Gut microbiota modulation via fecal microbiota transplantation mitigates hyperoxaluria and calcium oxalate crystal depositions induced by high oxalate diet
-
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 at day 45 after exposure to a 5% K₂Ox(Potassium Oxalate) diet that induces hyperoxaluria, evidenced by increased urinary oxalate excretion and renal CaOx(Calcium Oxalate) 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).
- arcsine square-root
- 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
Signature 1
Source: Figure 1e
Description: The different genera between the day 0 and day 45 of HDOx groups
Abundance in Group 1: increased abundance in 5%K₂Ox-45day
| NCBI | Quality Control | Links |
|---|---|---|
| Parasutterella | ||
| Ruminococcaceae bacterium UCG-005 |
Revision editor(s): Dorcas-od, Anne-mariesharp
Signature 2
Source: Figure 1e
Description: The different genera between the day 0 and day 45 of HDOx groups
Abundance in Group 1: decreased abundance in 5%K₂Ox-45day
Revision editor(s): Dorcas-od, Anne-mariesharp
Experiment 2
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Hydroxyproline measurement Hydroxyproline measurement,hydroxyproline measurement
- 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
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Rats at day 45 after exposure to a 5%Hyp(Hydroxyproline) oxalate precursor-diet that induces hyperoxaluria, evidenced by increased urinary oxalate excretion and renal CaOx(Calcium Oxalate) crystal deposition
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 1f
Description: The different genera between the day 0 and day 45 of HDOx groups
Abundance in Group 1: increased abundance in 5%Hyp-45day
| NCBI | Quality Control | Links |
|---|---|---|
| Alloprevotella | ||
| Bacteroides | ||
| Blautia | ||
| Fusicatenibacter | ||
| Oscillospira | ||
| Parasutterella | ||
| Ruminococcaceae bacterium UCG-005 |
Revision editor(s): Dorcas-od, Anne-mariesharp
Signature 2
Source: Figure 1f
Description: The different genera between the day 0 and day 45 of HDOx groups
Abundance in Group 1: decreased abundance in 5%Hyp-45day
| NCBI | Quality Control | Links |
|---|---|---|
| Eubacterium coprostanoligenes | ||
| Lactobacillus | ||
| uncultured Oscillospiraceae bacterium |
Revision editor(s): Dorcas-od, Anne-mariesharp
Experiment 3
Subjects
- 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 at day 45 after exposure to a 5% K₂Ox(Potassium Oxalate) diet that induces hyperoxaluria, evidenced by increased urinary oxalate excretion and renal CaOx(Calcium Oxalate) crystal deposition
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- Welch's T-Test
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 S1
Description: The differential phylum between indicated groups
Abundance in Group 1: increased abundance in 5%K₂Ox-45day
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomycetota | ||
| Bacteroidota |
Revision editor(s): Anne-mariesharp
Signature 2
Source: Figure S1
Description: The differential phylum between indicated groups
Abundance in Group 1: decreased abundance in 5%K₂Ox-45day
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillota |
Revision editor(s): Anne-mariesharp
Experiment 4
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- 5%K₂Ox-30day
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 S1
Description: The differential phylum between indicated groups
Abundance in Group 1: increased abundance in 5%K₂Ox-45day
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomycetota |
Revision editor(s): Anne-mariesharp
Experiment 5
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Normal Group (45 days)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- 5%K₂Ox (45 days)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Rats at day 45 after exposure to a 5% K2Ox diet that induces hyperoxaluria, evidenced by increased urinary oxalate excretion and renal CaOx crystal deposition
Lab analysis
Statistical Analysis
- Statistical test
- ANOVA
- Post-Hoc Pairwise
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 (45 days)
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomycetota | ||
| Bacteroidota | ||
| Pseudomonadota |
Revision editor(s): Dorcas-od, Anne-mariesharp
Signature 2
Source: Figure 4a
Description: The effects of FMT on gut microbiota and metabolism.
