The potential mechanism of the progression from latent to active tuberculosis based on the intestinal microbiota alterations
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Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI Uniform resource identifier for web resources.
Authors
Luo D, Shi CY, Wei NS, Yang BY, Qin K, Liu G, Dong BQ, Qin YX, Qin XL, Chen SY, Guo XJ, Gan L, Xu RL, Li H, Li J
Journal
Tuberculosis (Edinburgh, Scotland)
Year
2023
Keywords:
16S rDNA sequencing, Intestinal microbiota, LTBI, Tuberculosis
INTRODUCTION: Tuberculosis (TB) poses a serious challenge to global health systems. The altered intestinal microbiota is associated with the pathogenesis of TB, but the exact links remain unclear. METHODS: 16 S rDNA sequencing was performed to comprehensively detect the changes in the intestinal microbiota of feces from active TB (ATB), latent TB infection (LTBI) and healthy controls (HC). RESULTS: The rarefaction curves demonstrated the sequencing results' validity. The alpha diversity was lowest in ATB, while highest in HC. Boxplot of beta diversity showed significant differences in every two groups. LDA Effect Size (LEfSe) Analysis revealed differences in probiotic bacteria like Romboutsia, Bifidobacterium and Lactobacillus in LTBI, and pro-inflammatory bacteria like R. gnavus, Streptococcus and Erysipelatoclostridium in ATB, corresponding to the cluster analysis. PICRUST2 analysis revealed the pentose phosphate pathway was active in ATB and LTBI (more active in ATB). The differences between the groups are statistically significant at the P<0.05 level. CONCLUSION: Our study indicated that from LTBI to ATB, some intestinal microbiota inhibit the synthesis of interferon (INF)-γ and interleukin (IL)-17, promoting the survival and spread of Mycobacterium tuberculosis (M. tb). In addition, the metabolites secreted by intestinal microbiota and dysbiosis in intestine also have an effect on the development of LTBI to ATB.
Experiment 1
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
- Tuberculosis active tuberculosis,Kochs disease,TB,tuberculosis,tuberculosis disease,Tuberculosis
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- combination of active tuberculosis (ATB) and latent tuberculosis infection (LTBI)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- healthy controls
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- All cases had no previous history of tuberculosis
- Group 0 sample size Number of subjects in the control (unexposed) group
- 42
- Group 1 sample size Number of subjects in the case (exposed) group
- 11
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- previous history of treatment using antibiotics
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V5
- 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
- 4
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
- Richness Number of species
- increased
Signature 1
Source: Figure 5A-B
Description: The enrichment deviation diagram of three groups based on LEfSe analysis (selection criteria: P<0.05; LDA score ≥ 4). Histogram of LDA value of intestinal microbiota in three groups. The column represents LDA Score, and the colors represent the microbiota in three groups, respectively. LEfSe cladogram of LEfSe analysis.
Abundance in Group 1: increased abundance in healthy controls
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotellaceae | ||
| Prevotella | ||
| Holdemanella | ||
| Prevotella copriPrevotella copri | ||
| Negativicutes | ||
| Veillonellales selenomonadalesVeillonellales selenomonadales |
Revision editor(s): Nuerteye
Experiment 2
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- combination of healthy controls (HC) and latent tuberculosis infection (LTBI)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- active tuberculosis (ATB)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patents with ATB enrolled according to Technical Guidelines for Tuberculosis Prevention and Control in China [20] and all cases had no previous history of TB.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 24
- Group 1 sample size Number of subjects in the case (exposed) group
- 29
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- Not specified
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
Source: Figure 5A-B
Description: The enrichment deviation diagram of three groups based on LEfSe analysis (selection criteria: P<0.05; LDA score ≥ 4). Histogram of LDA value of intestinal microbiota in three groups. The column represents LDA Score, and the colors represent the microbiota in three groups, respectively. LEfSe cladogram of LEfSe analysis.
Abundance in Group 1: increased abundance in active tuberculosis (ATB)
Revision editor(s): Nuerteye
Experiment 3
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- combination of healthy controls (HC) and active tuberculosis (ATB)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- latent tuberculosis infection (LTBI)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Positive IGRAs and/or TST (nodule ≥15 mm, blister or necrosis), but had no clinical symptoms of TB.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 40
- Group 1 sample size Number of subjects in the case (exposed) group
- 13
Lab analysis
Statistical Analysis
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
Source: Figure 5A-B
Description: The enrichment deviation diagram of three groups based on LEfSe analysis (selection criteria: P<0.05; LDA score ≥ 4). Histogram of LDA value of intestinal microbiota in three groups. The column represents LDA Score, and the colors represent the microbiota in three groups, respectively. LEfSe cladogram of LEfSe analysis.
Abundance in Group 1: increased abundance in latent tuberculosis infection (LTBI)
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium | ||
| Bifidobacteriales | ||
| Bifidobacteriaceae | ||
| Lactobacillus | ||
| unclassified Lactobacillaceae | ||
| Romboutsia |
Revision editor(s): Nuerteye
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