
| Filobasidiaceae |
Revision editor(s): Scholastica
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