Altered intestinal microbiota and fecal metabolites in patients with latent and active pulmonary tuberculosis

Study information

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study design

cross-sectional observational, not case-control

Citation

PMID PubMed identifier for scientific articles.

39549509

DOI Digital object identifier for electronic documents.

10.1016/j.tube.2024.102577

URI Uniform resource identifier for web resources.

Authors

Zhang H, Xue M, He X, Sun L, He Q, Wang Y, Jin J

Journal

Tuberculosis (Edinburgh, Scotland)

Year

2024

Keywords:

16S rRNA gene sequencing, Fecal metabolites, Gut microbiota, Latent pulmonary tuberculosis, Pulmonary tuberculosis

BACKGROUND: Pulmonary tuberculosis (PTB) is the main cause of infection-related mortality and the most common infectious disease that develops resistance to antibiotics. Gut microbiota and their associated metabolites are assumed to induce and influence the development of PTB. However, the alterations of gut microbiota and metabolites in TB patients is currently unclear. METHODS: Fecal samples were collected from 13 PTB patients, 13 LTBI patients, and 13 healthy controls (HC). 16S rRNA sequencing and metabolomics were used to analyze the changes in the intestinal microbiota and the composition of fecal metabolites in groups. RESULTS: Our findings indicated that the α-diversity of the gut microbiota in patients with PTB and LTBI decreases compared to HC, and at the phylum level, the relative abundance of Firmicutes decreases and the relative abundance of Bacteroides increases. And six genera were notably enriched in PTB patients and four in LTBI patients. Metabolomic analysis showed alterations in metabolite levels, such as short-chain fatty acids and amino acids. CONCLUSIONS: we comprehensively explored the changes in the gut microbes and fecal metabolites in patients with PTB and LTBI from the perspective of the gut microbiota, which may provide potential diagnostic biomarkers and therapeutic targets for TB diagnosis and treatment.

Experiment 1

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Curated date: 2025/07/16

Curator: Nuerteye

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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

Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces

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

Healthy controls

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

Pulmonary tuberculosis patients

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

confirmed pulmonary tuberculosis

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

13

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

13

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

3

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: 2025/07/16

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Source: Figure 3A and B

Description: Identification of differential microbial biomarkers. (A, B and C) Evolutionary branching plots showing the most divergent taxa identified by LEfSe.

Abundance in Group 1: increased abundance in Pulmonary tuberculosis patients

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Erysipelotrichaceae
Erysipelotrichales
Erysipelotrichia
Prevotellaceae
Prevotellaceae bacterium
uncultured Lactobacillus sp.
Clostridium innocuumClostridium innocuum
uncultured Catenibacterium sp.uncultured Catenibacterium sp.
Clostridium innocuum group_unclassifiedClostridium innocuum group_unclassified

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Signature 2

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Source: Figure 3A and B

Description: Identification of differential microbial biomarkers. (A, B and C) Evolutionary branching plots showing the most divergent taxa identified by LEfSe.

Abundance in Group 1: decreased abundance in Pulmonary tuberculosis patients

NCBI	Quality Control	Links
Lachnospiraceae
Roseburia
Lachnospira
unclassified Dialister
Dialister
Ruminococcaceae UCG 013Ruminococcaceae UCG 013
Roseburia faecis
uncultured Roseburia sp.
unclassified Lachnospiraceae
Clostridiaceae
Clostridium
Ruminococcaceae NK4A214 groupRuminococcaceae NK4A214 group
Collinsella aerofaciens
uncultured Megasphaera sp.
Megasphaera
uncultured Clostridium sp.
Bacteroides sp_AR29Bacteroides sp_AR29

Revision editor(s): Nuerteye

Experiment 2

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Differences from previous experiment shown

Subjects

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

latent tuberculosis patients (LTBI)

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

pulmonary tuberculosis (PTB)

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

confirmed pulmonary tuberculosis patients

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

No prior antibiotics treatment

Lab analysis

16S variable region One or more hypervariable region(s) of the bacterial 16S gene

Not specified

Statistical Analysis

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

EditHistoryDelete

Mark reviewed

Your review change was submitted

Needs review

Curated date: 2025/07/16

Curator: Nuerteye

Revision editor(s): Nuerteye

Source: Fig. 3C and D

Description: Identification of differential microbial biomarkers. (A, B and C) Evolutionary branching plots showing the most divergent taxa identified by LEfSe. (B, D and F) Bar graphs showing LDA values for LEfSe analysis of bacterial abundance.

Abundance in Group 1: increased abundance in pulmonary tuberculosis (PTB)

NCBI	Quality Control	Links
Erysipelotrichaceae
Erysipelotrichales
Erysipelotrichia
Alloprevotella
Desulfovibrio sp.

Revision editor(s): Nuerteye

Signature 2

EditHistoryDelete

Mark reviewed

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Curated date: 2025/07/16

Curator: Nuerteye

Revision editor(s): Nuerteye

Source: Fig. 3C and D

Description: Identification of differential microbial biomarkers. (A, B and C) Evolutionary branching plots showing the most divergent taxa identified by LEfSe. (B, D and F) Bar graphs showing LDA values for LEfSe analysis of bacterial abundance.

Abundance in Group 1: decreased abundance in pulmonary tuberculosis (PTB)

NCBI	Quality Control	Links
Fusobacteriales
Fusobacteriia
Lachnospiraceae
unclassified Lachnospiraceae
FusobacteriaFusobacteria

Revision editor(s): Nuerteye