Microbiome diversity in the sputum of patients with pulmonary tuberculosis

From BugSigDB
Needs review
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI Uniform resource identifier for web resources.
Authors
Krishna P, Jain A, Bisen PS
Journal
European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology
Year
2016
TB is a worldwide pandemic. India has the highest burden of TB, with WHO statistics for 2013 giving an estimated incidence figure of 2.1 million cases for India out of a global incidence of 9 million. Microbiota have been shown to be associated with many disease conditions; however, only few studies have been reported for microbiota associated with TB infection. For the first time, we characterized the composition of microbiota of TB patients of India, using high-throughput 16S rRNA gene sequencing and compared it with healthy controls. Phylum-level analysis showed that the relative abundance of Firmicutes and Actinobacteria was significantly higher in TB samples and Neisseria and Veillonella were two dominant genera after Streptococcus. In our study, significantly different core genera in TB and normal population were found as compared with the reported studies. Also, the presence of diverse opportunistic pathogenic microbiota in TB patients increases the complexity and diversity of sputum microbiota. Characterization of the sputum microbiome is likely to provide important pathogenic insights into pulmonary tuberculosis.

Experiment 1


Needs review

Curated date: 2025/06/07

Curator: Nuerteye

Revision editor(s): Nuerteye

Subjects

Location of subjects
India
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
Sputum Expectoration,Sputum,sputum
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 (asymptomatic, TB negative)
Group 1 name Corresponds to the case (exposed) group for case-control studies
Tuberculosis patients (PTB)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Confirmed active pulmonary TB by sputum smear, culture, and RT‑PCR; no antibiotic use prior to sampling; HIV‑negative.
Group 0 sample size Number of subjects in the control (unexposed) group
16
Group 1 sample size Number of subjects in the case (exposed) group
23
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
None had taken antibiotics before sputum sampling (confirmed by clinical records).

Lab analysis

Sequencing type
16S
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
V6-V7
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Ion Torrent

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)
T-Test
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
Matched on Factors on which subjects have been matched on in a case-control study
age, sex
Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
ethnic group, HIV infection, antibiotic exposure, geographic area

Alpha Diversity

Pielou Quantifies how equal the community is numerically
unchanged
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
Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
decreased
Richness Number of species
decreased
Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
unchanged

Signature 1

Needs review

Curated date: 2025/06/07

Curator: Nuerteye

Revision editor(s): Nuerteye

Source: Fig. 2; Fig. 3; Table 2

Description: Phyla-level relative abundance of microbial composition in TB and normal patients groups. Genera-level relative abundance of microbial composition in TB and normal patients groups.

Abundance in Group 1: increased abundance in Tuberculosis patients (PTB)

NCBI Quality ControlLinks
Acinetobacter
Atopobium
Bacillus
Corynebacterium
Enterococcus
Lactobacillus
Lautropia
Leuconostoc
Megasphaera
Moraxella
Streptococcus
Veillonella
FirmicutesFirmicutes
ActinobacteriaActinobacteria

Revision editor(s): Nuerteye

Signature 2

Needs review

Curated date: 2025/06/07

Curator: Nuerteye

Revision editor(s): Nuerteye

Source: Fig. 2; Fig. 3; Table 2

Description: Phyla-level relative abundance of microbial composition in TB and normal patients groups. Genera-level relative abundance of microbial composition in TB and normal patients groups.

Abundance in Group 1: decreased abundance in Tuberculosis patients (PTB)

NCBI Quality ControlLinks
FusobacteriaFusobacteria
ProteobacteriaProteobacteria

Revision editor(s): Nuerteye

Experiment 2


Needs review

Curated date: 2025/06/07

Curator: Nuerteye

Revision editor(s): Nuerteye

Differences from previous experiment shown

Subjects

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
 Confirmed active pulmonary TB by sputum smear, culture, and RT‑PCR; no antibiotic use prior to sampling; HIV‑negative.
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
None had taken antibiotics before sputum sampling (confirmed by clinical records). 

Lab analysis

Statistical Analysis

Statistical test
Mann-Whitney (Wilcoxon)
PERMANOVA
T-Test
Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
0.05
Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
antibiotic exposure, HIV infection, geographic area, ethnic group

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