Predominance of Escherichia-Shigella in Gut Microbiome and Its Potential Correlation with Elevated Level of Plasma Tumor Necrosis Factor Alpha in Patients with Tuberculous Meningitis/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Aiyshaaaa on 2023-6-8
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
- Meningeal tuberculosis meningeal tuberculosis,TB meningitis,Meningeal tuberculosis
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy Control (HC)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Tuberculosis Meningitis (TBM)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The patients who have been diagnosed from Tuberculosis Meningitis (TBM).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 9
- Group 1 sample size Number of subjects in the case (exposed) group
- 9
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- proof of extensive antibiotic therapy for 1+ week in previous 6 months. also, prior treatment of systemic antituberculous therapy for more than 1 week.
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
- Welch's 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)?
- No
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
Signature 1
Reviewed Marked as Reviewed by Aiyshaaaa on 2023-6-8
Source: Supplementary Figure. 1 and 2(A)
Description: The Welch’s t-test was used to analyze phylum and genus level differences in microbiota compositions between pairs of groups: HC and TBM
Abundance in Group 1: increased abundance in Tuberculosis Meningitis (TBM)
| NCBI | Quality Control | Links |
|---|---|---|
| Pseudomonadota | ||
| Escherichia/Shigella sp. |
Revision editor(s): Aiyshaaaa
Signature 2
Reviewed Marked as Reviewed by Aiyshaaaa on 2023-6-8
Source: Supplementary Figure. 1 and 2(A)
Description: The Welch’s t-test was used to analyze phylum and genus level differences in microbiota compositions between pairs of groups: HC and TBM
Abundance in Group 1: decreased abundance in Tuberculosis Meningitis (TBM)
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomycetota | ||
| Bacillota | ||
| Blautia | ||
| Bifidobacterium | ||
| Fusicatenibacter | ||
| Parabacteroides | ||
| Roseburia | ||
| Romboutsia |
