Differences in salivary microbiome among children with tonsillar hypertrophy and/or adenoid hypertrophy/Experiment 4

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Curated date: 2024/10/09

Curator: Rahila

Revision editor(s): Rahila

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

Saliva Sailva normalis,Saliva atomaris,Saliva molecularis,Salivary gland secretion,Saliva,saliva

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

Hypertrophy Hypertrophy,hypertrophy

Group 0 name Corresponds to the control (unexposed) group for case-control studies

Smaller Tonsillar Hypertrophy (THS)

Group 1 name Corresponds to the case (exposed) group for case-control studies

Larger Tonsillar Hypertrophy (THL)

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

Salivary microbial profile in children with a larger tonsillar hypertrophy group diagnosed with Grade III tonsillar hypertrophy

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

20

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

26

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

3 months

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

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

2.0

Alpha Diversity

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

unchanged

Chao1 Abundance-based estimator of species richness

unchanged

Richness Number of species

unchanged

Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample

unchanged