Modulatory impact of Bifidobacterium longum subsp. longum BL21 on the gut-brain-ovary axis in polycystic ovary syndrome: insights into metabolic regulation, inflammation mitigation, and neuroprotection
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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.
- Mus musculus
- 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
- Polycystic ovary syndrome (PCOS) + Bifidobacterium longum subsp. longum (BL21) group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Control (CTL) group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group consists of pregnant mice used as controls.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 16
- Group 1 sample size Number of subjects in the case (exposed) group
- 8
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
- 2
Signature 1
Source: Figure 6A
Description: Results of the linear discriminant analysis effect size (LEfSe) analysis, showing the impact of BL21 treatment on differences in the abundance of bacterial taxa at the genus level. LEfSe analysis evaluates each significantly enriched bacterial taxonomic unit by calculating linear discriminant analysis (LDA) scores.
Abundance in Group 1: increased abundance in Control (CTL) group
| NCBI | Quality Control | Links |
|---|---|---|
| Parasutterella | ||
| Odoribacter | ||
| Bacteria incertae sedis | ||
| Colidextribacter | ||
| Helicobacter | ||
| Rs-E47 termite groupRs-E47 termite group |
Revision editor(s): Victoria
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Control (CTL) + Bifidobacterium longum subsp. longum (BL21) group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Polycystic ovary syndrome (PCOS) group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group consists of mice that were given dihydrotestosterone (DHT) to induce Polycystic ovary syndrome (PCOS).
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 6A
Description: Results of the linear discriminant analysis effect size (LEfSe) analysis, showing the impact of BL21 treatment on differences in the abundance of bacterial taxa at the genus level. LEfSe analysis evaluates each significantly enriched bacterial taxonomic unit by calculating linear discriminant analysis (LDA) scores.
Abundance in Group 1: increased abundance in Polycystic ovary syndrome (PCOS) group
Revision editor(s): Victoria
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Control (CTL) + Polycystic ovary syndrome (PCOS) group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Bifidobacterium longum subsp. longum (BL21) group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group consists of mice that were given dihydrotestosterone (DHT) to induce Polycystic ovary syndrome (PCOS) and then administered a daily oral dose of 1 × 109 CFU of BL21 continuously for a total of 8 weeks as treatment.
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 6A
Description: Results of the linear discriminant analysis effect size (LEfSe) analysis, showing the impact of BL21 treatment on differences in the abundance of bacterial taxa at the genus level. LEfSe analysis evaluates each significantly enriched bacterial taxonomic unit by calculating linear discriminant analysis (LDA) scores.
Abundance in Group 1: increased abundance in Bifidobacterium longum subsp. longum (BL21) group
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Butyricicoccus | ||
| Lachnospiraceae UCG-010Lachnospiraceae UCG-010 | ||
| Muribaculum | ||
| Muribaculaceae | ||
| Lactobacillus | ||
| Bifidobacterium | ||
| Rikenella | ||
| Blautia | ||
| Actinomyces |
Revision editor(s): Victoria
Experiment 4
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Control (CTL) group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Polycystic Ovary Syndrome (PCOS) group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group consists of mice that were given dihydrotestosterone (DHT) to induce Polycystic ovary syndrome (PCOS)—pre-BL21 intervention.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 8
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
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Figure 6B
Description: LEfSe analysis results at the genus level between the DHT-induced PCOS mouse model and the control (CTL) group.
Abundance in Group 1: increased abundance in Polycystic Ovary Syndrome (PCOS) group
Revision editor(s): Victoria
Signature 2
Source: Figure 6B
Description: LEfSe analysis results at the genus level between the DHT-induced PCOS mouse model and the control (CTL) group.
Abundance in Group 1: decreased abundance in Polycystic Ovary Syndrome (PCOS) group
| NCBI | Quality Control | Links |
|---|---|---|
| Parabacteroides | ||
| UCG-009UCG-009 | ||
| Rs-E47 termite groupRs-E47 termite group | ||
| Odoribacter | ||
| Lactobacillus | ||
| Bifidobacterium | ||
| Desulfovibrio | ||
| Alistipes |
Revision editor(s): Victoria
Experiment 5
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Polycystic Ovary Syndrome (PCOS) group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Bifidobacterium longum subsp. longum (BL21) group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group consists of mice that were given dihydrotestosterone (DHT) to induce Polycystic ovary syndrome (PCOS) and then administered a daily oral dose of 1 × 109 CFU of BL21 continuously for a total of 8 weeks as treatment.—post-BL21 intervention.
