Structural and functional profiles of the gut microbial community in polycystic ovary syndrome with insulin resistance (IR-PCOS): a pilot study
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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. 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
- Polycystic ovary syndrome Cystic disease of ovaries,hyperandrogenemia,Multicystic ovaries,multicystic ovaries,Ovarian Degeneration, Sclerocystic,Ovarian Syndrome, Polycystic,Ovarian Syndromes, Polycystic,Ovaries, Sclerocystic,Ovary Syndrome, Polycystic,Ovary, Sclerocystic,PCO - Polycystic ovaries,Pco1,PCOD - Polycystic ovarian disease,PCOS,Pcos,PCOS - Polycystic ovarian syndrome,PCOS1,Polycystic ovarian disease,polycystic ovarian disease,Polycystic ovarian syndrome,Polycystic ovaries,polycystic ovaries,Polycystic ovaries (disorder),polycystic ovary,polycystic ovary syndrome,polycystic ovary syndrome 1,Sclerocystic Ovarian Degeneration,Sclerocystic Ovaries,Sclerocystic Ovary,Sclerocystic Ovary Syndrome,Stein Leventhal Syndrome,Stein-Leventhal synd.,Stein-Leventhal Syndrome,Stein-Leventhal syndrome,Syndrome, Polycystic Ovary,Syndrome, Stein-Leventhal,Polycystic ovary syndrome
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- HC - Healthy Controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- NIR-PCOS - NIR(Non-Insulin Resistance)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- NIR-PCOS - PCOS without insulin resistance
- Group 0 sample size Number of subjects in the control (unexposed) group
- 8
- Group 1 sample size Number of subjects in the case (exposed) group
- 8
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Administration of antibiotics
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
- 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
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Source: Figure 3
Description: Identification of the bacterial taxa with statistically significant difference between groups using LEfSe software. LEfSe was performed in pairwise manner for HC vs. NIR-PCOS (A), HC vs. IR-PCOS (B) and NIR-PCOS vs. IR-PCOS (C). Cladograms show the taxonomic hierarchical structure and the circles from the inside to the outside indicate kingdom, phyla, class, order, family, genus. Taxa enriched in HC, NIR-PCOS and IR-PCOS group are colored by green, blue and red respectively (LDA > 2.0 and P < 0.05), relative abundance of these biomarkers are showed in the histogram (mean and standard deviation values are plotted) under the corresponding cladogram.
Abundance in Group 1: increased abundance in NIR-PCOS - NIR(Non-Insulin Resistance)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidaceae | ||
| Bacteroides | ||
| Lachnospira | ||
| Lachnospiraceae |
Revision editor(s): WikiWorks, Peace Sandy
Signature 2
Source: Figure 3
Description: Identification of the bacterial taxa with statistically significant difference between groups using LEfSe software. LEfSe was performed in pairwise manner for HC vs. NIR-PCOS (A), HC vs. IR-PCOS (B) and NIR-PCOS vs. IR-PCOS (C). Cladograms show the taxonomic hierarchical structure and the circles from the inside to the outside indicate kingdom, phyla, class, order, family, genus. Taxa enriched in HC, NIR-PCOS and IR-PCOS group are colored by green, blue and red respectively (LDA > 2.0 and P < 0.05), relative abundance of these biomarkers are showed in the histogram (mean and standard deviation values are plotted) under the corresponding cladogram.
Abundance in Group 1: decreased abundance in NIR-PCOS - NIR(Non-Insulin Resistance)
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotella | ||
| Prevotellaceae |
Revision editor(s): WikiWorks, Peace Sandy
Experiment 2
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- IR-PCOS IR-(Insulin Resistance)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- PCOS with Insulin resistance
- Group 1 sample size Number of subjects in the case (exposed) group
- 9
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Source: Figure 3
Description: Identification of the bacterial taxa with statistically significant difference between groups using LEfSe software. LEfSe was performed in pairwise manner for HC vs. NIR-PCOS (A), HC vs. IR-PCOS (B) and NIR-PCOS vs. IR-PCOS (C). Cladograms show the taxonomic hierarchical structure and the circles from the inside to the outside indicate kingdom, phyla, class, order, family, genus. Taxa enriched in HC, NIR-PCOS and IR-PCOS group are colored by green, blue and red respectively (LDA > 2.0 and P < 0.05), relative abundance of these biomarkers are showed in the histogram (mean and standard deviation values are plotted) under the corresponding cladogram.
Abundance in Group 1: increased abundance in IR-PCOS IR-(Insulin Resistance)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidaceae | ||
| Bacteroides | ||
| Lachnospira |
Revision editor(s): WikiWorks, Peace Sandy
Signature 2
Source: Figure 3
Description: Identification of the bacterial taxa with statistically significant difference between groups using LEfSe software. LEfSe was performed in pairwise manner for HC vs. NIR-PCOS (A), HC vs. IR-PCOS (B) and NIR-PCOS vs. IR-PCOS (C). Cladograms show the taxonomic hierarchical structure and the circles from the inside to the outside indicate kingdom, phyla, class, order, family, genus. Taxa enriched in HC, NIR-PCOS and IR-PCOS group are colored by green, blue and red respectively (LDA > 2.0 and P < 0.05), relative abundance of these biomarkers are showed in the histogram (mean and standard deviation values are plotted) under the corresponding cladogram.
Abundance in Group 1: decreased abundance in IR-PCOS IR-(Insulin Resistance)
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotella | ||
| Prevotellaceae |
Revision editor(s): WikiWorks, Peace Sandy
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- NIR-PCOS - NIR(Non-Insulin Resistance)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- PCOS with Insulin Resistance
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Source: Figure 3
Description: Identification of the bacterial taxa with statistically significant difference between groups using LEfSe software. LEfSe was performed in pairwise manner for HC vs. NIR-PCOS (A), HC vs. IR-PCOS (B) and NIR-PCOS vs. IR-PCOS (C). Cladograms show the taxonomic hierarchical structure and the circles from the inside to the outside indicate kingdom, phyla, class, order, family, genus. Taxa enriched in HC, NIR-PCOS and IR-PCOS group are colored by green, blue and red respectively (LDA > 2.0 and P < 0.05), relative abundance of these biomarkers are showed in the histogram (mean and standard deviation values are plotted) under the corresponding cladogram.
Abundance in Group 1: increased abundance in IR-PCOS IR-(Insulin Resistance)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidaceae | ||
| Bacteroidales | ||
| Bacteroides | ||
| Bacteroidia |
Revision editor(s): WikiWorks, Peace Sandy
Signature 2
Source: Figure 3
Description: Identification of the bacterial taxa with statistically significant difference between groups using LEfSe software. LEfSe was performed in pairwise manner for HC vs. NIR-PCOS (A), HC vs. IR-PCOS (B) and NIR-PCOS vs. IR-PCOS (C). Cladograms show the taxonomic hierarchical structure and the circles from the inside to the outside indicate kingdom, phyla, class, order, family, genus. Taxa enriched in HC, NIR-PCOS and IR-PCOS group are colored by green, blue and red respectively (LDA > 2.0 and P < 0.05), relative abundance of these biomarkers are showed in the histogram (mean and standard deviation values are plotted) under the corresponding cladogram.
Abundance in Group 1: decreased abundance in IR-PCOS IR-(Insulin Resistance)
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridia | ||
| Eubacteriales | ||
| Faecalibacterium | ||
| Lachnospiraceae | ||
| Bacillota |
Revision editor(s): WikiWorks, Peace Sandy
