Dysbiosis of the Saliva Microbiome in Patients With Polycystic Ovary Syndrome
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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
- Saliva Sailva normalis,Saliva atomaris,Saliva molecularis,Salivary gland secretion,Saliva,saliva
- 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
- Healthy control at Zeitgeber (ZT) 0
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- PCOS patients at Zeitgeber (ZT) 0
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Samples collected from patients with Polycystic Ovary Syndrome who were diagnosed according to the Rotterdam Criteria, who met two out of three of the following criteria: clinical/biochemical hyperandrogenism, oligo-/anovulation, and polycystic ovaries at Zeitgeber (ZT) 0
- Group 0 sample size Number of subjects in the control (unexposed) group
- 10
- Group 1 sample size Number of subjects in the case (exposed) group
- 10
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- use of antibiotics within 3 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
- 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)?
- No
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 4
- Matched on Factors on which subjects have been matched on in a case-control study
- body mass index, age, Matched on: "metabolic factors" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.metabolic factors
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
Source: Figure 3A
Description: Identification of specific bacterial taxa in PCOS patients and controls at different time points. Linear discriminant analysis (LDA) effect size (LEfSe) was used to identify biomarkers with significant differences between the two groups: Control.ZT0 vs. PCOS.ZT0
Abundance in Group 1: increased abundance in PCOS patients at Zeitgeber (ZT) 0
Revision editor(s): Idiaru angela
Signature 2
Source: Figure 3A
Description: Identification of specific bacterial taxa in PCOS patients and controls at different time points. Linear discriminant analysis (LDA) effect size (LEfSe) was used to identify biomarkers with significant differences between the two groups: Control.ZT0 vs. PCOS.ZT0
Abundance in Group 1: decreased abundance in PCOS patients at Zeitgeber (ZT) 0
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomycetota | ||
| Leptotrichia | ||
| Prevotella histicola |
Revision editor(s): Idiaru angela
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy control at Zeitgeber (ZT) 6
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- PCOS patients at Zeitgeber (ZT) 6
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Samples collected from patients with Polycystic Ovary Syndrome who were diagnosed according to the Rotterdam Criteria, who met two out of three of the following criteria: clinical/biochemical hyperandrogenism, oligo-/anovulation, and polycystic ovaries at Zeitgeber (ZT) 6
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Source: Figure 3B
Description: Identification of specific bacterial taxa in PCOS patients and controls at different time points. Linear discriminant analysis (LDA) effect size (LEfSe) was used to identify biomarkers with significant differences between the two groups: Control.ZT6 vs. PCOS.ZT6
Abundance in Group 1: increased abundance in PCOS patients at Zeitgeber (ZT) 6
| NCBI | Quality Control | Links |
|---|---|---|
| Fusobacteriaceae | ||
| Fusobacteriales | ||
| Fusobacteriia | ||
| Fusobacteriota | ||
| Fusobacterium | ||
| Fusobacterium periodonticum | ||
| SR1 bacterium oral taxon 875 |
Revision editor(s): Idiaru angela
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy control at Zeitgeber (ZT) 12
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- PCOS patients at Zeitgeber (ZT) 12
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Samples collected from patients with Polycystic Ovary Syndrome who were diagnosed according to the Rotterdam Criteria, who met two out of three of the following criteria: clinical/biochemical hyperandrogenism, oligo-/anovulation, and polycystic ovaries at Zeitgeber (ZT) 12
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Source: Figure 3C
Description: Identification of specific bacterial taxa in PCOS patients and controls at different time points. Linear discriminant analysis (LDA) effect size (LEfSe) was used to identify biomarkers with significant differences between the two groups: Control.ZT12 vs. PCOS.ZT12
Abundance in Group 1: increased abundance in PCOS patients at Zeitgeber (ZT) 12
| NCBI | Quality Control | Links |
|---|---|---|
| Fusobacterium | ||
| Fusobacteriaceae | ||
| Fusobacterium periodonticum |
Revision editor(s): Idiaru angela
Signature 2
Source: Figure 3C
Description: Identification of specific bacterial taxa in PCOS patients and controls at different time points. Linear discriminant analysis (LDA) effect size (LEfSe) was used to identify biomarkers with significant differences between the two groups: Control.ZT12 vs. PCOS.ZT12
Abundance in Group 1: decreased abundance in PCOS patients at Zeitgeber (ZT) 12
| NCBI | Quality Control | Links |
|---|---|---|
| Leptotrichia | ||
| Prevotella histicola |
Revision editor(s): Idiaru angela
Experiment 4
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy control at Zeitgeber (ZT) 18
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- PCOS patients at Zeitgeber (ZT) 18
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Samples collected from patients with Polycystic Ovary Syndrome who were diagnosed according to the Rotterdam Criteria, who met two out of three of the following criteria: clinical/biochemical hyperandrogenism, oligo-/anovulation, and polycystic ovaries at Zeitgeber (ZT) 18
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Source: Figure 3D
Description: Identification of specific bacterial taxa in PCOS patients and controls at different time points. Linear discriminant analysis (LDA) effect size (LEfSe) was used to identify biomarkers with significant differences between the two groups: Control.ZT18 vs. PCOS.ZT18
Abundance in Group 1: increased abundance in PCOS patients at Zeitgeber (ZT) 18
Revision editor(s): Idiaru angela
Signature 2
Source: Figure 3D
Description: Identification of specific bacterial taxa in PCOS patients and controls at different time points. Linear discriminant analysis (LDA) effect size (LEfSe) was used to identify biomarkers with significant differences between the two groups: Control.ZT18 vs. PCOS.ZT18
Abundance in Group 1: decreased abundance in PCOS patients at Zeitgeber (ZT) 18
| NCBI | Quality Control | Links |
|---|---|---|
| Neisseria flava | ||
| unclassified Cyanobacteriota | ||
| Cyanobacteriota | ||
| Leptotrichiaceae | ||
| Leptotrichia | ||
| Prevotella histicola | ||
| unclassified Prevotellaceae |
Revision editor(s): Idiaru angela
Experiment 5
Subjects
- 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
- 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
- PCOS Patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- PCOS patients who were diagnosed according to the Rotterdam Criteria, who met two out of three of the following criteria: clinical/biochemical hyperandrogenism, oligo-/anovulation, and polycystic ovaries
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Supplemental Figure 5E
Description: The microbiota that showed significant differences between the two groups as analysed by LEfSe with an LDA score threshold of 4.0.
Abundance in Group 1: decreased abundance in PCOS Patients
| NCBI | Quality Control | Links |
|---|---|---|
| Blautia | ||
| Streptococcus | ||
| Streptococcaceae | ||
| Streptococcus thermophilus | ||
| Bifidobacterium adolescentis |
Revision editor(s): Idiaru angela
