The oral microbiome of newly diagnosed tuberculosis patients; a pilot study/Experiment 2

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Curated date: 2025/06/07

Curator: Nuerteye

Revision editor(s): Nuerteye

Subjects

Location of subjects

Pakistan

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

Oral cavity Bucca,Buccal cavity,Cavity of mouth,Oral cavity,oral cavity

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

Extrapulmonary tuberculosis Extrapulmonary tuberculosis,extrapulmonary tuberculosis

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

Healthy controls

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

Newly diagnosed, treatment‑naive pulmonary TB patients

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

Confirmed active pulmonary TB (sputum smear microscopy and Xpert MTB/RIF assay, per national guidelines).

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

20

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

Excluded if currently or recently receiving broad‑spectrum antibiotics or prescription mouthwashes.

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

PERMANOVA

DESeq2

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)?

Yes

LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool

2

Matched on Factors on which subjects have been matched on in a case-control study

age, Matched on: "gender" 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.gender

Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment

socioeconomic status, education level, oral hygiene

Alpha Diversity

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

increased

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

increased

Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa

increased

Richness Number of species

increased