Formulation of traditional Chinese medicine and its application on intestinal flora of constipated rats
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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
- Traditional Chinese medicine type TCM type,Traditional Chinese medicine type,traditional Chinese medicine type
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Functional constipation (FC) model (control) group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Low dose group (DI)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Rats in this group were treated with a low dose 5.15 g/(kg d) of traditional Chinese medicine
- 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
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
- ANOVA
- 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
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Figure 2C
Description: Relative abundance of significant taxa between Functional constipation (FC) and Low Dose (DI) groups
Abundance in Group 1: increased abundance in Low dose group (DI)
NCBI | Quality Control | Links |
---|---|---|
Bacteroidota |
Revision editor(s): Tosin
Signature 2
Source: Figure 2B
Description: Relative abundance of significant taxa between Functional constipation (FC) and Low Dose (DI) groups
Abundance in Group 1: decreased abundance in Low dose group (DI)
NCBI | Quality Control | Links |
---|---|---|
Bacillota |
Revision editor(s): Tosin
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Blank control (KO) group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Functional constipation (FC) model group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Rats in this group were given 4 ml normal saline every time and gavage for 2 weeks.
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
- Richness Number of species
- unchanged
Signature 1
Source: Figure 2B
Description: Relative abundance between Functional constipation (FC) model group and Blank control (KO) group
Abundance in Group 1: increased abundance in Functional constipation (FC) model group
NCBI | Quality Control | Links |
---|---|---|
Bacillota |
Revision editor(s): Tosin
Signature 2
Source: Figure 2C
Description: Relative abundance between Functional constipation (FC) model and Blank control (KO) groups
Abundance in Group 1: decreased abundance in Functional constipation (FC) model group
NCBI | Quality Control | Links |
---|---|---|
Bacteroidota |
Revision editor(s): Tosin
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low dose (DI) group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Medium dose (ZH) group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Rats in this group were treated with a medium dose 10.3 g/(kg d) of traditional Chinese medicine
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
- Richness Number of species
- decreased
Signature 1
Source: Figure 2B, 2F
Description: Relative abundance between Low dose group (DI) and Medium dose group (ZH)
Abundance in Group 1: increased abundance in Medium dose (ZH) group
NCBI | Quality Control | Links |
---|---|---|
Bacillota | ||
Lactobacillus |
Revision editor(s): Tosin
Signature 2
Source: Figure 2C, 2E
Description: Relative abundance between Low dose (DI) group and Medium dose (ZH) group
Abundance in Group 1: decreased abundance in Medium dose (ZH) group
NCBI | Quality Control | Links |
---|---|---|
Lachnospiraceae | ||
Bacteroidota |
Revision editor(s): Tosin
Experiment 4
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Blank control (KO) group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High dose (GA) group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Rats in this group were treated with a high dose 20.6 g/(kg d) of traditional Chinese medicine
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
- Richness Number of species
- decreased
Signature 1
Source: Figure 2B, 2F
Description: Relative abundance between Blank control (KO) group and High dose group (GA)
Abundance in Group 1: increased abundance in High dose (GA) group
NCBI | Quality Control | Links |
---|---|---|
Lactobacillus | ||
Bacillota |
Revision editor(s): Tosin
Experiment 5
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Functional constipation (FC) model (control) group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Mosapride (MO) group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Rats in this group were given mosapride 2 mg/(kg d) gavage, with a volume of 4ml per animal each time
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
- Richness Number of species
- increased
Signature 1
Source: Figure 2E
Description: Relative abundance between Functional constipation (FC) group and Mosapride (MO) group
Abundance in Group 1: decreased abundance in Mosapride (MO) group
NCBI | Quality Control | Links |
---|---|---|
Lachnospiraceae |
Revision editor(s): Tosin
Experiment 6
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Blank control (KO) group
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
- Richness Number of species
- unchanged
Signature 1
Source: Figure 2E
Description: Relative abundance between Blank control (KO) group and Mosapride (MO) group
Abundance in Group 1: decreased abundance in Mosapride (MO) group
NCBI | Quality Control | Links |
---|---|---|
Lachnospiraceae |
Revision editor(s): Tosin
Experiment 7
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Medium dose (ZH) group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High dose (GA) group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Rats in this group were treated with a high dose 20.6 g/(kg d) of traditional Chinese medicine
