Parasite-Derived Excretory-Secretory Products Alleviate Gut Microbiota Dysbiosis and Improve Cognitive Impairment Induced by a High-Fat 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
Curated date: 2024/10/30
Curator:
Revision editor(s):
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
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low-Fat Diet (LF) group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High-Fat Diet (HF) group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group includes mice receiving the High Fat diet (60% fat by weight) and intraperitoneally injected with 200 ml vehicle control twice a week in the Shannon Index.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 12
- Group 1 sample size Number of subjects in the case (exposed) group
- 12
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
- 3
- Matched on Factors on which subjects have been matched on in a case-control study
- body weight, Matched on: "fat mass" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.fat mass
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- body weight, diet, antibiotic, Confounders controlled for: "fat mass" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.fat mass
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
Signature 1
Curated date: 2024/11/04
Curator: Joiejoie
Revision editor(s): WikiWorks, MyleeeA, KateRasheed, Joiejoie
Source: Figure 5I
Description: Relative abundance of taxa in the LF vs HF groups
Abundance in Group 1: increased abundance in
Revision editor(s): WikiWorks, MyleeeA, KateRasheed, Joiejoie
Signature 2
Curated date: 2024/11/04
Curator: Joiejoie
Revision editor(s): WikiWorks, MyleeeA, KateRasheed, Joiejoie
Source: Figure 5I
Description: Relative abundance of taxa between the LF and HF groups
Abundance in Group 1: decreased abundance in
NCBI | Quality Control | Links |
---|---|---|
Bacteroidales | ||
Bacteroidia | ||
Bacteroidota | ||
Muribaculaceae | ||
Parabacteroides | ||
Parasutterella |
Revision editor(s): WikiWorks, MyleeeA, KateRasheed, Joiejoie
Experiment 2
Curated date: 2024/11/13
Curator:
Revision editor(s):
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- High-Fat Diet with Excretory-secretory products (HFE) group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group includes mice receiving the High Fat diet (60% fat by weight) and intraperitoneally injected with 200 ml vehicle control twice a week for the Shannon Index.
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
Signature 1
Curated date: 2024/11/13
Curator: MyleeeA
Revision editor(s): WikiWorks, MyleeeA, KateRasheed, Joiejoie
Source: Figure 5J
Description: Relative abundance of taxa in the HF and HFE groups
Abundance in Group 1: increased abundance in
NCBI | Quality Control | Links |
---|---|---|
Lactobacillus intestinalis | ||
Odoribacter | ||
Romboutsia | ||
unclassified Eubacteriales |
Revision editor(s): WikiWorks, MyleeeA, KateRasheed, Joiejoie
Signature 2
Curated date: 2024/11/13
Curator: MyleeeA
Revision editor(s): WikiWorks, MyleeeA, KateRasheed, Joiejoie
Source: Figure 5J
Description: Relative abundance of taxa between the HF and HFE groups
Abundance in Group 1: decreased abundance in
Revision editor(s): WikiWorks, MyleeeA, KateRasheed, Joiejoie
Experiment 3
Curated date: 2024/12/27
Curator:
Revision editor(s):
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low-Fat Diet (LF) group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group includes mice receiving the High Fat diet (60% fat by weight) and intraperitoneally injected with 200 ml vehicle control twice a week in the Simpson Index.
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- log transformation
- Statistical test
- ANOVA
- 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
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
Signature 1
Source: Fig. 5E
Description: Relative abundance of taxa in the HF and LF groups using ANOVA
Abundance in Group 1: decreased abundance in
NCBI | Quality Control | Links |
---|---|---|
Bacteroidota |
Revision editor(s): KateRasheed, WikiWorks
Signature 2
Source: Fig. 5D, 5G, 5K
Description: Relative abundance of taxa in the HF and LF groups using ANOVA
Abundance in Group 1: increased abundance in
NCBI | Quality Control | Links |
---|---|---|
Bacillota | ||
Deltaproteobacteria | ||
Desulfovibrionaceae | ||
Desulfovibrionales | ||
Pseudomonadota |
Revision editor(s): KateRasheed, WikiWorks
Experiment 4
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- High-Fat Diet with Excretory-secretory products (HFE) group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group includes mice receiving the High Fat diet (60% fat by weight) and intraperitoneally injected with 200 ml vehicle control twice a week for the Simpson Index.
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
Signature 1
Source: Fig. 5L
Description: Relative abundance of taxa in the HF and HFE groups using ANOVA
Abundance in Group 1: increased abundance in High-Fat Diet (HF) group
NCBI | Quality Control | Links |
---|---|---|
Odoribacter |
Revision editor(s): KateRasheed, WikiWorks
Signature 2
Source: Fig. 5D, 5G, 5K
Description: Relative abundance of taxa in the HF and HFE groups using ANOVA
Abundance in Group 1: decreased abundance in High-Fat Diet (HF) group
NCBI | Quality Control | Links |
---|---|---|
Bacillota | ||
Pseudomonadota | ||
Desulfovibrionaceae | ||
Desulfovibrionales | ||
Deltaproteobacteria |
Revision editor(s): KateRasheed, WikiWorks
Experiment 21
Curated date: 2025/02/02
Curator:
Revision editor(s):
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High-Fat ESPs supplement with antibiotics (HFE+AB) group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group includes the HFE group given a cocktail of antibiotics ( HFE+Ab) in the drinking water to investigate the role of gut microbiota in ESPs intervention.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 6
- Group 1 sample size Number of subjects in the case (exposed) group
- 6