Changes in the gut microbiota structure and function in rats with doxorubicin-induced heart failure
-
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
- Treatment outcome measurement Treatment outcome measurement,treatment outcome measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Control (Con-J) group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Doxorubicin-A (Dox-A) group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The rats in the DOX-A group were administered 2mg/kg of doxorubicin via the tail vein for 6 weeks to induce heart failure, and their body weights decreased to varying degrees.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 9
- Group 1 sample size Number of subjects in the case (exposed) group
- 9
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- 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
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 8 & 9
Description: Histogram and Cladogram analyzed by LEfSe (LDA = 4.0, P < 0.05) showing the phylogenetic distribution of the bacterial lineages in the CON group and DOX group.
Abundance in Group 1: increased abundance in Doxorubicin-A (Dox-A) group
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotellaceae | ||
| Alloprevotella | ||
| unclassified Actinomycetota | ||
| Actinomycetota | ||
| Odoribacter | ||
| Marinifilaceae |
Revision editor(s): Victoria
Signature 2
Source: Figure 8 & 9
Description: Histogram and Cladogram analyzed by LEfSe (LDA = 4.0, P < 0.05) showing the phylogenetic distribution of the bacterial lineages in the CON group and DOX group.
Abundance in Group 1: decreased abundance in Doxorubicin-A (Dox-A) group
| NCBI | Quality Control | Links |
|---|---|---|
| Ruminococcus | ||
| Bacteroides rodentium | ||
| Eubacteriales | ||
| Bacteroidaceae | ||
| Bacteroides | ||
| Ligilactobacillus murinus | ||
| Ligilactobacillus | ||
| Lactobacillaceae | ||
| Clostridia | ||
| Bacillota |
Revision editor(s): Victoria
Experiment 2
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Doxorubicin-B (Dox-B) group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The rats in the DOX-B group were administered 2.5mg/kg of doxorubicin via the tail vein for 6 weeks to induce heart failure, and their body weights decreased to varying degrees.
- Group 1 sample size Number of subjects in the case (exposed) group
- 8
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
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- decreased
Signature 1
Source: Figure 8 & 9
Description: Histogram and Cladogram analyzed by LEfSe (LDA = 4.0, P < 0.05) showing the phylogenetic distribution of the bacterial lineages in the CON group and DOX group.
Abundance in Group 1: increased abundance in Doxorubicin-B (Dox-B) group
Revision editor(s): Victoria
Signature 2
Source: Figure 8 & 9
Description: Histogram and Cladogram analyzed by LEfSe (LDA = 4.0, P < 0.05) showing the phylogenetic distribution of the bacterial lineages in the CON group and DOX group.
Abundance in Group 1: decreased abundance in Doxorubicin-B (Dox-B) group
Revision editor(s): Victoria
Experiment 3
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Doxorubicin-C (Dox-C) group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The rats in the DOX-C group were administered 3mg/kg of doxorubicin via the tail vein for 6 weeks to induce heart failure, and their body weights decreased to varying degrees.
- 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
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- decreased
Signature 1
Source: Figure 8 & 9
Description: Histogram and Cladogram analyzed by LEfSe (LDA = 4.0, P < 0.05) showing the phylogenetic distribution of the bacterial lineages in the CON group and DOX group.
Abundance in Group 1: increased abundance in Doxorubicin-C (Dox-C) group
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium pseudolongum | ||
| Escherichia/Shigella sp. | ||
| Escherichia coli | ||
| Enterobacteriaceae | ||
| Gammaproteobacteria | ||
| Pseudomonadota | ||
| Enterobacterales | ||
| Rikenellaceae | ||
| Alistipes |
Revision editor(s): Victoria
Signature 2
Source: Figure 8 & 9
Description: Histogram and Cladogram analyzed by LEfSe (LDA = 4.0, P < 0.05) showing the phylogenetic distribution of the bacterial lineages in the CON group and DOX group.
