High-fat feeding rather than obesity drives taxonomical and functional changes in the gut microbiota in mice
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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
- Denmark
- 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
- Obesity Adiposis,Adiposity,Obese,Obese (finding),obesity,Obesity (disorder),Obesity [Ambiguous],obesity disease,obesity disorder,Obesity NOS,Obesity, unspecified,Overweight and obesity,Obesity
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- BL6- Low Fat
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Sv129- Low Fat
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- (BL6): C57BL/6JBomTac mouse strain, (Sv129): the obesity-resistant mouse strain 129S6/SvEvTac . LF: (LF)low-fat diet, (HF) high fat diet without indomethacin, (HFI) high fat diet supplemented with indomethacin.
- 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
- 7
Lab analysis
- Sequencing type
- WMS
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
- 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
- Mann-Whitney (Wilcoxon)
- 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)?
- Yes
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
Signature 1
Source: Data S4,S7,S8,S9,S10,S11,S13,S14
Description: Relative abundance at the bacterial phylum, genus and species levesl between two strain mices fed low fat diet, fed high fat diet and high fat diet + indomethacin
Abundance in Group 1: increased abundance in Sv129- Low Fat
Signature 2
Source: Data S4,S7,S8,S9,S10,S11,S13,S14
Description: Relative abundance at the bacterial phylum, genus and species levesl between two strain mices fed low fat diet, fed high fat diet and high fat diet + indomethacin
Abundance in Group 1: decreased abundance in Sv129- Low Fat
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- BL6-High Fat without enomithacin
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Sv129-High Fat without enomithacin
- 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
- unchanged
Signature 1
Source: Data S4,S7,S8,S9,S10,S11,S13,S14
Description: Relative abundance at the bacterial phylum, genus and species levesl between two strain mices fed low fat diet, fed high fat diet and high fat diet + indomethacin
Abundance in Group 1: increased abundance in Sv129-High Fat without enomithacin
Signature 2
Source: Data S4,S7,S8,S9,S10,S11,S13,S14
Description: Relative abundance at the bacterial phylum, genus and species levesl between two strain mices fed low fat diet, fed high fat diet and high fat diet + indomethacin
Abundance in Group 1: decreased abundance in Sv129-High Fat without enomithacin
| NCBI | Quality Control | Links |
|---|---|---|
| Akkermansia | ||
| Akkermansia muciniphila | ||
| Planctomycetota | ||
| Verrucomicrobiota | ||
| Holdemanella biformis |
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- BL6-High Fat with enomithacin
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Sv129-High Fat with enomithacin
- 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
- unchanged
Signature 1
Source: Data S4,S7,S8,S9,S10,S11,S13,S14
Description: Relative abundance at the bacterial phylum, genus and species levesl between two strain mices fed low fat diet, fed high fat diet and high fat diet + indomethacin
Abundance in Group 1: increased abundance in Sv129-High Fat with enomithacin
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Bacteroidota | ||
| Cyanobacteriota | ||
| Chlorobiota | ||
| Fibrobacterota |
Revision editor(s): WikiWorks
Signature 2
Curated date: 2021/01/10
Curator: Shaimaa Elsafoury
Source: Data S4,S7,S8,S9,S10,S11,S13,S14
Description: Relative abundance at the bacterial phylum, genus and species levesl between two strain mices fed low fat diet, fed high fat diet and high fat diet + indomethacin
Abundance in Group 1: decreased abundance in Sv129-High Fat with enomithacin
