Metagenomic analysis of the lung microbiome in pulmonary tuberculosis - a pilot study

Study information

Needs review

study design

case-control

Citation

PMID PubMed identifier for scientific articles.

32552447

DOI Digital object identifier for electronic documents.

10.1080/22221751.2020.1783188

URI Uniform resource identifier for web resources.

Authors

Hu Y, Cheng M, Liu B, Dong J, Sun L, Yang J, Yang F, Chen X, Jin Q

Journal

Emerging microbes & infections

Year

2020

Keywords:

16S rDNA, Lung microbiome, bronchoalveolar lavage, metagenomic analysis, tuberculosis

The lung microbiome plays an important role in the pathophysiological processes associated with pulmonary tuberculosis (PTB). However, only a few studies using 16S rDNA amplicon sequencing have been reported, and the interactions between Mycobacterium tuberculosis (MTB) and the lung microbiome remain poorly understood. Patients with respiratory symptoms and imaging abnormalities compatible with tuberculosis (TB) were enrolled. We analyzed the lung microbiome in bronchoalveolar lavage (BAL) samples from 30 MTB-positive (MTB+) subjects and 30 MTB negative (MTB-) subjects by shotgun metagenomic sequencing. Alpha diversity tended to be lower in the MTB+ group than in the MTB- group. There was a significant difference in beta diversity between the MTB+ and MTB- subjects. MTB+ lung samples were dominated by MTB, while MTB- samples were enriched with Streptococcus, Prevotella, Nesseria, Selenomonas and Bifidobacterium, which more closely resemble the microbial composition of a healthy lung. Network analysis suggested that MTB could greatly impact the microbial community structure. MTB+ and MTB- communities showed distinct functional signatures. Fungal communities were also found to be associated with the presence or absence of MTB. Furthermore, it was confirmed that 16S rDNA amplicon sequencing underrepresents Mycobacterium. This pilot study is the first to explore the interplay between MTB and the host microbiome by using metagenomic sequencing. MTB dominates the lung microbiome of MTB+ subjects, while MTB- subjects have a Streptococcus-enriched microbiome. The 16S approach underrepresents Mycobacterium and is not the best way to study the TB-associated microbiome.

Experiment 1

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Curated date: 2025/07/05

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: Mycobacterium tuberculosis (MTB−)

Group 1 name Corresponds to the case (exposed) group for case-control studies: Mycobacterium tuberculosis (MTB+)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Mycobacterium tuberculosis (MTB) detected by smear, culture, PCR, or GeneXpert.

Group 0 sample size Number of subjects in the control (unexposed) group: 30

Group 1 sample size Number of subjects in the case (exposed) group: 30

Lab analysis

Sequencing type: 16S

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: Mann-Whitney (Wilcoxon)

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

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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Source: Figure 2

Description: Average relative taxon abundance comparisons between the MTB+ and MTB- groups at the genus level.

Abundance in Group 1: increased abundance in Mycobacterium tuberculosis (MTB+)

NCBI	Quality Control	Links
Mycobacterium tuberculosis

Revision editor(s): Nuerteye

Signature 2

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Curated date: 2025/07/05

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Source: Figure 2

Description: Average relative taxon abundance comparisons between the MTB+ and MTB- groups at the genus level.

Abundance in Group 1: decreased abundance in Mycobacterium tuberculosis (MTB+)

NCBI	Quality Control	Links
Streptococcus
Prevotella
Neisseria
Selenomonas
Bifidobacterium

Revision editor(s): Nuerteye