Airway microbiome signature accurately discriminates Mycobacterium tuberculosis infection status

Study information

Needs review

study design

prospective cohort
time series / longitudinal observational

Citation

PMID PubMed identifier for scientific articles.

38904070

DOI Digital object identifier for electronic documents.

10.1016/j.isci.2024.110142

URI Uniform resource identifier for web resources.

Authors

Kayongo A, Ntayi ML, Olweny G, Kyalo E, Ndawula J, Ssengooba W, Kigozi E, Kalyesubula R, Munana R, Namaganda J, Caroline M, Sekibira R, Bagaya BS, Kateete DP, Joloba ML, Jjingo D, Sande OJ, Mayanja-Kizza H

Journal

iScience

Year

2024

Keywords:

Bacteriology, Microbiology, Microbiome

Mycobacterium tuberculosis remains one of the deadliest infectious agents globally. Amidst efforts to control TB, long treatment duration, drug toxicity, and resistance underscore the need for novel therapeutic strategies. Despite advances in understanding the interplay between microbiome and disease in humans, the specific role of the microbiome in predicting disease susceptibility and discriminating infection status in tuberculosis still needs to be fully investigated. We investigated the impact of M.tb infection and M.tb-specific IFNγ immune responses on airway microbiome diversity by performing TB GeneXpert and QuantiFERON-GOLD assays during the follow-up phase of a longitudinal HIV-Lung Microbiome cohort of individuals recruited from two large independent cohorts in rural Uganda. M.tb rather than IFNγ immune response mainly drove a significant reduction in airway microbiome diversity. A microbiome signature comprising Streptococcus, Neisseria, Fusobacterium, Prevotella, Schaalia, Actinomyces, Cutibacterium, Brevibacillus, Microbacterium, and Beijerinckiacea accurately discriminated active TB from Latent TB and M.tb-uninfected individuals.

Experiment 1

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Curated date: 2025/07/16

Curator: Nuerteye

Revision editor(s): Nuerteye

Subjects

Location of subjects: Uganda

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: Sputum Expectoration,Sputum,sputum

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Pulmonary tuberculosis lung TB,lung tuberculosis,pulmonary TB,pulmonary tuberculosis,Tuberculosis, Pulmonary,Pulmonary tuberculosis

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Non‑Tuberculosis (M.tb-uninfected)

Group 1 name Corresponds to the case (exposed) group for case-control studies: Active tuberculosis patients (PTB)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Active tuberculosis defined by GeneXpert

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): no history of prior antibiotic use in the past two weeks

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

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, sex, smoking status

Alpha Diversity

Pielou Quantifies how equal the community is numerically: decreased

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

Chao1 Abundance-based estimator of species richness: decreased

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

Richness Number of species: decreased

Signature 1

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Curated date: 2025/07/17

Curator: Nuerteye

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Source: Figure 4C

Description: Bar plots showing linear discriminant analysis (LDA) effect size scores of OTUs in active TB versus LTBI and M.tb-uninfected groups.

Abundance in Group 1: increased abundance in Active tuberculosis patients (PTB)

NCBI	Quality Control	Links
ActinobacteriaActinobacteria
Brevibacillus
Microbacterium
Streptomyces
Beijerinckiaceae
Mycobacterium tuberculosis

Revision editor(s): Nuerteye

Signature 2

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Mark reviewed

Your review change was submitted

Needs review

Curated date: 2025/07/17

Curator: Nuerteye

Revision editor(s): Nuerteye

Source: Figure 4C

Description: Bar plots showing linear discriminant analysis (LDA) effect size scores of OTUs in active TB versus LTBI and M.tb-uninfected groups.

Abundance in Group 1: decreased abundance in Active tuberculosis patients (PTB)

NCBI	Quality Control	Links
Streptococcus
Bacteroides
Prevotella
Stenotrophomonas
XanthomonadaceaeXanthomonadaceae
Fusobacterium
Negativicutes
Neisseria
Burkholderia
Pasteurella
Sphingomonas
RothiaRothia
Veillonella
Haemophilus
Alloprevotella
Leptotrichia
SchaaliiSchaalii
Granulicatella

Revision editor(s): Nuerteye