Abundance in Group 1: decreased abundance in 5%K₂Ox (45 days)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillota |
Revision editor(s): Dorcas-od
Experiment 6
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Response to transplant Response to transplant,response to transplant
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- 5%K₂OxFMT (45 days)
- 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 and treated with fecal microbiota transplantation (FMT) from healthy rat donors every two days for 45 days
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 4a
Description: The effects of FMT on gut microbiota and metabolism.
Abundance in Group 1: increased abundance in 5%K₂OxFMT (45 days)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidota | ||
| Pseudomonadota |
Revision editor(s): Dorcas-od, Anne-mariesharp
Signature 2
Source: Figure 4a
Description: The effects of FMT on gut microbiota and metabolism.
Abundance in Group 1: decreased abundance in 5%K₂OxFMT (45 days)
| 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 (45 days)
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 4a
Description: The effects of FMT on gut microbiota and metabolism.
Abundance in Group 1: increased abundance in 5%K₂OxFMT (45 days)
| 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%K₂OxFMT (45 days)
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomycetota | ||
| Bacteroidota |
Revision editor(s): Dorcas-od, Anne-mariesharp
Experiment 8
Curated date: 2025/04/06
Curator: Dorcas-od
Revision editor(s): Dorcas-od, Anne-mariesharp, KateRasheed
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Hydroxyproline measurement Hydroxyproline measurement,hydroxyproline measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Normal Group (45 days)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- 5%Hyp (45 days)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Rats at day 45 after exposure to a 5%Hyp(Hydroxyproline) oxalate precursor-diet that induces hyperoxaluria, evidenced by increased urinary oxalate excretion and renal CaOx(Calcium Oxalate) 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
- unchanged
Signature 1
Source: Figure 4a
Description: The effects of FMT on gut microbiota and metabolism.
Abundance in Group 1: increased abundance in 5%Hyp (45 days)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidota | ||
| Verrucomicrobiota |
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%Hyp (45 days)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillota |
Revision editor(s): Dorcas-od
Experiment 9
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
- 5%Hyp (45 days)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- 5%HypFMT (45 days)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Rats exposed to a 5%Hyp(Hydroxyproline) oxalate precursor-diet and treated with fecal microbiota transplantation (FMT) from healthy rat donors every two days for 45 days
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 4a
Description: The effects of FMT on gut microbiota and metabolism.
Abundance in Group 1: increased abundance in 5%HypFMT (45 days)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillota |
Revision editor(s): Dorcas-od, Anne-mariesharp
Signature 2
Source: Figure 4a
Description: The effects of FMT on gut microbiota and metabolism.
Abundance in Group 1: decreased abundance in 5%HypFMT (45 days)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidota | ||
| Verrucomicrobiota |
Revision editor(s): Dorcas-od, Anne-mariesharp
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 and treated with fecal microbiota transplantation (FMT) from healthy rat donors
Lab analysis
Statistical Analysis
- Statistical test
- Welch's T-Test
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 S7a
Description: The effects of FMT on HDOx-induced differential bacteria (genus level)
Abundance in Group 1: increased abundance in 5%K₂OxFMT
| NCBI | Quality Control | Links |
|---|---|---|
| Ruminococcus_2Ruminococcus_2 | ||
| Prevotella_9Prevotella_9 |
Revision editor(s): Dorcas-od, Anne-mariesharp
Signature 2
Source: Figure 4b, Figure S7a, c
Description: The effects of FMT on HDOx-induced differential bacteria (genus level)
Abundance in Group 1: decreased abundance in 5%K₂OxFMT
| NCBI | Quality Control | Links |
|---|---|---|
| Parasutterella | ||
| Butyricimonas | ||
| Papillibacter | ||
| Coriobacteriaceae_UCG-002Coriobacteriaceae_UCG-002 |
Revision editor(s): Anne-mariesharp
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
- Rats exposed to a 5%Hyp(Hydroxyproline) oxalate precursor-diet and treated with fecal microbiota transplantation (FMT) from healthy rat donors
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
- increased
Signature 1
Source: Figure 4c, Figure S7b, d
Description: The effects of FMT on HDOx-induced differential bacteria (genus level)
Abundance in Group 1: increased abundance in 5%HypFMT
Revision editor(s): Dorcas-od, Anne-mariesharp
Signature 2
Source: Figure 4c, Figure S7b, d
Description: The effects of FMT on HDOx-induced differential bacteria (genus level)
Abundance in Group 1: decreased abundance in 5%HypFMT
