Chronic stress is associated with altered gut microbiota profile and relevant metabolites in adolescents
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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.
- Homo sapiens
- 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
- Stress-related disorder Stress-related disorder,stress-related disorder
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- low stress + medium stress
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- high stress
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants with high chronic stress levels
- Group 0 sample size Number of subjects in the control (unexposed) group
- 83
- Group 1 sample size Number of subjects in the case (exposed) group
- 41
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 3 months
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
- 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
- 2
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
- decreased
- Richness Number of species
- decreased
Signature 2
Source: Figure 2a
Description: Linear discriminant analysis (LDA) scores for the bacterial taxa differentially abundant in adolescents with different chronic stress levels (LDA > 2).
Abundance in Group 1: increased abundance in high stress
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomycetota | ||
| Alphaproteobacteria | ||
| Bacteria | ||
| Pseudomonas plecoglossicida | ||
| Sphingomonadaceae | ||
| Sphingomonadales | ||
| Sphingomonas | ||
| unclassified Sphingomonas |
Revision editor(s): Appleeyes
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- low stress
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants with high chronic stress levels for the metagenomic subset
- 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
- 30
Lab analysis
- Sequencing type
- WMS
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
Statistical Analysis
Signature 1
Source: figure 3c
Description: The specific bacteria taxa of two stress groups based on Linear Discriminant Analysis Effect Size (LEfSe) analysis.
Abundance in Group 1: increased abundance in high stress
| NCBI | Quality Control | Links |
|---|---|---|
| Ascomycota | ||
| Saccharomyces | ||
| Saccharomycetaceae | ||
| Saccharomycetales | ||
| Saccharomycetes |
Revision editor(s): Appleeyes
Experiment 3
Subjects
Lab analysis
Statistical Analysis
- Statistical test
- Mann-Whitney (Wilcoxon)
- 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
- Not specified
Signature 1
Source: figure 3e
Description: The Wilcoxon rank-sum test was used to analyze the difference in the relative abundances in adolescents with low- and high-chronic stress. These analyses were based on gut microbial species that were significantly correlated with chronic stress, as identified by Spearman’s rank correlation.
Abundance in Group 1: decreased abundance in high stress
Revision editor(s): Appleeyes
Signature 2
Source: figure 3e
Description: The Wilcoxon rank-sum test was used to analyze the difference in the relative abundances in adolescents with low- and high-chronic stress. These analyses were based on gut microbial species that were significantly correlated with chronic stress, as identified by Spearman’s rank correlation.
Abundance in Group 1: increased abundance in high stress
| NCBI | Quality Control | Links |
|---|---|---|
| Achromobacter insuavis | ||
| Bifidobacterium catenulatum | ||
| Bifidobacterium pseudocatenulatum CAG:263 | ||
| Desulfovibrio sp. 3_1_syn3 | ||
| Clostridium sp. AM25-23AC |
Revision editor(s): Appleeyes
Experiment 4
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- low stress + medium stress
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants with high chronic stress levels
- Group 0 sample size Number of subjects in the control (unexposed) group
- 83
- Group 1 sample size Number of subjects in the case (exposed) group
- 41
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V4
Statistical Analysis
- Statistical test
- Kruskall-Wallis
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
- decreased
- Richness Number of species
- decreased
Signature 1
Source: figure 2c and 2e
Description: The Kruskal-Wallis test was used to analyze differences in the relative abundances of bacteria taxa at the phylum and genus levels among adolescents with varying stress levels.
Abundance in Group 1: decreased abundance in high stress
| NCBI | Quality Control | Links |
|---|---|---|
| Akkermansia | ||
| Bacteroides | ||
| Bacteroidota | ||
| Faecalibacterium | ||
| Ruminococcus | ||
| Thermodesulfobacteriota | ||
| Verrucomicrobiota | ||
| unclassified Lachnospiraceae |
Revision editor(s): Appleeyes
Signature 2
Source: figure 2c and 2e
Description: The Kruskal-Wallis test was used to analyze differences in the relative abundances of bacteria taxa at the phylum and genus levels among adolescents with varying stress levels.
Abundance in Group 1: increased abundance in high stress
| NCBI | Quality Control | Links |
|---|---|---|
| Chloroflexia |
Revision editor(s): Appleeyes
Experiment 5
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- low stress
- 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
- 30
Lab analysis
- Sequencing type
- WMS
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
Statistical Analysis
- Statistical test
- Logistic Regression
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, body mass index, sex, Confounders controlled for: "fruit consumption" 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.fruit consumption
Signature 1
Source: figure 3f
Description: Logistic regression analysis was used to analyze the adjusted associations between chronic stress and gut microbial species, identified in Fig. 3 (e). The logistic regression analysis adjusted for sex, age, food consumption, and body mass index as covariates.
