Sputum microbiota profiles of patients with rifampicin-resistant tuberculosis during the intensive-phase treatment

Study information

Needs review

study design

case-control

Citation

PMID PubMed identifier for scientific articles.

40597612

DOI Digital object identifier for electronic documents.

10.1186/s12866-025-04091-4

URI Uniform resource identifier for web resources.

Authors

Cai X, Lin Y, Wu B, Luo Y, Li K

Journal

BMC microbiology

Year

2025

Keywords:

16S rRNA gene sequencing, Rifampicin-resistant tuberculosis, Sputum microbiota

BACKGROUND: The respiratory microbiome plays a crucial role in respiratory health and influences the onset and progression of tuberculosis (TB). However, changes in the respiratory microbiota of patients with rifampicin-resistant TB (RR-TB) during the intensive-phase treatment have not been assessed. This study aimed to investigate the impact of a six-month intensive-phase treatment of second-line anti-TB drugs on the respiratory microbiota of RR-TB patients. METHODS: Sputum samples were collected from 14 RR-TB patients and 14 healthy controls. Microbiota composition was analyzed using 16S rRNA gene sequencing, and functional predictions were performed to assess metabolic pathway changes. RESULTS: RR-TB patients exhibited significantly lower alpha diversity compared to healthy controls, but no significant changes were observed after six months of treatment. Beta diversity analysis revealed distinct clustering patterns between RR-TB patients and healthy controls, with no significant differences between pre- and post-treatment groups. Functional analysis showed reduced microbial functions related to pyruvate fermentation and amino acid metabolism in RR-TB patients. CONCLUSIONS: These findings highlight the specific effects of second-line anti-TB drugs on the respiratory microbiota and suggest potential roles of respiratory ecological imbalance in RR-TB pathogenesis. Future studies could explore microbiome-based diagnostic and therapeutic strategies for RR-TB. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-025-04091-4.

Experiment 1

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Curated date: 2025/07/07

Curator: Nuerteye

Revision editor(s): Nuerteye

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: Sputum Expectoration,Sputum,sputum

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Tuberculosis active tuberculosis,Kochs disease,TB,tuberculosis,tuberculosis disease,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: rifampicin-resistant tuberculosis (RR-TB) patients

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Smear/Xpert-confirmed rifampicin‑resistant pulmonary tuberculosis.

Group 0 sample size Number of subjects in the control (unexposed) group: 14

Group 1 sample size Number of subjects in the case (exposed) group: 14

Lab analysis

Sequencing type: 16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V1-V3

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)?: Yes

LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool: 4

Matched on Factors on which subjects have been matched on in a case-control study: age, sex

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on 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: 2025/07/08

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Source: Figure 4A–B

Description: (A) Significantly different taxa in terms of relative abundance (LDA score ≥ 4); (B) Cladogram highlighting significantly different taxa (LDA score ≥ 4)

Abundance in Group 1: increased abundance in rifampicin-resistant tuberculosis (RR-TB) patients

NCBI	Quality Control	Links
Streptococcus
Granulicatella
Lautropia
BacteroidetesBacteroidetes
Haemophilus
Bacteroidales
Bacteroidia
Pasteurellaceae
Pasteurellales
Bacilli
Lactobacillales
Carnobacteriaceae
Burkholderiaceae
ActinobacteriaActinobacteria
MucilaginosaMucilaginosa

Revision editor(s): Nuerteye

Signature 2

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Curated date: 2025/07/08

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Source: Figure 4A–B

Description: (A) Significantly different taxa in terms of relative abundance (LDA score ≥ 4); (B) Cladogram highlighting significantly different taxa (LDA score ≥ 4)

Abundance in Group 1: decreased abundance in rifampicin-resistant tuberculosis (RR-TB) patients

NCBI	Quality Control	Links
Fusobacterium
Fusobacteriaceae
Fusobacteriia
FusobacteriaFusobacteria
ParaprevotellaceaeParaprevotellaceae
Prevotella

Revision editor(s): Nuerteye