Sleep deprivation-induced anxiety-like behaviors are associated with alterations in the gut microbiota and metabolites
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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
- Anxiety disorder anxiety,anxiety disorder,anxiety disorders,anxiety neuroses,anxiety neurosis,anxiety state,anxiety/mood disorders,chronic stress,mood and anxiety disorder,mood and anxiety disorders,neurotic anxiety states,Anxiety disorder
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Baseline samples (BSL)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Post sleep deprivation samples (7d-SD)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Samples collected from rats after being subjected to 7 days of sleep deprivation (7d-SD).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 30
- Group 1 sample size Number of subjects in the case (exposed) group
- 29
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).
- centered log-ratio
- 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)?
- Yes
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 3
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: Fig.3d
Description: LEfSe analysis identified bacteria species that significantly differed (FDR <0.05 and LDA >3) among samples.
Abundance in Group 1: increased abundance in Post sleep deprivation samples (7d-SD)
Revision editor(s): Iman-Ngwepe, Aleru Divine
Signature 2
Source: Fig.3d
Description: LEfSe analysis identified bacteria species that significantly differed (FDR <0.05 and LDA >3) among samples.
Abundance in Group 1: decreased abundance in Post sleep deprivation samples (7d-SD)
Revision editor(s): Iman-Ngwepe, Aleru Divine
Experiment 2
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Saline supplementation - SA (21d-SA)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Samples collected from rats after 14 days of saline supplementation (21d-SA).
- Group 1 sample size Number of subjects in the case (exposed) group
- 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: Fig.3d
Description: LEfSe analysis identified bacteria species that significantly differed (FDR <0.05 and LDA >3) among samples.
Abundance in Group 1: increased abundance in Saline supplementation - SA (21d-SA)
Revision editor(s): Aleru Divine
Signature 2
Source: Fig.3d
Description: LEfSe analysis identified bacteria species that significantly differed (FDR <0.05 and LDA >3) among samples.
Abundance in Group 1: decreased abundance in Saline supplementation - SA (21d-SA)
Revision editor(s): Aleru Divine
Experiment 3
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Multi-probiotic supplementation - MP (21d-MP)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Samples collected from rats after 14 days of multi-probiotic supplementation (21d-MP).
- Group 1 sample size Number of subjects in the case (exposed) group
- 14
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: Fig.3d
Description: LEfSe analysis identified bacteria species that significantly differed (FDR <0.05 and LDA >3) among samples.
Abundance in Group 1: increased abundance in Multi-probiotic supplementation - MP (21d-MP)
Revision editor(s): Aleru Divine
Signature 2
Source: Fig.3d
Description: LEfSe analysis identified bacteria species that significantly differed (FDR <0.05 and LDA >3) among samples.
Abundance in Group 1: decreased abundance in Multi-probiotic supplementation - MP (21d-MP)
Revision editor(s): Aleru Divine
Experiment 4
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Post sleep deprivation samples (7d-SD)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Saline supplementation - SA (21d-SA)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Samples collected from rats after 14 days of saline supplementation (21d-SA).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 29
- Group 1 sample size Number of subjects in the case (exposed) group
- 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: Fig.3d
Description: LEfSe analysis identified bacteria species that significantly differed (FDR <0.05 and LDA >3) among samples.
Abundance in Group 1: increased abundance in Saline supplementation - SA (21d-SA)
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotella sp. P2-180 | ||
| Lactobacillus johnsonii | ||
| Corynebacterium stationis | ||
| Prevotella sp. MGM2 | ||
| Streptococcus hyointestinalis | ||
| Prevotella sp. CAG:1031 | ||
| Aerococcaceae bacterium |
Revision editor(s): Aleru Divine
Signature 2
Source: Fig.3d
Description: LEfSe analysis identified bacteria species that significantly differed (FDR <0.05 and LDA >3) among samples.
Abundance in Group 1: decreased abundance in Saline supplementation - SA (21d-SA)
Revision editor(s): Aleru Divine
Experiment 5
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Multi-probiotic supplementation - MP (21d-MP)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Samples collected from rats after 14 days of multi-probiotic supplementation (21d-MP).
- Group 1 sample size Number of subjects in the case (exposed) group
- 14
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: Fig.3d
Description: LEfSe analysis identified bacteria species that significantly differed (FDR <0.05 and LDA >3) among samples.
Abundance in Group 1: increased abundance in Multi-probiotic supplementation - MP (21d-MP)
Revision editor(s): Aleru Divine
Signature 2
Source: Fig.3d
Description: LEfSe analysis identified bacteria species that significantly differed (FDR <0.05 and LDA >3) among samples.
Abundance in Group 1: decreased abundance in Multi-probiotic supplementation - MP (21d-MP)
Revision editor(s): Aleru Divine
Experiment 6
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Saline supplementation - SA (21d-SA)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 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: Fig.3d
Description: LEfSe analysis identified bacteria species that significantly differed (FDR <0.05 and LDA >3) among samples.
Abundance in Group 1: increased abundance in Multi-probiotic supplementation - MP (21d-MP)
Revision editor(s): Aleru Divine
Signature 2
Source: Fig.3d
Description: LEfSe analysis identified bacteria species that significantly differed (FDR <0.05 and LDA >3) among samples.
Abundance in Group 1: decreased abundance in Multi-probiotic supplementation - MP (21d-MP)
Revision editor(s): Aleru Divine