Abundance in Group 1: decreased abundance in Doxorubicin-C (Dox-C) group
Revision editor(s): Victoria
Experiment 4
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Doxorubicin-D (Dox-D) group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The rats in the DOX-D group were administered doxorubicin via the tail vein in the following concentrations: 3mg/kg in weeks 1, 3, and 5, and 1mg/kg in weeks 2, 4 & 6 to induce heart failure, and their body weights decreased to varying degrees.
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 8 & 9
Description: Histogram and Cladogram analyzed by LEfSe (LDA = 4.0, P < 0.05) showing the phylogenetic distribution of the bacterial lineages in the CON group and DOX group.
Abundance in Group 1: increased abundance in Doxorubicin-D (Dox-D) group
| NCBI | Quality Control | Links |
|---|---|---|
| Enterobacteriaceae | ||
| Enterobacterales | ||
| Escherichia coli | ||
| Escherichia/Shigella sp. | ||
| Rikenellaceae | ||
| Alistipes | ||
| Odoribacter | ||
| Marinifilaceae |
Revision editor(s): Victoria
Signature 2
Source: Figure 8 & 9
Description: Histogram and Cladogram analyzed by LEfSe (LDA = 4.0, P < 0.05) showing the phylogenetic distribution of the bacterial lineages in the CON group and DOX group.
Abundance in Group 1: decreased abundance in Doxorubicin-D (Dox-D) group
| NCBI | Quality Control | Links |
|---|---|---|
| Oscillospiraceae | ||
| Ruminococcus | ||
| Bacteroides rodentium | ||
| Bacteroides | ||
| Bacteroidaceae | ||
| Ligilactobacillus murinus | ||
| Ligilactobacillus | ||
| Bacillota |
Revision editor(s): Victoria
Experiment 5
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Doxorubicin-E (Dox-E) group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The rats in the DOX-E group were administered doxorubicin via the tail vein in the following concentrations: 3.5mg/kg in weeks 1, 3, and 5, and 1.5mg/kg in weeks 2, 4 & 6 to induce heart failure, and their body weights decreased to varying degrees.
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
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Figure 8 & 9
Description: Histogram and Cladogram analyzed by LEfSe (LDA = 4.0, P < 0.05) showing the phylogenetic distribution of the bacterial lineages in the CON group and DOX group.
Abundance in Group 1: increased abundance in Doxorubicin-E (Dox-E) group
| NCBI | Quality Control | Links |
|---|---|---|
| Escherichia/Shigella sp. | ||
| Enterobacteriaceae | ||
| Enterobacterales | ||
| Escherichia coli | ||
| Pseudomonadota | ||
| Gammaproteobacteria | ||
| Odoribacter | ||
| Marinifilaceae | ||
| Alistipes | ||
| Rikenellaceae |
Revision editor(s): Victoria
Signature 2
Source: Figure 8 & 9
Description: Histogram and Cladogram analyzed by LEfSe (LDA = 4.0, P < 0.05) showing the phylogenetic distribution of the bacterial lineages in the CON group and DOX group.
Abundance in Group 1: decreased abundance in Doxorubicin-E (Dox-E) group
Revision editor(s): Victoria
Experiment 6
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Doxorubicin-F (Dox-F) group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The rats in the DOX-F group were administered doxorubicin via the tail vein in the following concentrations: 4mg/kg in weeks 1, 3, and 5, and 2mg/kg in weeks 2, 4 & 6 to induce heart failure, and their body weights decreased to varying degrees.
- Group 1 sample size Number of subjects in the case (exposed) group
- 7
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
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- decreased
Signature 1
Source: Figure 8 & 9
Description: Histogram and Cladogram analyzed by LEfSe (LDA = 4.0, P < 0.05) showing the phylogenetic distribution of the bacterial lineages in the CON group and DOX group.
Abundance in Group 1: increased abundance in Doxorubicin-F (Dox-F) group
Revision editor(s): Victoria
Signature 2
Source: Figure 8 & 9
Description: Histogram and Cladogram analyzed by LEfSe (LDA = 4.0, P < 0.05) showing the phylogenetic distribution of the bacterial lineages in the CON group and DOX group.
