Gut microbiota modulation via fecal microbiota transplantation mitigates hyperoxaluria and calcium oxalate crystal depositions induced by high oxalate diet
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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.
- Rattus norvegicus
- 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
- Oxalate measurement Oxalate measurement,oxalate measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- 5%K2Ox-0day
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- 5%K2Ox-45day
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Rats exposed to a 5% K2Ox diet that induces hyperoxaluria, evidenced by increased urinary oxalate excretion and renal CaOx crystal deposition
- 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
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
- MaAsLin2
- 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
- 3.5
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 1e
Description: The differential genera between the Normal group and the HDOx groups at day 45.
Abundance in Group 1: increased abundance in 5%K2Ox-45day
Revision editor(s): Dorcas-od
Signature 2
Source: Figure 1e-h
Description: (e, f) The differential genera between the Normal group and the HDOx groups at day 45.
Abundance in Group 1: decreased abundance in 5%K2Ox-45day
| NCBI | Quality Control | Links |
|---|---|---|
| Parasutterella | ||
| Ruminococcaceae_UCG-005Ruminococcaceae_UCG-005 |
Revision editor(s): Dorcas-od
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- 5%Hyp-0day
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- 5%Hyp-45day
Lab analysis
Statistical Analysis
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 1f
Description: The differential genera between the Normal group and the HDOx groups at day 45.
Abundance in Group 1: increased abundance in 5%Hyp-45day
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillus | ||
| Ruminococcaceae_UCG-014Ruminococcaceae_UCG-014 | ||
| Eubacterium coprostanoligenes |
Revision editor(s): Dorcas-od
Signature 2
Source: Figure 1f
Description: The differential genera between the Normal group and the HDOx groups at day 45.
Abundance in Group 1: decreased abundance in 5%Hyp-45day
| NCBI | Quality Control | Links |
|---|---|---|
| Blautia | ||
| Ruminococcaceae_UCG-005Ruminococcaceae_UCG-005 | ||
| Bacteroidia | ||
| Parasutterella | ||
| Alloprevotella | ||
| Fusicatenibacter | ||
| Oscillospira |
Revision editor(s): Dorcas-od
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Normal-45day
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- 5%K2Ox-45day
Lab analysis
Statistical Analysis
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 1g
Description: The different genera between the day 0 and day 45 of HDOx groups. ns: no significance. & : p < 0.05. ### : p < 0.001. **** ,#### ,^^^^ and &&&& : p < 0.001.
Abundance in Group 1: increased abundance in 5%K2Ox-45day
Revision editor(s): Dorcas-od
Signature 2
Source: Figure 1g
Description: The different genera between the day 0 and day 45 of HDOx groups. ns: no significance. & : p < 0.05. ### : p < 0.001. **** ,#### ,^^^^ and &&&& : p < 0.001.
Abundance in Group 1: decreased abundance in 5%K2Ox-45day
Revision editor(s): Dorcas-od
Experiment 4
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- 5%Hyp-45day
Lab analysis
Statistical Analysis
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 1h
Description: The different genera between the day 0 and day 45 of HDOx groups. ns: no significance. & : p < 0.05. ### : p < 0.001. **** ,#### ,^^^^ and &&&& : p < 0.001.
Abundance in Group 1: increased abundance in 5%Hyp-45day
Revision editor(s): Dorcas-od
Signature 2
Source: Figure 1h
Description: The different genera between the day 0 and day 45 of HDOx groups. ns: no significance. & : p < 0.05. ### : p < 0.001. **** ,#### ,^^^^ and &&&& : p < 0.001.
Abundance in Group 1: decreased abundance in 5%Hyp-45day
Revision editor(s): Dorcas-od
Experiment 5
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Response to transplant Response to transplant,response to transplant
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Normal Group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- 5%K2Ox
Lab analysis
Statistical Analysis
- Statistical test
- ANOVA
- LEfSe
- Spearman Correlation
- Welch's T-Test
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 4a
Description: The effects of FMT on gut microbiota and metabolism.
Abundance in Group 1: increased abundance in 5%K2Ox
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidota | ||
| Pseudomonadota | ||
| Actinomycetota |
Revision editor(s): Dorcas-od
Signature 2
Source: Figure 4a
Description: The effects of FMT on gut microbiota and metabolism.
Abundance in Group 1: decreased abundance in 5%K2Ox
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillota |
Revision editor(s): Dorcas-od
Experiment 6
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- 5%K2OxFMT
Lab analysis
Statistical Analysis
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 4a
Description: The effects of FMT on gut microbiota and metabolism.
Abundance in Group 1: increased abundance in 5%K2OxFMT
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomycetota | ||
| Bacteroidota | ||
| Pseudomonadota |
Revision editor(s): Dorcas-od
Signature 2
Source: Figure 4a
Description: The effects of FMT on gut microbiota and metabolism.
Abundance in Group 1: decreased abundance in 5%K2OxFMT
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillota |
Revision editor(s): Dorcas-od
Experiment 7
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- 5%K2Ox
Lab analysis
Statistical Analysis
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 4a
Description: The effects of FMT on gut microbiota and metabolism.
Abundance in Group 1: increased abundance in 5%K2OxFMT
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillota |
Revision editor(s): Dorcas-od
Experiment 8
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Normal Group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- 5%Hyp
Lab analysis
Statistical Analysis
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 4a
Description: The effects of FMT on gut microbiota and metabolism.
Abundance in Group 1: increased abundance in 5%Hyp
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidota | ||
| Verrucomicrobiota |
Revision editor(s): Dorcas-od
Experiment 9
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- 5%Hyp
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- 5%HypFMT
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The effects of FMT on gut microbiota and metabolism.
Lab analysis
Statistical Analysis
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 4a
Description: The effects of FMT on gut microbiota and metabolism.
Abundance in Group 1: increased abundance in 5%HypFMT
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillota |
Revision editor(s): Dorcas-od
Signature 2
Source: Figure 4a
Description: The effects of FMT on gut microbiota and metabolism.
Abundance in Group 1: decreased abundance in 5%HypFMT
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidota | ||
| Verrucomicrobiota |
Revision editor(s): Dorcas-od
Experiment 10
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- 5%K2Ox
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- 5%K2OxFMT
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Rats exposed to a 5% K2Ox diet that induces hyperoxaluria, evidenced by increased urinary oxalate excretion and renal CaOx crystal deposition
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
Experiment 11
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- 5%Hyp
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- 5%HypFMT
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Not specified
- Group 0 sample size Number of subjects in the control (unexposed) group
- Not specified
- Group 1 sample size Number of subjects in the case (exposed) group
- Not specified
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Rats exposed to a 5% K2Ox diet that induces hyperoxaluria, evidenced by increased urinary oxalate excretion and renal CaOx crystal deposition
Lab analysis
Statistical Analysis
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 4c
Description: The effects of FMT on gut microbiota and metabolism.
Abundance in Group 1: increased abundance in 5%HypFMT
| NCBI | Quality Control | Links |
|---|---|---|
| Parasutterella |
Revision editor(s): Dorcas-od