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
- Richness Number of species
- increased
Signature 1
Source: Figure 6C
Description: Post-intervention LEfSe analysis results at the genus level between the DHT-induced PCOS mouse model and the BL21 treatment group.
Abundance in Group 1: increased abundance in Bifidobacterium longum subsp. longum (BL21) group
| NCBI | Quality Control | Links |
|---|---|---|
| Ruminococcus | ||
| Rikenella | ||
| Lactobacillus | ||
| Lachnospiraceae NK4A136 groupLachnospiraceae NK4A136 group | ||
| Bifidobacterium | ||
| Bacteroides |
Revision editor(s): Victoria
Signature 2
Source: Figure 6C
Description: Post-intervention LEfSe analysis results at the genus level between the DHT-induced PCOS mouse model and the BL21 treatment group.
Abundance in Group 1: decreased abundance in Bifidobacterium longum subsp. longum (BL21) group
| NCBI | Quality Control | Links |
|---|---|---|
| Odoribacter | ||
| Lachnoclostridium | ||
| Muribaculaceae | ||
| Helicobacter | ||
| Alistipes |
Revision editor(s): Victoria
Experiment 6
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Bifidobacterium longum subsp. longum (BL21_Baseline) group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Bifidobacterium longum subsp. longum (BL21_End) group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group consists of mice that were given dihydrotestosterone (DHT) to induce Polycystic ovary syndrome (PCOS) and then administered a daily oral dose of 1 × 109 CFU of BL21 continuously for a total of 8 weeks as treatment (after BL21 intervention).
Lab analysis
Statistical Analysis
- Statistical test
- Kruskall-Wallis
- Mann-Whitney (Wilcoxon)
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- Not specified
Signature 1
Source: Figure 5B
Description: Violin plots illustrating differences in gut microbiota abundance at the phylum level before and after BL21 intervention at different time points. Different letters indicate statistically significant differences between groups.
Abundance in Group 1: increased abundance in Bifidobacterium longum subsp. longum (BL21_End) group
| NCBI | Quality Control | Links |
|---|---|---|
| Thermodesulfobacteriota |
Revision editor(s): Victoria
Experiment 7
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Control (CTL_Baseline) group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Control (CTL_End) group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group consists of pregnant mice used as controls (after BL21 intervention)
Signature 1
Source: Figure 5B
Description: Violin plots illustrating differences in gut microbiota abundance at the phylum level before and after BL21 intervention at different time points.
Abundance in Group 1: increased abundance in Control (CTL_End) group
| NCBI | Quality Control | Links |
|---|---|---|
| Thermodesulfobacteriota | ||
| Campylobacterota |
Revision editor(s): Victoria
Signature 2
Source: Figure 5B
Description: Violin plots illustrating differences in gut microbiota abundance at the phylum level before and after BL21 intervention at different time points.
Abundance in Group 1: decreased abundance in Control (CTL_End) group
| NCBI | Quality Control | Links |
|---|---|---|
| Pseudomonadota |
Revision editor(s): Victoria
Experiment 8
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Polycystic Ovary Syndrome (PCOS_Baseline) group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Polycystic Ovary Syndrome (PCOS_End) group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group consists of mice that were given dihydrotestosterone (DHT) to induce Polycystic ovary syndrome (PCOS) (after BL21 intervention).
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 5B
Description: Violin plots illustrating differences in gut microbiota abundance at the phylum level before and after BL21 intervention at different time points. Different letters indicate statistically significant differences between groups.
Abundance in Group 1: increased abundance in Polycystic Ovary Syndrome (PCOS_End) group
| NCBI | Quality Control | Links |
|---|---|---|
| Thermodesulfobacteriota |
Revision editor(s): Victoria
Signature 2
Source: Figure 5B
Description: Violin plots illustrating differences in gut microbiota abundance at the phylum level before and after BL21 intervention at different time points. Different letters indicate statistically significant differences between groups.
Abundance in Group 1: decreased abundance in Polycystic Ovary Syndrome (PCOS_End) group
| NCBI | Quality Control | Links |
|---|---|---|
| Campylobacterota | ||
| Bacillota |
Revision editor(s): Victoria