| NCBI | Quality Control | Links |
|---|---|---|
| Akkermansia | ||
| Alloprevotella | ||
| Bacteroides | ||
| Butyricimonas | ||
| Oscillospira | ||
| Parasutterella | ||
| Prevotellaceae_UCG-001Prevotellaceae_UCG-001 | ||
| Clostridium |
Revision editor(s): Dorcas-od, Anne-mariesharp
Experiment 12
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Timepoint Timepoint,timepoint
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Normal-0day
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Normal-15day
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Healthy rats fed with a standard pellet diet, and had their sample collected at day 15
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 S1
Description: The differential phylum between indicated groups
Abundance in Group 1: increased abundance in Normal-15day
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillota | ||
| Pseudomonadota |
Revision editor(s): Dorcas-od, Anne-mariesharp
Signature 2
Source: Figure S1
Description: The differential phylum between indicated groups
Abundance in Group 1: decreased abundance in Normal-15day
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidota |
Revision editor(s): Dorcas-od, Anne-mariesharp
Experiment 13
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Normal-30day
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Healthy rats fed with a standard pellet diet, and had their sample collected at day 30
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 S1
Description: The differential phylum between indicated groups
Abundance in Group 1: increased abundance in Normal-30day
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillota |
Revision editor(s): Dorcas-od, Anne-mariesharp
Signature 2
Source: Figure S1
Description: The differential phylum between indicated groups
Abundance in Group 1: decreased abundance in Normal-30day
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidota |
Revision editor(s): Dorcas-od, Anne-mariesharp
Experiment 14
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Normal-45day
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Healthy rats fed with a standard pellet diet, and had their sample collected at day 45
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 S1
Description: The differential phylum between indicated groups
Abundance in Group 1: increased abundance in Normal-45day
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillota |
Revision editor(s): Dorcas-od, Anne-mariesharp
Signature 2
Source: Figure S1
Description: The differential phylum between indicated groups
Abundance in Group 1: decreased abundance in Normal-45day
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidota |
Revision editor(s): Dorcas-od, Anne-mariesharp
Experiment 15
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Normal-15day
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Normal-30day
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Healthy rats fed with a standard pellet diet, and had their sample collected at day 30
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 2
Source: Figure S1
Description: The differential phylum between indicated groups
Abundance in Group 1: decreased abundance in Normal-30day
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomycetota | ||
| Pseudomonadota |
Revision editor(s): Dorcas-od, Anne-mariesharp
Experiment 16
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Normal-45day
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Healthy rats fed with a standard pellet diet, and had their sample collected at day 45
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 2
Source: Figure S1
Description: The differential phylum between indicated groups
Abundance in Group 1: decreased abundance in Normal-45day
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomycetota | ||
| Pseudomonadota |
Revision editor(s): Dorcas-od, Anne-mariesharp
Experiment 17
Subjects
- 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
- 3%K₂Ox-0day
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- 3%K₂Ox-15day
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Rats at day 15 after exposure to a 3% K₂Ox(Potassium Oxalate) diet that induces hyperoxaluria, evidenced by increased urinary oxalate excretion and renal CaOx(Calcium Oxalate) crystal deposition
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 S1
Description: The differential phylum between indicated groups
Abundance in Group 1: increased abundance in 3%K₂Ox-15day
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidota |
Revision editor(s): Dorcas-od, Anne-mariesharp
Signature 2
Source: Figure S1
Description: The differential phylum between indicated groups
Abundance in Group 1: decreased abundance in 3%K₂Ox-15day
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillota |
Revision editor(s): Dorcas-od, Anne-mariesharp
Experiment 18
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- 3%K₂Ox-15day
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- 3%K₂Ox-30day
