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

Study information

Needs review

study design

cross-sectional observational, not case-control

Citation

PMID PubMed identifier for scientific articles.

35073343

DOI Digital object identifier for electronic documents.

https://doi.org/10.1371/journal.pone.0262806

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

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Curated date: 2024/03/26

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 media 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 group

Group 1 name Corresponds to the case (exposed) group for case-control studies: patients with otitis media

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: patients suffering from 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: 48

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

Experiment 2

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Curated date: 2024/03/31

Curator: Alcantara.m

Revision editor(s): Alcantara.m

Differences from previous experiment shown

Subjects

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 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)