Changes in the nasopharyngeal and oropharyngeal microbiota in pediatric obstructive sleep apnea before and after surgery: a prospective study
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Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
Experiment 1
Subjects
- Location of subjects
- China
- 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
- Throat Gula,Throat,throat
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Obstructive sleep apnea Apnea, Obstructive Sleep,apnea, obstructive sleep,Apneas, Obstructive Sleep,Apneas, obstructive sleep,obstructive sleep apnea,Obstructive Sleep Apnea Syndrome,obstructive sleep apnea syndrome,Obstructive Sleep Apneas,obstructive sleep Apneas,Osa,OSAHS,sleep apnea hypopnea syndrome,Sleep Apnea Syndrome, Obstructive,sleep apnea syndrome, obstructive,Sleep Apnea, Obstructive,sleep apnea/hypopnea syndrome,Sleep Apneas, Obstructive,sleep Apneas, obstructive,Syndrome, Obstructive Sleep Apnea,syndrome, obstructive sleep apnea,Syndrome, Sleep Apnea, Obstructive,syndrome, sleep apnea, obstructive,Syndrome, Upper Airway Resistance, Sleep Apnea,syndrome, upper airway resistance, sleep apnea,Upper Airway Resistance Sleep Apnea Syndrome,upper airway resistance sleep apnea syndrome,Obstructive sleep apnea
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Combination of non-OSA group B(surface of palatine tonsil), C (palatine tonsillar capsule after tonsillectomy) and D (adenoid: nasopharynx site)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Non-OSA group A (oropharynx site)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants (children) with obstructive apnea hypopnea index [OAHI] categorized into severity (< 1 events/h) whose sample was obtained from the tongue base (oropharynx site).
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-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).
- relative abundances
- Statistical test
- Kruskall-Wallis
- 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
Signature 1
Source: Figure 5A
Description: Species differentially abundant in non- OSA group A(mucosa of the patient’s tongue base: oropharynx site), B(surface of palatine tonsil), C( palatine tonsillar capsule after tonsillectomy) and D(adenoid :nasopharynx site).
Abundance in Group 1: increased abundance in Non-OSA group A (oropharynx site)
NCBI | Quality Control | Links |
---|---|---|
Veillonella |
Revision editor(s): Tosin
Signature 2
Source: Figure 5A
Description: Species differentially abundant in non- OSA group A(mucosa of the patient’s tongue base: oropharynx site), B(surface of palatine tonsil), C( palatine tonsillar capsule after tonsillectomy) and D(adenoid :nasopharynx site).
Abundance in Group 1: decreased abundance in Non-OSA group A (oropharynx site)
NCBI | Quality Control | Links |
---|---|---|
Fusobacteriia | ||
Treponema |
Revision editor(s): Tosin
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Non Obstructive sleep apnea (OSA)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Obstructive sleep apnea (OSA)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants (Children)with Obstructive sleep apnea categorized into mild OSA (OAHI, 1–5 events/h), moderate OSA (OAHI, 6–10 events/h), and severe OSA (OAHI>10 events/h).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 10
- Group 1 sample size Number of subjects in the case (exposed) group
- 30
Signature 1
Source: Figure 5E
Description: Species differentially abundant in the Obstructive Sleep Apnea (OSA) group and the Non-Obstructive Sleep Apnea group (OSA)
Abundance in Group 1: increased abundance in Obstructive sleep apnea (OSA)
NCBI | Quality Control | Links |
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Alloprevotella |
Revision editor(s): MyleeeA
Signature 2
Source: Figure 5E
Description: Species differentially abundant in the Obstructive Sleep Apnea (OSA) group and the Non-Obstructive Sleep Apnea group (OSA)
Abundance in Group 1: decreased abundance in Obstructive sleep apnea (OSA)
NCBI | Quality Control | Links |
---|---|---|
Neisseria | ||
Haemophilus |
Revision editor(s): MyleeeA
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Combination of Mild OSA group B(surface of palatine tonsil), C(palatine tonsillar capsule after tonsillectomy) and D(adenoid: nasopharynx site)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Mild OSA group A (oropharynx site)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants (children) with obstructive apnea hypopnea index [OAHI] categorized into severity (1–5 events/h) whose sample was obtained from the tongue base (oropharynx site).
- Group 0 sample size Number of subjects in the control (unexposed) group
- Not specified
- Group 1 sample size Number of subjects in the case (exposed) group
- Not specified
Signature 1
Source: Figure 5B
Description: Species differentially abundant in Mild OSA group A(mucosa of the patient’s tongue base: oropharynx site), B(surface of palatine tonsil), C( palatine tonsillar capsule after tonsillectomy) and D(adenoid :nasopharynx site).
Abundance in Group 1: increased abundance in Mild OSA group A (oropharynx site)
NCBI | Quality Control | Links |
---|---|---|
Veillonella |
Revision editor(s): Tosin
Signature 2
Source: Figure 5B
Description: Species differentially abundant in Mild OSA group A(mucosa of the patient’s tongue base: oropharynx site), B(surface of palatine tonsil), C( palatine tonsillar capsule after tonsillectomy) and D(adenoid :nasopharynx site).
