Alterations in the intestinal microbiota associated with active tuberculosis and latent tuberculosis infection

Study information

Needs review

study design

case-control

Citation

PMID PubMed identifier for scientific articles.

38045157

DOI Digital object identifier for electronic documents.

10.1016/j.heliyon.2023.e22124

URI Uniform resource identifier for web resources.

Authors

Huang Y, Tang J, Cai Z, Qi Y, Jiang S, Ma T, Yue Y, Huang F, Yang H, Ma Y

Journal

Heliyon

Year

2023

Keywords:

16S rDNA sequencing, Active tuberculosis (ATB), Human gut microbiota, Latent tuberculosis infection (LTBI), Microbial diversity, Mycobacterium tuberculosis

OBJECTIVES: To study the characteristics of intestinal microbiota at different stages of Mycobacterium tuberculosis infection. METHODS: Fecal samples of 19 active tuberculosis (ATB) patients, 21 latent tuberculosis infection (LTBI) individuals, and 20 healthy controls (HC) were collected. Gut microbiota of all the participants were analyzed by 16S rDNA sequencing. Clinical information of ATB patients was also collected and analyzed. RESULTS: Both ATB and LTBI groups showed significant decreases in microbial diversity and decline of Clostridia. For ATB patients, bacteria within phylum Proteobacteria increased. While for LTBI individuals, genera Prevotella and Rosburia enriched. The abundance of Faecalibacterium, Clostridia and Gammaproteobacteria has the potential to diagnose ATB, with the area under the curve (AUC) of 0.808, 0.784 and 0.717. And Prevotella and Rosburia has the potential to diagnose LTBI, with the AUC of 0.689 and 0.689. Notably, in ATB patients, the relative abundance of Blautia was negatively correlated with the proportions of peripheral T cells and CD8+T cells. And serum direct bilirubin was positively correlated with Bacteroidales, while negatively correlated with Clostridiales in ATB patients. CONCLUSIONS: The specifically changed bacteria are promising markers for ATB and LTBI diagnosis. Some gut bacteria contribute to anti-MTB immunity through interactions with T cells and bilirubin.

Experiment 1

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Curated date: 2025/06/27

Curator: Nuerteye

Revision editor(s): Nuerteye, Ese

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: Active TB

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Clinical and microbiologically confirmed pulmonary TB, treatment-naïve.

Group 0 sample size Number of subjects in the control (unexposed) group: 20

Group 1 sample size Number of subjects in the case (exposed) group: 19

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): 2 months

Lab analysis

Sequencing type: PCR

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: Not specified

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; Linear Discriminant Analysis

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: 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

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: 2025/06/27

Curator: Nuerteye

Revision editor(s): Nuerteye

Source: Figure 5A and B

Description: (A) Column diagram of LDA analysis of fecal microbiome in the three groups (HC, LTBI and ATB) (P < 0.05; LDA score >4.0). (B) Pairwise LDA effect size (LEfSe) analysis table of fecal microbiome. The phyla and subsequent taxonomic levels are sorted alphabetically, and the corresponding LDA score for each pairwise analysis is indicated in the column (P < 0.05; LDA score >4.0)

Abundance in Group 1: increased abundance in Active TB

NCBI	Quality Control	Links
Enterobacteriaceae
EnterobacterialesEnterobacteriales
Gammaproteobacteria
ProteobacteriaProteobacteria
ErysipelatoclostridiumErysipelatoclostridium

Revision editor(s): Nuerteye

Signature 2

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Mark reviewed

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Curated date: 2025/06/27

Curator: Nuerteye

Revision editor(s): Nuerteye

Source: Figure 5A and B

Description: (A) Column diagram of LDA analysis of fecal microbiome in the three groups (HC, LTBI and ATB) (P < 0.05; LDA score >4.0). (B) Pairwise LDA effect size (LEfSe) analysis table of fecal microbiome. The phyla and subsequent taxonomic levels are sorted alphabetically, and the corresponding LDA score for each pairwise analysis is indicated in the column (P < 0.05; LDA score >4.0).

Abundance in Group 1: decreased abundance in Active TB

NCBI	Quality Control	Links
BifidobacterialeBifidobacteriale
Bifidobacteriaceae
Bifidobacterium
Clostridia
ClostridialesClostridiales
OscillospiraceaeOscillospiraceae
Ruminococcus
Faecalibacterium
Lachnospiraceae
Agathobacter
Fusicatenibacter

Revision editor(s): Nuerteye