Abundance in Group 1: decreased abundance in high stress
Revision editor(s): Appleeyes
Signature 2
Source: figure 3f
Description: Logistic regression analysis was used to analyze the adjusted associations between chronic stress and gut microbial species, identified in Fig. 3 (e). The logistic regression analysis adjusted for sex, age, food consumption, and body mass index as covariates.
Abundance in Group 1: increased abundance in high stress
| NCBI | Quality Control | Links |
|---|---|---|
| Achromobacter insuavis | ||
| Bifidobacterium catenulatum | ||
| Bifidobacterium pseudocatenulatum CAG:263 | ||
| Desulfovibrio sp. 3_1_syn3 | ||
| Clostridium sp. AM25-23AC |
Revision editor(s): Appleeyes
Experiment 6
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- medium stress + high stress
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- low stress
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants with low chronic stress levels
- Group 0 sample size Number of subjects in the control (unexposed) group
- 82
- Group 1 sample size Number of subjects in the case (exposed) group
- 42
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V4
Statistical Analysis
- Statistical test
- LEfSe
- 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
- 2
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- Not specified
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
- Richness Number of species
- increased
Signature 1
Source: figure 2a
Description: Linear discriminant analysis (LDA) scores for the bacterial taxa differentially abundant in adolescents with different chronic stress levels (LDA > 2).
Abundance in Group 1: increased abundance in low stress
Revision editor(s): Appleeyes
Experiment 7
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- low stress + high stress
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- medium stress
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants with medium chronic stress levels
- Group 0 sample size Number of subjects in the control (unexposed) group
- 83
- Group 1 sample size Number of subjects in the case (exposed) group
- 41
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 2a
Description: Linear discriminant analysis (LDA) scores for the bacterial taxa differentially abundant in adolescents with different chronic stress levels (LDA > 2).
Abundance in Group 1: increased abundance in medium stress
Revision editor(s): Appleeyes
Experiment 8
Subjects
Lab analysis
Statistical Analysis
- Statistical test
- Kruskall-Wallis
- 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
- Not specified
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 2c and 2e
Description: The Kruskal-Wallis test was used to analyze differences in the relative abundances of bacteria taxa at the phylum and genus levels among adolescents with varying stress levels.
Abundance in Group 1: decreased abundance in medium stress
| NCBI | Quality Control | Links |
|---|---|---|
| Thermodesulfobacteriota | ||
| Chloroflexia | ||
| Faecalibacterium | ||
| Lachnospiraceae | ||
| Ruminococcus |
Revision editor(s): Appleeyes
Signature 2
Source: figure 2c and 2e
Description: The Kruskal-Wallis test was used to analyze differences in the relative abundances of bacteria taxa at the phylum and genus levels among adolescents with varying stress levels.
Abundance in Group 1: increased abundance in medium stress
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidota | ||
| Verrucomicrobiota | ||
| Bacteroides | ||
| Akkermansia |
Revision editor(s): Appleeyes
Experiment 9
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- medium stress + high stress
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- low stress
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants with low chronic stress levels
- Group 0 sample size Number of subjects in the control (unexposed) group
- 82
- Group 1 sample size Number of subjects in the case (exposed) group
- 42
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
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
- Richness Number of species
- increased
Signature 1
Source: figure 2c and 2e
Description: The Kruskal-Wallis test was used to analyze differences in the relative abundances of bacteria taxa at the phylum and genus levels among adolescents with varying stress levels.
Abundance in Group 1: decreased abundance in low stress
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidota | ||
| Verrucomicrobiota | ||
| Chloroflexia | ||
| Bacteroides | ||
| Akkermansia | ||
| Ruminococcus |
Revision editor(s): Appleeyes
Signature 2
Source: figure 2c and 2e
Description: The Kruskal-Wallis test was used to analyze differences in the relative abundances of bacteria taxa at the phylum and genus levels among adolescents with varying stress levels.
Abundance in Group 1: increased abundance in low stress
| NCBI | Quality Control | Links |
|---|---|---|
| Thermodesulfobacteriota | ||
| Faecalibacterium | ||
| Lachnospiraceae |
Revision editor(s): Appleeyes
