Changes in the nasopharyngeal and oropharyngeal microbiota in pediatric obstructive sleep apnea before and after surgery: a prospective study

Study information

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study design

prospective cohort

Citation

PMID PubMed identifier for scientific articles.

38459431

DOI Digital object identifier for electronic documents.

10.1186/s12866-024-03230-7

URI

Authors

Fang L, Tuohuti A, Cai W, Chen X

Journal

BMC microbiology

Year

2024

Keywords:

16S rRNA sequencing, Biomarker, Microbiome, Pediatric OSA, Upper airway

OBJECTIVE: To explore the changes and potential mechanisms of microbiome in different parts of the upper airway in the development of pediatric OSA and observe the impact of surgical intervention on oral microbiome for pediatric OSA. METHODS: Before adeno-tonsillectomy, we collected throat swab samples from different parts of the oropharynx and nasopharynx of 30 OSA patients and 10 non-OSA patients and collected throat swab samples from the oropharynx of the above patients one month after the adeno-tonsillectomy. The 16 S rRNA V3-V4 region was sequenced to identify the microbial communities. The correlation analysis was conducted based on clinical characteristics. RESULTS: There was a significant difference of alpha diversity in different parts of the upper airway of pediatric OSA, but this difference was not found in children with non-OSA. Beta diversity was significantly different between non-OSA and pediatric OSA. At the genus level, the composition of flora in different parts is different between non-OSA and pediatric OSA. The correlation analysis revealed that the relative abundance of Neisseria was significantly correlated with obstructive apnea hypopnea index. Furthermore, the functional prediction revealed that pathways related to cell proliferation and material metabolism were significantly different between non-OSA and pediatric OSA. Besides, the adeno-tonsillectomy has minimal impact on oral microbiota composition in short term. CONCLUSION: The changes in upper airway microbiome are highly associated with pediatric OSA. The relative abundance of some bacteria was significantly different between OSA and non-OSA. These bacteria have the potential to become new diagnostic and early warning biomarkers.

Experiment 1

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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

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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)

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Veillonella

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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)

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Fusobacteriia
Treponema

Revision editor(s): Tosin

Experiment 2

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Differences from previous experiment shown

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

Lab analysis

Statistical Analysis

Statistical test

Mann-Whitney (Wilcoxon)

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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)

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Alloprevotella

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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)

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Neisseria
Haemophilus

Revision editor(s): MyleeeA

Experiment 3

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Differences from previous experiment shown

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

Lab analysis

Statistical Analysis

Statistical test

Kruskall-Wallis

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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)

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Veillonella
Neisseria

Revision editor(s): Tosin, Aleru Divine

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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)

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Fusobacterium
Treponema

Revision editor(s): Tosin, Aleru Divine

Experiment 4

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Differences from previous experiment shown

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

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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

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Haemophilus
Neisseria

Revision editor(s): MyleeeA

Experiment 5

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Differences from previous experiment shown

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

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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)

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Veillonella

Revision editor(s): Tosin

Experiment 6

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Differences from previous experiment shown

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

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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).

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Veillonella

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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).

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Corynebacterium

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Experiment 7

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Differences from previous experiment shown

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

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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.

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Haemophilus
Neisseria
Treponema

Revision editor(s): Tosin

Experiment 8

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Differences from previous experiment shown

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

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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.

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Prevotella

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Experiment 9

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Differences from previous experiment shown

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

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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

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Porphyromonas
Treponema

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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

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Moraxella

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Experiment 10

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Differences from previous experiment shown

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

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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

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Acetobacteraceae
Alcanivoracaceae
Alcanivorax
Alicyclobacillaceae
Arcicella
Brachybacterium
Brucellaceae
Corynebacteriaceae
Corynebacterium
Dermabacteraceae
Devosia
Hydrogenophaga
Legionella
Legionellaceae
Legionellales
Mollicutes
Mycoplasma
Mycoplasmataceae
Mycoplasmatales
Mycoplasmatota
Opitutaceae
Opitutales
Opitutus
Ornithinimicrobium
Pseudochrobactrum
Pseudoxanthomonas
Rhodocista
Slackia
Variovorax
Verrucomicrobiota

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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

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Eikenella
Lautropia
Moraxella
Rothia
Stomatobaculum

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Experiment 11

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Differences from previous experiment shown

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

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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

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Altererythrobacter
Desulfovibrio
Anaerococcus
Bulleidia
Curvibacter
Deltaproteobacteria
Desulfovibrionaceae
Desulfovibrionales
Eikenella
Erythrobacteraceae
Filifactor
Nocardioidaceae
Nocardioides
Novosphingobium
Proteus
Schwartzia
Chromatiaceae
Chromatiales
Alloprevotella
Rheinheimera
Spirochaetales
Spirochaetia
Spirochaetota
Spirochaetaceae
Treponema

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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

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Pseudomonadota
Pasteurellaceae
Pasteurellales
Haemophilus
Betaproteobacteria
Neisseriales
Neisseria
Neisseriaceae
Gammaproteobacteria
Bacilli
Lactobacillales
Streptococcus
Streptococcaceae
Actinomycetales
Rothia
Micrococcaceae
Flavobacteriales
Flavobacteriia
Flavobacteriaceae
Capnocytophaga
Oribacterium
Anaerovorax

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Experiment 12

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Differences from previous experiment shown

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

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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

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Bifidobacteriaceae
Bifidobacteriales
Bifidobacterium
Bulleidia
Cellulomonadaceae
Cellulomonas
Chromatiaceae
Chromatiales
Lachnospiraceae incertae sedis
Novosphingobium
Oscillibacter
Rheinheimera
Roseburia
Rubellimicrobium
Verrucomicrobiota
Ruminococcus

Revision editor(s): Tosin

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Reviewed Marked as Reviewed by Svetlana up on 2024-12-13

Curated date: 2024/11/03

Curator: Tosin

Revision editor(s): Tosin

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

NCBI	Quality Control	Links
Pseudomonadota
Pasteurellaceae
Pasteurellales
Haemophilus
Betaproteobacteria
Neisseriales
Neisseriaceae
Neisseria
Porphyromonas
Porphyromonadaceae
Leptotrichia
Capnocytophaga
Burkholderiaceae

Revision editor(s): Tosin

Experiment 13

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Reviewed Marked as Reviewed by Svetlana up on 2024-12-13

Curated date: 2024/11/04

Curator: MyleeeA

Revision editor(s): MyleeeA

Differences from previous experiment shown

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

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Reviewed Marked as Reviewed by Svetlana up on 2024-12-13

Curated date: 2024/11/04

Curator: MyleeeA

Revision editor(s): MyleeeA

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)

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Neisseria
Veillonella
Prevotella

Revision editor(s): MyleeeA

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EditHistoryDelete

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Reviewed Marked as Reviewed by Svetlana up on 2024-12-13

Curated date: 2024/11/04

Curator: MyleeeA

Revision editor(s): MyleeeA

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