Characteristic gut microbiota and metabolic changes in patients with pulmonary tuberculosis/Experiment 1

From BugSigDB


Needs review

Curated date: 2025/06/17

Curator: Nuerteye

Revision editor(s): Nuerteye

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
PTB patients
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Clinically and/or bacteriologically confirmed active PTB, T-SPOT.TB positive, pre-treatment
Group 0 sample size Number of subjects in the control (unexposed) group
52
Group 1 sample size Number of subjects in the case (exposed) group
83
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
No antibiotics or pre/probiotics within 1 month prior to sampling; all PTB patients were treatment-naïve.

Lab analysis

Sequencing type
16S
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
V3-V4
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
LEfSe
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
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
Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
HIV infection

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

Needs review

Curated date: 2025/06/17

Curator: Nuerteye

Revision editor(s): Nuerteye

Source: Figure 2D

Description: LDA, linear discriminant analysis. The circular cladogram was derived from the LEfSe analysis and showed the relationship between the most differentially abundant taxa in the patients with PTB (green) and the HCs (red). HCs, healthy controls; LEfSe, linear discriminant analysis effect size; PTB, pulmonary tuberculosis.

Abundance in Group 1: increased abundance in PTB patients

NCBI Quality ControlLinks
Bacteroidales
Prevotellaceae
Bacteroides vulgatusBacteroides vulgatus

Revision editor(s): Nuerteye

Signature 2

Needs review

Curated date: 2025/06/17

Curator: Nuerteye

Revision editor(s): Nuerteye

Source: Figure 2D

Description: LDA, linear discriminant analysis. The circular cladogram was derived from the LEfSe analysis and showed the relationship between the most differentially abundant taxa in the patients with PTB (green) and the HCs (red). HCs, healthy controls; LEfSe, linear discriminant analysis effect size; PTB, pulmonary tuberculosis.

Abundance in Group 1: decreased abundance in PTB patients

NCBI Quality ControlLinks
Blautia wexlerae
Lachnospiraceae
ClostridialesClostridiales
FirmicutesFirmicutes
RuminococcaceaeRuminococcaceae
ActinobacteriaActinobacteria
Bifidobacteriales

Revision editor(s): Nuerteye