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Rats at day 30 after exposure to a 3% K₂Ox(Potassium Oxalate) diet that induces hyperoxaluria, evidenced by increased urinary oxalate excretion and renal CaOx(Calcium Oxalate) crystal deposition
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 S1
Description: The differential phylum between indicated groups
Abundance in Group 1: decreased abundance in 3%K₂Ox-30day
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidota |
Revision editor(s): Dorcas-od, Anne-mariesharp
Experiment 19
Subjects
- 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-15day
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Rats at day 15 after exposure to a 5% K₂Ox(Potassium Oxalate) diet that induces hyperoxaluria, evidenced by increased urinary oxalate excretion and renal CaOx(Calcium Oxalate) crystal deposition
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 S1
Description: The differential phylum between indicated groups
Abundance in Group 1: increased abundance in 5%K₂Ox-15day
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidota |
Revision editor(s): Dorcas-od, Anne-mariesharp
Signature 2
Source: Figure S1
Description: The differential phylum between indicated groups
Abundance in Group 1: decreased abundance in 5%K₂Ox-15day
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillota |
Revision editor(s): Dorcas-od, Anne-mariesharp
Experiment 20
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- 5%K₂Ox-30day
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Rats at day 30 after exposure to a 5% K₂Ox(Potassium Oxalate) diet that induces hyperoxaluria, evidenced by increased urinary oxalate excretion and renal CaOx(Calcium Oxalate) crystal deposition
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 S1
Description: The differential phylum between indicated groups
Abundance in Group 1: increased abundance in 5%K₂Ox-30day
| NCBI | Quality Control | Links |
|---|---|---|
| Pseudomonadota |
Revision editor(s): Dorcas-od, Anne-mariesharp
Experiment 22
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- 5%K₂Ox-15day
- 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 at day 45 after exposure to a 5% K₂Ox(Potassium Oxalate) diet that induces hyperoxaluria, evidenced by increased urinary oxalate excretion and renal CaOx(Calcium Oxalate) crystal deposition
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 S1
Description: The differential phylum between indicated groups
Abundance in Group 1: increased abundance in 5%K₂Ox-45day
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomycetota |
Revision editor(s): Dorcas-od, Anne-mariesharp
Experiment 23
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Hydroxyproline measurement Hydroxyproline measurement,hydroxyproline measurement
- 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-30day
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Rats at day 30 after exposure to a 5%Hyp(Hydroxyproline) oxalate precursor-diet that induces hyperoxaluria, evidenced by increased urinary oxalate excretion and renal CaOx(Calcium Oxalate) crystal deposition
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 S1
Description: The differential phylum between indicated groups
Abundance in Group 1: increased abundance in 5%Hyp-30day
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillota |
Revision editor(s): Dorcas-od, Anne-mariesharp
Signature 2
Source: Figure S1
Description: The differential phylum between indicated groups
Abundance in Group 1: decreased abundance in 5%Hyp-30day
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidota |
Revision editor(s): Dorcas-od, Anne-mariesharp
Experiment 24
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- 5%Hyp-30days
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- 5%Hyp-45days
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Rats at day 45 after exposure to a 5%Hyp(Hydroxyproline) oxalate precursor-diet that induces hyperoxaluria, evidenced by increased urinary oxalate excretion and renal CaOx(Calcium Oxalate) crystal deposition
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 S1
Description: The differential phylum between indicated groups
Abundance in Group 1: increased abundance in 5%Hyp-45days
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidota |
Revision editor(s): Anne-mariesharp
Signature 2
Source: Figure S1
Description: The differential phylum between indicated groups
Abundance in Group 1: decreased abundance in 5%Hyp-45days
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillota |
Revision editor(s): Anne-mariesharp
Experiment 25
Subjects
- 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-45days
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Normal-45days
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Healthy rats fed with a standard pellet diet, and had their sample collected at day 45
Lab analysis
Statistical Analysis
- Statistical test
- LEfSe
- 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
- increased
- Chao1 Abundance-based estimator of species richness
- increased
Signature 1
Source: Figure S2a
Description: LEfSe analysis identified the most differentially abundant genera between the Normal group and the HDOx groups on day 45.
