Disorders of gut microbiota and fecal-serum metabolic patterns are associated with pulmonary tuberculosis and pulmonary tuberculosis comorbid type 2 diabetes mellitus
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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
Wang Y, He X, Gao Y, Xue M, Zhang H, Sun L, He Q, Jin J
Journal
Microbiology spectrum
Year
2025
Keywords:
diabetes mellitus, fecal metabolites, gut microbiota, metabolic pathways, pulmonary tuberculosis
UNLABELLED: Pulmonary tuberculosis (PTB) and diabetes mellitus (DM) are prevalent chronic diseases with substantial implications for human health. DM patients are more susceptible to PTB, which exacerbates diabetes-related complications. However, the complex molecular mechanisms underlying the enhanced susceptibility of DM patients to PTB infection remain poorly understood. In this study, α- and β-diversity of gut microbiota was significantly reduced in PTB patients and PTB-DM patients. The abundances of families Lachnospiraceae and Ruminococcaceae in the the Firmicutes phylum were reduced in PTB patients and further diminished in PTB-DM patients. On the other hand, untargeted metabolomics in frozen serum and stool samples indicated that phenylalanine, tyrosine, and tryptophan biosynthesis, metabolites of arginine, proline, tryptophan, and histidine were consistently altered in PTB patients and PTB-DM patients, with significant upregulation of most metabolites. Amino acids like serine, proline, and histidine were both remarkably elevated in PTB and PTB-DM patients. The correlation network analysis reveals the relationships between the shared microbial biomarkers and the shared metabolic pathways. This research contributes to the exploration of pivotal diagnostic biomarkers for both patients with PTB and PTB accompanied by diabetes. Specifically, shared reductions were identified in the genera g-Roseburia, g-Ruminococcaceae_UCG.013, g-Ruminococcaceae_NK4A214, g-Lachnospiraceae_unclassified, and g-Firmicutes_unclassified in addition to notable regulation of amino acids, like glycine, serine, and histidine in patients with PTB and PTB-DM. Our study expands the comprehension of the intricate connections linking gut microbiota, fecal metabolites, and serum metabolites in PTB and PTB-DM patients. IMPORTANCE: This study expands the understanding of the complex links between gut microbiota, fecal metabolites, and serum metabolites in patients with PTB and PTB-DM through multi-omics techniques. It is helpful for us to understand the complex molecular mechanism of increased susceptibility to PTB infection in diabetic patients.
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
- Pulmonary tuberculosis , Diabetes mellitus lung TB,lung tuberculosis,pulmonary TB,pulmonary tuberculosis,Tuberculosis, Pulmonary,Pulmonary tuberculosis,Diabetes,diabetes,diabetes mellitus,diabetes mellitus (disease),Diabetes mellitus (disorder),Diabetes mellitus, NOS,Diabetes NOS,DM,DM - Diabetes mellitus,Diabetes mellitus
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Combination of healthy volunteers (Health) and pulmonary tuberculosis patients with diabetes mellitus (PTB-DM)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- pulmonary tuberculosis (PTB) patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Diagnosed via TB-PCR, AFB, Xpert, plus clinical TB
- Group 0 sample size Number of subjects in the control (unexposed) group
- 26
- Group 1 sample size Number of subjects in the case (exposed) group
- 13
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Not received any anti-tuberculosis antibiotics or other treatments for tuberculosis prior to sample collection
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
- 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
- 2
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
Signature 1
Source: Figure 3A and 3B
Description: Identification of differential microbial biomarkers. Cladogram visualized the most differentially abundant taxa identified by LEfSe among the three groups. Comparisons of microbiota bacteria among the three groups. The histogram showed the LDA score computed for genera differentially abundant between groups and identified using LEfSe. Health: healthy people, PTB: pulmonary tuberculosis, PTB-DM: pulmonary tuberculosis patients with diabetes mellitus.
Abundance in Group 1: increased abundance in pulmonary tuberculosis (PTB) patients
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 pulmonary tuberculosis (PTB) and pulmonary tuberculosis patients with diabetes mellitus (PTB-DM) group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Healthy participants in our study had normal lifestyles. In terms of diet, they maintained a balanced diet with a variety of foods. Their sleep patterns were regular, ensuring an adequate amount of sleep every night. They also engaged in regular physical exercise and had effective stress control methods.
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- none of the healthy participants had taken antibiotics within 1 year prior to sampling.
Lab analysis
Statistical Analysis
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
Signature 1
Source: Figure 3A and 3B
Description: Identification of differential microbial biomarkers. Cladogram visualized the most differentially abundant taxa identified by LEfSe among the three groups. Comparisons of microbiota bacteria among the three groups. The histogram showed the LDA score computed for genera differentially abundant between groups and identified using LEfSe. Health: healthy people, PTB: pulmonary tuberculosis, PTB-DM: pulmonary tuberculosis patients with diabetes mellitus.
Abundance in Group 1: increased abundance in pulmonary tuberculosis (PTB) patients
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 volunteers (Health) and pulmonary tuberculosis (PTB) group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- pulmonary tuberculosis and diabetes mellitus (PTB–DM)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Individuals presenting typical diabetic symptoms (polyuria, polydipsia, unexplained weight loss), fasting blood glucose ≥11.1 mmol or random blood glucose levels ≥ 11.1 mmol/L, and age between 18 and 65 years
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Not specified
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
Signature 1
Source: Figure 3A and 3B
Description: Identification of differential microbial biomarkers. Cladogram visualized the most differentially abundant taxa identified by LEfSe among the three groups. Comparisons of microbiota bacteria among the three groups. The histogram showed the LDA score computed for genera differentially abundant between groups and identified using LEfSe. Health: healthy people, PTB: pulmonary tuberculosis, PTB-DM: pulmonary tuberculosis patients with diabetes mellitus.
Abundance in Group 1: increased abundance in pulmonary tuberculosis and diabetes mellitus (PTB–DM)
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillales | ||
| Bacilli | ||
| Fusobacteriales | ||
| Fusobacteriaceae | ||
| Fusobacterium | ||
| Fusobacterium mortiferum | ||
| Clostridium innocuumClostridium innocuum | ||
| Faecalibacterium |
Revision editor(s): Nuerteye
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