Insights into the Unique Lung Microbiota Profile of Pulmonary Tuberculosis Patients Using Metagenomic Next-Generation Sequencing

Study information

Reviewed Marked as Reviewed by Svetlana up on 2024-8-1

study design

case-control

Citation

PMID PubMed identifier for scientific articles.

35196800

DOI Digital object identifier for electronic documents.

https://doi.org/10.1128/spectrum.01901-21

URI

Authors

Guohui Xiao, Guoliang Zhang, Juanjuan Zhang, Lei Liu, Liang Yang yangl@sustech.edu.cn, Lili Ren, Min Ou, Minfei Yu, Peikun Guan, Qinglong Guo, Taosheng Ye, Xiangdong Fu, Yimin Tang, Zhao Cai, Zhaoqin Wang

Journal

Insights into the Unique Lung Microbiota Profile of Pulmonary Tuberculosis Patients Using Metagenomic Next-Generation Sequencing

Year

2022

Pages:

15

First page:

Keywords:

tuberculosis, Mycobacterium tuberculosis, anti-TB treatment, antibiotic resistance genes, lung microbiota, metagenomics

The microbiota plays an important role in human health and disease development.

The lung microbiota profile in pulmonary tuberculosis (TB) patients and the effects of anti-TB treatment on the profile need to be determined thoroughly and comprehensively. This study primarily aimed to determine the lung microbiota profile associated with pulmonary TB and characterize the longitudinal changes during anti-TB treatment. A total of 53 participants, comprising 8 healthy individuals, 12 untreated pulmonary TB patients, 15 treated pulmonary TB patients, 11 cured pulmonary TB patients, and 7 lung cancer patients, were recruited in the present study. Bronchioalveolar lavage fluid (BALF) samples were collected from the above participants, and throat swabs were taken from healthy individuals. Microbiomes in the samples were examined using metagenomic next-generation sequencing (mNGS). Differences in microbiota profiles were determined through a comparison of the indicated groups. Our findings indicated that the BALF samples displayed decreased richness and diversity of the microbiota compared to those of the throat swab samples, and these two kinds of samples exhibited obvious separation on principal-coordinate analysis (PCoA) plots. Untreated pulmonary TB patients displayed a unique lung microbiota signature distinct from that of healthy individuals and lung cancer patients. Our data first demonstrated that anti-TB treatment with first-line drugs increases alpha diversity and significantly affects the beta diversity of the lung microbiota, while it also induces antibiotic resistance genes (ARGs).

Experiment 1

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Curated date: 2024/03/17

Curator: BSpac126

Revision editor(s): BSpac126, Victoria, Scholastica

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: Throat Gula,Throat,throat

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Mycobacterium tuberculosis , Lung cancer Bacillus tuberculosis,Bacterium tuberculosis,Mycobacterium tuberculosis typus humanus,Mycobacterium tuberculosis var. hominis,Mycobacterium tuberculosis,mycobacterium tuberculosis,alveolar cell carcinoma,cancer of lung,lung cancer,lung cancer, protection against,lung neoplasm,malignant lung neoplasm,malignant lung tumor,malignant neoplasm of lung,malignant neoplasm of the lung,malignant tumor of lung,malignant tumor of the lung,Nonsmall cell lung cancer,Lung cancer

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Healthy Control Group (HCG)

Group 1 name Corresponds to the case (exposed) group for case-control studies: Untreated TB Group (UTG) and lung cancer patient group (LCG)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: This group consists of patients who have untreated pulmonary tuberculosis group (UTG; 5 males, 7 females) and lung cancer patient group (LCG; 5 males, 2 females)

Group 0 sample size Number of subjects in the control (unexposed) group: 8

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

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

MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?: No

LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool: 4.0

Signature 1

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Curated date: 2024/03/17

Curator: BSpac126

Revision editor(s): BSpac126, Victoria, Scholastica

Source: Fig 3C

Description: Differentially enriched taxa identified by linear discriminant analysis effect size (LEfSe) among the three groups.

Abundance in Group 1: decreased abundance in Untreated TB Group (UTG) and lung cancer patient group (LCG)

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Ralstonia pickettii
Staphylococcus haemolyticus

Revision editor(s): BSpac126, Victoria, Scholastica

Experiment 2

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Curated date: 2024/03/19

Curator: BSpac126

Revision editor(s): BSpac126, Victoria, Scholastica

Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Mycobacterium tuberculosis Bacillus tuberculosis,Bacterium tuberculosis,Mycobacterium tuberculosis typus humanus,Mycobacterium tuberculosis var. hominis,Mycobacterium tuberculosis,mycobacterium tuberculosis

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Healthy Control Group (HCG) and Lung Cancer Group (LCG)

Group 1 name Corresponds to the case (exposed) group for case-control studies: Untreated TB Group (UTG)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: This group consists of patients who have Untreated Pulmonary Tuberculosis and are not taking any antibiotics.

Group 0 sample size Number of subjects in the control (unexposed) group: 15

Group 1 sample size Number of subjects in the case (exposed) group: 12

Lab analysis

Statistical Analysis

Signature 1

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Curated date: 2024/03/20

Curator: BSpac126

Revision editor(s): BSpac126, Victoria

Source: Fig 3C

Description: Differentially enriched taxa identified by linear discriminant analysis effect size (LEfSe) among the three groups.

Abundance in Group 1: increased abundance in Untreated TB Group (UTG)

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Pasteurella multocida
Staphylococcus aureus
Ralstonia solanacearum

Revision editor(s): BSpac126, Victoria

Experiment 3

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Curated date: 2024/03/22

Curator: BSpac126

Revision editor(s): BSpac126, Victoria, Scholastica

Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Lung cancer alveolar cell carcinoma,cancer of lung,lung cancer,lung cancer, protection against,lung neoplasm,malignant lung neoplasm,malignant lung tumor,malignant neoplasm of lung,malignant neoplasm of the lung,malignant tumor of lung,malignant tumor of the lung,Nonsmall cell lung cancer,Lung cancer

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Healthy Control Group (HCG) and Untreated TB Group (UTG)

Group 1 name Corresponds to the case (exposed) group for case-control studies: Lung cancer patient group (LCG)

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

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: 7

Lab analysis

Statistical Analysis

Signature 1

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Curated date: 2024/03/22

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Source: Fig 4D

Description: Differentially enriched taxa identified by linear discriminant analysis effect size (LEfSe) among the three groups.

Abundance in Group 1: increased abundance in Lung cancer patient group (LCG)

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Prevotella intermedia
Streptomyces sp. ICC4

Revision editor(s): BSpac126, Victoria, Scholastica

Experiment 4

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Curated date: 2024/07/31

Curator: Scholastica

Revision editor(s): Scholastica

Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Mycobacterium tuberculosis Bacillus tuberculosis,Bacterium tuberculosis,Mycobacterium tuberculosis typus humanus,Mycobacterium tuberculosis var. hominis,Mycobacterium tuberculosis,mycobacterium tuberculosis

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Treated pulmonary TB group (TTG) and cured pulmonary TB group (CTG)

Group 1 name Corresponds to the case (exposed) group for case-control studies: Untreated pulmonary TB group (UTG)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: This group consists of patients who have Untreated Pulmonary Tuberculosis and are not taking any antibiotics.