Altered Middle Ear Microbiome in Children With Chronic Otitis Media With Effusion and Respiratory Illnesses/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Svetlana up on 2024-5-16
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
Reviewed Marked as Reviewed by Svetlana up on 2024-5-16
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
Reviewed Marked as Reviewed by Svetlana up on 2024-5-16
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
