Alterations of Gut Microbiota in Patients With Graves' Disease/Experiment 2
From BugSigDB
Needs review
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
- Graves disease Basedow disease,Basedow's disease,exophthalmic goiter,Flajani-Basedow-Graves disease,grave's disease,Graves disease,Graves' disease,Graves' hyperthyroidism,parry disease,toxic diffuse goiter,graves disease
- 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
- Graves’ disease (GD)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients diagnosed with Graves’ disease (GD)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 48
- Group 1 sample size Number of subjects in the case (exposed) group
- 55
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Two months
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)?
- Yes
- Matched on Factors on which subjects have been matched on in a case-control study
- age, body mass index, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Needs review
Source: Figure 2C
Description: Differentially abundant taxa from the phylum to genus level were further analyzed by STAMP analysis using Welch’s t-test (p < 0.05, q < 0.05) (C).
Abundance in Group 1: increased abundance in Graves’ disease (GD)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidota | ||
| Actinomycetota | ||
| Tannerellaceae | ||
| Erysipelotrichaceae | ||
| Coriobacteriaceae | ||
| Prevotellaceae | ||
| Actinomycetaceae | ||
| Parabacteroides | ||
| Collinsella | ||
| Prevotella | ||
| Schaalia odontolytica |
Revision editor(s): Aleru Divine
Signature 2
Needs review
Source: Figure 2C
Description: Differentially abundant taxa from the phylum to genus level were further analyzed by STAMP analysis using Welch’s t-test (p < 0.05, q < 0.05) (C).
Abundance in Group 1: decreased abundance in Graves’ disease (GD)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillota | ||
| Lachnospiraceae |
Revision editor(s): Aleru Divine