Abundance in Group 1: decreased abundance in Mild OSA group A (oropharynx site)
NCBI | Quality Control | Links |
---|---|---|
Fusobacterium | ||
Neisseria | ||
Treponema |
Revision editor(s): Tosin
Experiment 4
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Non-OSA, mild OSA and severe OSA
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Moderate OSA
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants (Children) in the moderate OSA group were categorized based on (OAHI, 6–10 events/h)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 30
- Group 1 sample size Number of subjects in the case (exposed) group
- 10
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 5f
Description: Species differentially abundant in the Moderate Obstructive Sleep Apnea (OSA) group and the None, Mild and Severe Obstructive Sleep Apnea groups (OSA)
Abundance in Group 1: decreased abundance in Moderate OSA
NCBI | Quality Control | Links |
---|---|---|
Haemophilus | ||
Neisseria |
Revision editor(s): MyleeeA
Experiment 5
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Combination of Moderate OSA group B(surface of palatine tonsil), C(palatine tonsillar capsule after tonsillectomy) and D(adenoid: nasopharynx site)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Moderate OSA group A (oropharynx site)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants (children) with obstructive apnea hypopnea index [OAHI] categorized into severity (6–10 events/h) whose sample was obtained from the tongue base (oropharynx site)(Part A).
- Group 0 sample size Number of subjects in the control (unexposed) group
- Not specified
- Group 1 sample size Number of subjects in the case (exposed) group
- Not specified
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 5C
Description: Species differentially abundant in Moderate OSA group A(mucosa of the patient’s tongue base: oropharynx site), B(surface of palatine tonsil), C( palatine tonsillar capsule after tonsillectomy) and D(adenoid :nasopharynx site).
Abundance in Group 1: increased abundance in Moderate OSA group A (oropharynx site)
NCBI | Quality Control | Links |
---|---|---|
Veillonella |
Revision editor(s): Tosin
Experiment 6
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Combination of Severe OSA group B(surface of palatine tonsil), C(palatine tonsillar capsule after tonsillectomy) and D(adenoid: nasopharynx site)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Severe OSA group A (oropharynx site).
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants (children) with obstructive apnea hypopnea index [OAHI], severity > 10 events/h whose sample was obtained from tongue base (oropharynx site)(Part A).
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 5D
Description: Species differentially abundant in Severe OSA group A(mucosa of the patient’s tongue base: oropharynx site), B(surface of palatine tonsil), C( palatine tonsillar capsule after tonsillectomy) and D(adenoid :nasopharynx site).
Abundance in Group 1: increased abundance in Severe OSA group A (oropharynx site).
NCBI | Quality Control | Links |
---|---|---|
Veillonella |
Revision editor(s): Tosin
Signature 2
Source: Figure 5D
Description: Species differentially abundant in Severe OSA group A(mucosa of the patient’s tongue base: oropharynx site), B(surface of palatine tonsil), C( palatine tonsillar capsule after tonsillectomy) and D(adenoid :nasopharynx site).
Abundance in Group 1: decreased abundance in Severe OSA group A (oropharynx site).
NCBI | Quality Control | Links |
---|---|---|
Corynebacterium |
Revision editor(s): Tosin
Experiment 7
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Non OSA group B
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Combination of Mild OSA group B, Moderate OSA group B and Severe OSA group B.
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients in the Mild, Moderate and Severe groups who completed the collection of oral microbiota samples in surface of palatine tonsils (Part B).
Lab analysis
Statistical Analysis
Signature 1
Source: Figure S5B
Description: The differences in the relative abundance of key bacterias among four groups (None, Mild, Moderate, Severe) in surface of palatine tonsils (Part B).
Abundance in Group 1: decreased abundance in Combination of Mild OSA group B, Moderate OSA group B and Severe OSA group B.
NCBI | Quality Control | Links |
---|---|---|
Haemophilus | ||
Neisseria | ||
Treponema |
Revision editor(s): Tosin
Experiment 8
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Non OSA group C
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Combination of Mild OSA group C, Moderate OSA group C and Severe OSA group C.
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients in the Mild, Moderate and Severe groups who completed the collection of oral microbiota samples in palatine tonsillar capsule after tonsillectomy (Part C).
Lab analysis
Statistical Analysis
Signature 1
Source: Figure S5C
Description: The differences in the relative abundance of key bacterias among four groups (None, Mild, Moderate, Severe) in palatine tonsillar capsule after tonsillectomy (Part C).
Abundance in Group 1: decreased abundance in Combination of Mild OSA group C, Moderate OSA group C and Severe OSA group C.
NCBI | Quality Control | Links |
---|---|---|
Prevotella |
Revision editor(s): Tosin
Experiment 9
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Preoperative Severe OSA patients
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Postoperative Severe OSA patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients who completed the collection of oral microbiota samples in tongue base (oropharynx site) after surgery one month after undergoing adeno-tonsillectomy
Lab analysis
Statistical Analysis
- Statistical test
- Mann-Whitney (Wilcoxon)
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Figure 6F
Description: Species differentially abundant in the Preoperative Severe Obstructive Sleep Apnea (OSA) patient and Postoperative Severe Obstructive Sleep Apnea (OSA) patients.
