Alterations in the oral microbiome in HIV-infected participants after antiretroviral therapy administration are influenced by immune status/Experiment 1

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Reviewed Marked as Reviewed by Folakunmi on 2024-1-8

Curated date: 2023/10/10

Curator: MyleeeA

Revision editor(s): MyleeeA, Folakunmi

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

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

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

Viral load viral burden,viral titer,viral titre,Viral load,viral load

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

High viral load at baseline

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

Low viral load at baseline

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

Participants with viral load less than 100 000 copies/ml at baseline

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

9

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)

N/A

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).

relative abundances

Statistical test

Mann-Whitney (Wilcoxon)

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

Alpha Diversity

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

unchanged

Richness Number of species

unchanged