Microbiome Alteration in Lung Tissues of Tuberculosis Patients Revealed by Metagenomic Next-Generation Sequencing and Immune-Related Transcriptional Profile Identified by Transcriptome Sequencing

Study information

Needs review

study design

case-control

Citation

PMID PubMed identifier for scientific articles.

37975314

DOI Digital object identifier for electronic documents.

10.1021/acsinfecdis.3c00416

URI Uniform resource identifier for web resources.

Authors

Liu H, Ji S, Fang Y, Yi X, Wu F, Xing F, Wang C, Zhou H, Xu J, Sun W

Journal

ACS infectious diseases

Year

2023

Keywords:

mNGS, microbiome, transcriptional profile, transcriptome sequencing, tuberculosis

This study explored alterations in the respiratory microbiome and transcriptome after Mycobacterium tuberculosis infection in tuberculosis (TB) patients. Metagenomic next-generation sequencing (mNGS) was adopted to reveal the microbiome in lung tissues from 110 TB and 25 nontuberculous (NonTB) patients. Transcriptome sequencing was performed in TB tissues (n = 3), tissues adjacent to TB (ParaTB, n = 3), and NonTB tissues (n = 3) to analyze differentially expressed genes (DEGs) and functional pathways. The microbial β diversity (p = 0.01325) in TB patients differed from that in the NonTB group, with 17 microbial species distinctively distributed. Eighty-three co-up-regulated DEGs were identified in the TB versus NonTB and the TB versus ParaTB comparison groups, and six were associated with immune response to Mtb. These DEGs were significantly enriched in the signaling pathways such as immune response, NF-κB, and B cell receptor. Data in the lung tissue microbiome and transcriptome in TB patients offer a sufficient understanding of the pathogenesis of TB.

Experiment 1

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Curated date: 2025/07/20

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: Lung Pulmo,Lung,lung

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: patients with Non-tuberculosis

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

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Mtb-positive in the bacteriological examination, including sputum smear or sputum culture, mNGS, acid-fast staining, T-spot, adenosine deaminase, PCR, and interferon-gamma release assay; clinical manifestations such as constitutional symptoms and imaging manifestations; improvement following initiation of anti-TB therapy.

Group 0 sample size Number of subjects in the control (unexposed) group: 25

Group 1 sample size Number of subjects in the case (exposed) group: 110

Lab analysis

Sequencing type: WMS

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

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

Alpha Diversity

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

Chao1 Abundance-based estimator of species richness: unchanged

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

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

Signature 1

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Curated date: 2025/07/20

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Source: Figure 2C

Description: Microbial distribution in lung tissues of TB and NonTB patients. LEfSe analyses were performed to determine the microbial features with significant differences in the relative abundance.

Abundance in Group 1: increased abundance in patients with tuberculosis

NCBI	Quality Control	Links
Pseudomonas pharmacofabricaePseudomonas pharmacofabricae
Enterobius vermicularisEnterobius vermicularis
Delftia tsuruhatensis
Streptosporangium violaceochromogenes
Actinomadura cremeaActinomadura cremea
Micobacterium saperdaeMicobacterium saperdae

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Signature 2

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Source: Figure 2C

Description: Microbial distribution in lung tissues of TB and NonTB patients. LEfSe analyses were performed to determine the microbial features with significant differences in the relative abundance.

Abundance in Group 1: decreased abundance in patients with tuberculosis

NCBI	Quality Control	Links
Fusobacterium nucleatum
Prevotella melaninogenica
Ralstonia insidiosa
Paracoccus versutusParacoccus versutus
Stenotrophomonas tumulicolaStenotrophomonas tumulicola
Staphylococcus haemolyticus
Bradyrhizobium brasilenceBradyrhizobium brasilence
Afipia clevelandensisAfipia clevelandensis
Bradyrhizobium embrapenseBradyrhizobium embrapense
Rhizobium oryzihabitansRhizobium oryzihabitans
Methylorubrum populi

Revision editor(s): Nuerteye