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
- Richness Number of species
- decreased
Signature 1
Source: Figure 2F
Description: Relative abundance between Medium dose (ZH) group and High dose (GA) group
Abundance in Group 1: increased abundance in High dose (GA) group
NCBI | Quality Control | Links |
---|---|---|
Lactobacillus |
Revision editor(s): Tosin
Signature 2
Source: Figure 2C, 2E
Description: Relative abundance between Medium dose (ZH) group and High dose (GA) group
Abundance in Group 1: decreased abundance in High dose (GA) group
NCBI | Quality Control | Links |
---|---|---|
Bacteroidota | ||
Lachnospiraceae |
Revision editor(s): Tosin
Experiment 8
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Functional constipation (FC) model (control) group
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
- Richness Number of species
- unchanged
Signature 1
Source: Figure 2F
Description: Relative abundance between Functional constipation (FC) model (control) group and High dose (GA) group
Abundance in Group 1: increased abundance in High dose (GA) group
NCBI | Quality Control | Links |
---|---|---|
Lactobacillus |
Revision editor(s): Tosin
Experiment 9
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Combination of Blank control (KO), Functional constipation model (FC), Mosapride (MO), Low dose (DI) and High dose (GA) groups
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Medium dose (ZH) group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Rats in this group were treated with a medium dose 10.3 g/(kg d) of traditional Chinese medicine
- Group 0 sample size Number of subjects in the control (unexposed) group
- 50
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
- 2
Signature 1
Source: Figure 3a
Description: Taxonomic cladogram obtained from LEfSe at six groups.
Abundance in Group 1: increased abundance in Medium dose (ZH) group
NCBI | Quality Control | Links |
---|---|---|
Christensenellaceae | ||
Erysipelotrichaceae | ||
Erysipelotrichales | ||
Erysipelotrichia | ||
Methanobacteria | ||
Methanobacteriaceae | ||
Methanobacteriales |
Revision editor(s): Tosin
Experiment 10
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Combination of Blank control (KO), Functional constipation (FC) , Low dose (DI), Medium dose (ZH) and High dose (GA) groups
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Mosapride (MO) group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Rats in this group were given mosapride 2 mg/(kg d) gavage, with a volume of 4ml per animal each time
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 3a
Description: Taxonomic cladogram obtained from LEfSe at six groups.
Abundance in Group 1: increased abundance in Mosapride (MO) group
Revision editor(s): Tosin
Experiment 11
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Combination of Blank control (KO), Functional constipation (FC), Mosapride (MO), Medium dose (ZH) and High dose (GA) groups
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Low dose group (DI)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Rats in this group were treated with a low dose 5.15 g/(kg d) of traditional Chinese medicine
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 3a
Description: Taxonomic cladogram obtained from LEfSe at six groups.
Abundance in Group 1: increased abundance in Low dose group (DI)
NCBI | Quality Control | Links |
---|---|---|
Porphyromonadaceae | ||
Lachnospiraceae |
Revision editor(s): Tosin
Experiment 12
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Combination of Blank control (KO), Functional constipation (FC), Mosapride (MO), Low dose (DI), Medium dose (ZH) groups
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High dose (GA) group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Rats in this group were treated with a high dose 20.6 g/(kg d) of traditional Chinese medicine
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 3a
Description: Taxonomic cladogram obtained from LEfSe at six groups.
Abundance in Group 1: increased abundance in High dose (GA) group
NCBI | Quality Control | Links |
---|---|---|
Lactobacillaceae | ||
Lactobacillales | ||
Bacilli | ||
Peptostreptococcaceae |
Revision editor(s): Tosin
Experiment 13
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Combination of Functional constipation (FC), Mosapride (MO), Low dose (DI), Medium dose (ZH) and High dose (GA) groups
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Blank control (KO) group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Rats in this group were fed SPF standard diet until the end of the experiment and given 4 ml normal saline every time and gavage for 2 weeks.
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 3a
Description: Taxonomic cladogram obtained from LEfSe at six groups.
Abundance in Group 1: increased abundance in Blank control (KO) group
Revision editor(s): Tosin
Experiment 14
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Combination of Blank control (KO), Mosapride (MO), Low dose (DI), Medium dose (ZH) and High dose (GA) groups
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Functional constipation (FC) model (control) group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Rats in this group were given 4 ml normal saline every time and gavage for 2 weeks.
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 3a
Description: Taxonomic cladogram obtained from LEfSe at six groups.
Abundance in Group 1: increased abundance in Functional constipation (FC) model (control) group
NCBI | Quality Control | Links |
---|---|---|
Carnobacteriaceae | ||
Clostridia | ||
Eubacteriales |
Revision editor(s): Tosin