Self-Balance of Intestinal Flora in Spouses of Patients With Rheumatoid Arthritis
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Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
Experiment 1
Subjects
- Location of subjects
- China
- Host species Species from which microbiome was sampled (if applicable)
- 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
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- rheumatoid arthritis Arthritis or polyarthritis, rheumatic,arthritis or polyarthritis, rheumatic,Arthritis, Rheumatoid,arthritis, rheumatoid,atrophic Arthritis,atrophic arthritis,autoimmune arthritis,Chronic rheumatic arthritis,Proliferative arthritis,RA,RA - Rheumatoid arthritis,RhA - Rheumatoid arthritis,Rheumatic gout,rheumatoid arthritis,Rheumatoid arthritis (disorder),Rheumatoid arthritis NOS,Rheumatoid arthritis NOS (disorder),rheumatoid arthritis, susceptibility to,Rheumatoid 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
- rheumatoid arthritis patient
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- rheumatoid arthritis patient
- Group 0 sample size Number of subjects in the control (unexposed) group
- 20
- Group 1 sample size Number of subjects in the case (exposed) group
- 30
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Potential volunteer enrolees (including patients and or healthy individuals) were excluded from this study if having: (1) ingested antibiotics in the last 6 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
- Statistical test
- LEfSe
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- .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
- 2
- Matched on Factors on which subjects have been matched on in a case-control study
- sex, age
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 3, text
Description: Discriminant analysis of LEfSe multistage species difference.
Abundance in Group 1: decreased abundance in rheumatoid arthritis patient
NCBI | Quality Control | Links |
---|---|---|
Roseburia | ||
Lachnoclostridium |
Revision editor(s): Tislam
Signature 2
Source: Figure 3, text
Description: Discriminant analysis of LEfSe multistage species difference. It can be seen from the figure that, among the three groups, the abundance peaks of species with significant differences were distributed in RA and HC, respectively, and there was no peak in the SP group.
Abundance in Group 1: decreased abundance in rheumatoid arthritis patient
Revision editor(s): Tislam
Signature 3
Source: Figure 3, text
Description: Discriminant analysis of LEfSe multistage species difference. It can be seen from the figure that, among the three groups, the abundance peaks of species with significant differences were distributed in RA and HC, respectively, and there was no peak in the SP group.
Abundance in Group 1: decreased abundance in rheumatoid arthritis patient
NCBI | Quality Control | Links |
---|---|---|
Revision editor(s): Tislam
Signature 5
Source: Figure 3, text
Description: Discriminant analysis of LEfSe multistage species difference.
Abundance in Group 1: decreased abundance in rheumatoid arthritis patient
NCBI | Quality Control | Links |
---|---|---|
Roseburia |
Revision editor(s): Tislam
Signature 6
Source: Figure 3, text
Description: Discriminant analysis of LEfSe multistage species difference.
Abundance in Group 1: decreased abundance in rheumatoid arthritis patient
NCBI | Quality Control | Links |
---|---|---|
Roseburia |
Revision editor(s): Tislam
Signature 8
Source: Figure1
Description:
Abundance in Group 1: decreased abundance in rheumatoid arthritis patient
NCBI | Quality Control | Links |
---|---|---|
Acetitomaculum |
Revision editor(s): Fatima