Altered Middle Ear Microbiome in Children With Chronic Otitis Media With Effusion and Respiratory Illnesses

Study information

Reviewed Marked as Reviewed by Svetlana up on 2024-5-16

study design

cross-sectional observational, not case-control

Citation

PMID PubMed identifier for scientific articles.

31637220

DOI Digital object identifier for electronic documents.

10.3389/fcimb.2019.00339

URI

Authors

Kolbe AR, Castro-Nallar E, Preciado D, Pérez-Losada M

Journal

Frontiers in cellular and infection microbiology

Year

2019

Keywords:

amplicon sequence variants, asthma, bronchiolitis, middle ear microbiome, otitis media

Chronic otitis media with effusion (COME) is a common childhood disease characterized by an accumulation of fluid behind the eardrum. COME often requires surgical intervention and can also lead to significant hearing loss and subsequent learning disabilities. Recent characterization of the middle ear fluid (MEF) microbiome in pediatric patients has led to an improved understanding of the microbiota present in the middle ear during COME. However, it is not currently known how the MEF microbiome might vary due to other conditions, particularly respiratory disorders. Here, we apply an amplicon sequence variant (ASV) pipeline to MEF 16S rRNA high-throughput sequencing data from 50 children with COME (ages 3-176 months) undergoing tube placement. We achieve a more detailed taxonomic resolution than previously reported, including species and genus level resolution. Additionally, we provide the first report of the functional roles of the MEF microbiome and demonstrate that despite high taxonomic diversity, the functional capacity of the MEF microbiome remains uniform between patients. Furthermore, we analyze microbiome differences between children with COME with and without a history of lower airway disease (i.e., asthma or bronchiolitis). The MEF microbiome was less diverse in participants with lower airway disease than in patients without, and phylogenetic β-diversity (weighted UniFrac) was significantly different based on lower airway disease status. Differential abundance between patients with lower airway disease and those without was observed for the genera Haemophilus, Moraxella, Staphylococcus, Alloiococcus, and Turicella. These findings support previous suggestions of a link between COME and respiratory illnesses and emphasize the need for future study of the middle ear and respiratory tract microbiomes in diseases such as asthma and bronchiolitis.

Experiment 1

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Reviewed Marked as Reviewed by Svetlana up on 2024-5-16

Curated date: 2024/05/06

Curator: Scholastica

Revision editor(s): Scholastica, WikiWorks

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: Middle ear Auris media,Middle ear,middle ear

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

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Chronic Otitis Media With Effusion (COME) without asthma or bronchiolitis

Group 1 name Corresponds to the case (exposed) group for case-control studies: Chronic Otitis Media With Effusion (COME) with asthma or bronchiolitis

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Children from 3 to 176 months of age, with Chronic Otitis Media With Effusion (COME) with a history of lower airway disease (i.e., asthma or bronchiolitis), defined by a history of pulmonary physician-diagnosed asthma; documented chronic wheezing being treated with a daily respiratory inhaler; or PCR (+) for rhinovirus bronchiolitis diagnosis.

Group 0 sample size Number of subjects in the control (unexposed) group: 37

Group 1 sample size Number of subjects in the case (exposed) group: 13

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): 2 weeks

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).: raw counts

Statistical test: DESeq2

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

Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment: age, sex, Confounders controlled for: "significant hearing loss" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.significant hearing loss, Confounders controlled for: "mucoid/serous effusion" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.mucoid/serous effusion, Confounders controlled for: "presence of Muc5B and/or Muc5AC" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.presence of Muc5B and/or Muc5AC

Alpha Diversity

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

Richness Number of species: decreased

Signature 1

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Source: Figure 5

Description: Differentially abundant genera/species (p-adjusted < 0.05) in middle ear fluid (MEF) of patients with lower airway disease diagnosis (i.e., asthma or bronchiolitis) compared to those without.

Abundance in Group 1: increased abundance in Chronic Otitis Media With Effusion (COME) with asthma or bronchiolitis

NCBI	Quality Control	Links
Haemophilus
Staphylococcus
Moraxella

Revision editor(s): Scholastica, WikiWorks

Signature 2

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Reviewed Marked as Reviewed by Svetlana up on 2024-5-16

Curated date: 2024/05/06

Curator: Scholastica

Revision editor(s): Scholastica, WikiWorks

Source: Figure 5

Description: Differentially abundant genera/species (p-adjusted < 0.05) in middle ear fluid (MEF) of patients with lower airway disease diagnosis (i.e., asthma or bronchiolitis) compared to those without.

Abundance in Group 1: decreased abundance in Chronic Otitis Media With Effusion (COME) with asthma or bronchiolitis

NCBI	Quality Control	Links
Alloiococcus otitis
Corynebacterium otitidis

Revision editor(s): Scholastica, WikiWorks