Abundance in Group 1: decreased abundance in Doxorubicin-F (Dox-F) group
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides rodentium | ||
| Clostridia UCG-014Clostridia UCG-014 | ||
| Lachnospiraceae | ||
| Lachnospirales | ||
| Ligilactobacillus murinus | ||
| Ligilactobacillus | ||
| Clostridia |
Revision editor(s): Victoria
Experiment 7
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Control (Con-K) group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Doxorubicin-G (Dox-G) group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The rats in the DOX-G group were administered doxorubicin intraperitoneally in the following concentrations: 3mg/kg in weeks 1, 3, and 5, and 1mg/kg in weeks 2, 4 & 6 to induce heart failure, and their body weights increased to varying degrees.
- 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
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
- Richness Number of species
- increased
Signature 1
Source: Figure 8 & 9
Description: Histogram and Cladogram analyzed by LEfSe (LDA = 4.0, P < 0.05) showing the phylogenetic distribution of the bacterial lineages in the CON group and DOX group.
Abundance in Group 1: increased abundance in Doxorubicin-G (Dox-G) group
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomycetota | ||
| Bifidobacterium | ||
| Bifidobacteriales | ||
| unclassified Acidimicrobiia | ||
| Bifidobacterium pseudolongum | ||
| Bifidobacteriaceae |
Revision editor(s): Victoria
Signature 2
Source: Figure 8 & 9
Description: Histogram and Cladogram analyzed by LEfSe (LDA = 4.0, P < 0.05) showing the phylogenetic distribution of the bacterial lineages in the CON group and DOX group.
Abundance in Group 1: decreased abundance in Doxorubicin-G (Dox-G) group
| NCBI | Quality Control | Links |
|---|---|---|
| Lachnospirales | ||
| Lachnospiraceae | ||
| Bacteroides rodentium | ||
| Oscillospiraceae | ||
| Bacteroides | ||
| Bacteroidaceae | ||
| Clostridia UCG-014Clostridia UCG-014 | ||
| Eubacteriales | ||
| Clostridia |
Revision editor(s): Victoria
Experiment 8
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Doxorubicin-H (Dox-H) group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The rats in the DOX-H group were administered doxorubicin intraperitoneally in the following concentrations: 3.5mg/kg in weeks 1, 3, and 5, and 1.5mg/kg in weeks 2, 4 & 6 to induce heart failure, and their body weights increased to varying degrees.
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
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
- Richness Number of species
- increased
Signature 1
Source: Figure 8 & 9
Description: Histogram and Cladogram analyzed by LEfSe (LDA = 4.0, P < 0.05) showing the phylogenetic distribution of the bacterial lineages in the CON group and DOX group.
Abundance in Group 1: increased abundance in Doxorubicin-H (Dox-H) group
Revision editor(s): Victoria
Signature 2
Source: Figure 8 & 9
Description: Histogram and Cladogram analyzed by LEfSe (LDA = 4.0, P < 0.05) showing the phylogenetic distribution of the bacterial lineages in the CON group and DOX group.
Abundance in Group 1: decreased abundance in Doxorubicin-H (Dox-H) group
Revision editor(s): Victoria
Experiment 9
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Doxorubicin-I (Dox-I) group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The rats in the DOX-I group were administered doxorubicin intraperitoneally in the following concentrations: 4mg/kg in weeks 1, 3, and 5, and 2mg/kg in weeks 2, 4 & 6 to induce heart failure, and their body weights increased to varying degrees.
- Group 1 sample size Number of subjects in the case (exposed) group
- 7
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
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
- Richness Number of species
- unchanged
Signature 1
Source: Figure 8 & 9
Description: Histogram and Cladogram analyzed by LEfSe (LDA = 4.0, P < 0.05) showing the phylogenetic distribution of the bacterial lineages in the CON group and DOX group.
Abundance in Group 1: increased abundance in Doxorubicin-I (Dox-I) group
Revision editor(s): Victoria
Signature 2
Source: Figure 8 & 9
Description: Histogram and Cladogram analyzed by LEfSe (LDA = 4.0, P < 0.05) showing the phylogenetic distribution of the bacterial lineages in the CON group and DOX group.
Abundance in Group 1: decreased abundance in Doxorubicin-I (Dox-I) group
Revision editor(s): Victoria