Abundance in Group 1: increased abundance in Postoperative Severe OSA patients
NCBI | Quality Control | Links |
---|---|---|
Porphyromonas | ||
Treponema |
Revision editor(s): MyleeeA
Signature 2
Source: Figure 6F
Description: Species differentially abundant in the Preoperative Severe Obstructive Sleep Apnea (OSA) patient and Postoperative Severe Obstructive Sleep Apnea (OSA) patients.
Abundance in Group 1: decreased abundance in Postoperative Severe OSA patients
NCBI | Quality Control | Links |
---|---|---|
Moraxella |
Revision editor(s): MyleeeA
Experiment 10
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Non Obstructive sleep apnea (OSA)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Obstructive sleep apnea (OSA) Severe
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants (Children) with Obstructive sleep apnea categorized into severe OSA (OAHI>10 events/h).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 10
- Group 1 sample size Number of subjects in the case (exposed) group
- 10
Lab analysis
Statistical Analysis
- Statistical test
- LEfSe
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
Signature 1
Source: Supplementary Figure 7C
Description: Species differentially abundant in the Obstructive sleep apnea (OSA) Severe and None Obstructive sleep apnea (OSA) patients.
Abundance in Group 1: increased abundance in Obstructive sleep apnea (OSA) Severe
Revision editor(s): MyleeeA
Signature 2
Source: Supplementary Figure 7C
Description: Species differentially abundant in the Obstructive sleep apnea (OSA) Severe and None Obstructive sleep apnea (OSA) patients.
Abundance in Group 1: decreased abundance in Obstructive sleep apnea (OSA) Severe
NCBI | Quality Control | Links |
---|---|---|
Eikenella | ||
Lautropia | ||
Moraxella | ||
Rothia | ||
Stomatobaculum |
Revision editor(s): MyleeeA
Experiment 11
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Obstructive sleep apnea (OSA) Mild
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants (children) with obstructive apnea hypopnea index [OAHI] categorized into severity (1–5 events/h).
Lab analysis
Statistical Analysis
Signature 1
Source: Figure S7A
Description: Species differentially abundant in the non-Obstructive sleep apnea (OSA) and Obstructive sleep apnea (OSA) Mild patients.
Abundance in Group 1: increased abundance in Obstructive sleep apnea (OSA) Mild
Revision editor(s): Tosin
Signature 2
Source: Figure S7A
Description: Species differentially abundant in the non-Obstructive sleep apnea (OSA) and Obstructive sleep apnea (OSA) Mild participants.
Abundance in Group 1: decreased abundance in Obstructive sleep apnea (OSA) Mild
Revision editor(s): Tosin
Experiment 12
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Obstructive sleep apnea (OSA) Moderate
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants (children) with obstructive apnea hypopnea index [OAHI] severity 6-10 events/h.
Lab analysis
Statistical Analysis
Signature 1
Source: Figure S7B
Description: Species differentially abundant in the non-Obstructive sleep apnea (OSA) and Obstructive sleep apnea (OSA) Moderate participants.
Abundance in Group 1: increased abundance in Obstructive sleep apnea (OSA) Moderate
Revision editor(s): Tosin
Signature 2
Source: Figure S7B
Description: Species differentially abundant in the non-Obstructive sleep apnea (OSA) and Obstructive sleep apnea (OSA) Moderate participants.
Abundance in Group 1: decreased abundance in Obstructive sleep apnea (OSA) Moderate
Revision editor(s): Tosin
Experiment 13
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Non OSA ( Postoperative)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Mild OSA, Moderate OSA and severe OSA (Postoperative)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients in the Mild, Moderate and Severe groups who completed the collection of oral microbiota samples in tongue base (oropharynx site) one month after undergoing adeno-tonsillectomy.
- Group 0 sample size Number of subjects in the control (unexposed) group
- Not specified
- Group 1 sample size Number of subjects in the case (exposed) group
- Not specified
Lab analysis
Statistical Analysis
- Statistical test
- Kruskall-Wallis
- 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
- Not specified
Signature 1
Source: Figure 6B
Description: Genus abundance of predominant bacteria between the Non-Obstructive sleep apnea (OSA) and Obstructive sleep apnea (OSA) Mild, Moderate and Severe in the postoperative groups.
Abundance in Group 1: increased abundance in Mild OSA, Moderate OSA and severe OSA (Postoperative)
NCBI | Quality Control | Links |
---|---|---|
Neisseria | ||
Veillonella | ||
Prevotella |
Revision editor(s): MyleeeA
Signature 2
Source: Figure 6B
Description: Genus abundance of predominant bacteria between the Non-Obstructive sleep apnea (OSA) and Obstructive sleep apnea (OSA) Mild, Moderate and Severe in the postoperative groups.
Abundance in Group 1: decreased abundance in Mild OSA, Moderate OSA and severe OSA (Postoperative)
NCBI | Quality Control | Links |
---|---|---|
Treponema | ||
Fusobacterium | ||
Streptococcus |
Revision editor(s): MyleeeA