Abundance in Group 1: increased abundance in Normal-45days
Revision editor(s): Anne-mariesharp
Signature 2
Source: Figure S2a
Description: LEfSe analysis identified the most differentially abundant genera between the Normal group and the HDOx groups on day 45.
Abundance in Group 1: decreased abundance in Normal-45days
Revision editor(s): Anne-mariesharp
Experiment 26
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Hydroxyproline measurement Hydroxyproline measurement,hydroxyproline measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- 5%Hyp-45days
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
- unchanged
Signature 1
Source: Figure S2a
Description: LEfSe analysis identified the most differentially abundant genera between the Normal group and the HDOx groups on day 45.
Abundance in Group 1: increased abundance in Normal-45days
Revision editor(s): Anne-mariesharp
Signature 2
Source: Figure S2a
Description: LEfSe analysis identified the most differentially abundant genera between the Normal group and the HDOx groups on day 45.
Abundance in Group 1: decreased abundance in Normal-45days
Revision editor(s): Anne-mariesharp
Experiment 27
Subjects
- 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-45days
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Rats at day 45 after exposure to a 5% K₂Ox diet that induces hyperoxaluria, evidenced by increased urinary oxalate excretion and renal CaOx crystal deposition
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- log transformation
- Statistical test
- Linear Regression
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- Not specified
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 S2c
Description: Differentially abundant genera of HDOx groups between the day 0 and day 45
Abundance in Group 1: increased abundance in 5%K₂Ox-45days
Revision editor(s): Anne-mariesharp
Signature 2
Source: Figure S2c
Description: Differentially abundant genera of HDOx groups between the day 0 and day 45
Abundance in Group 1: decreased abundance in 5%K₂Ox-45days
Revision editor(s): Anne-mariesharp
Experiment 28
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Hydroxyproline measurement Hydroxyproline measurement,hydroxyproline measurement
- 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-45days
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Rats at day 45 after exposure to a 5%Hyp(Hydroxyproline) oxalate precursor-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
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Source: Figure S2c
Description: Differentially abundant genera of HDOx groups between the day 0 and day 45
Abundance in Group 1: increased abundance in 5%Hyp-45days
Revision editor(s): Anne-mariesharp
Signature 2
Source: Figure S2c
Description: Differentially abundant genera of HDOx groups between the day 0 and day 45
Abundance in Group 1: decreased abundance in 5%Hyp-45days
| NCBI | Quality Control | Links |
|---|---|---|
| Bacilli | ||
| Lactobacillus | ||
| Lactobacillaceae | ||
| Ruminococcaceae bacterium UCG-005 | ||
| Lactobacillales |
Revision editor(s): Anne-mariesharp
Contents
- 1 Experiment 1
- 2 Experiment 2
- 3 Experiment 3
- 4 Experiment 4
- 5 Experiment 5
- 6 Experiment 6
- 7 Experiment 7
- 8 Experiment 8
- 9 Experiment 9
- 10 Experiment 10
- 11 Experiment 11
- 12 Experiment 12
- 13 Experiment 13
- 14 Experiment 14
- 15 Experiment 15
- 16 Experiment 16
- 17 Experiment 17
- 18 Experiment 18
- 19 Experiment 19
- 20 Experiment 20
- 21 Experiment 22
- 22 Experiment 23
- 23 Experiment 24
- 24 Experiment 25
- 25 Experiment 26
- 26 Experiment 27
- 27 Experiment 28
