Differences in gut microbiota associated with age, sex, and stool consistency in healthy Japanese subjects
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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
- Japan
- 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
- Biological sex Biological sex,biological sex
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Male
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Female
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Female subjects investigated for gut microbiota
- Group 0 sample size Number of subjects in the control (unexposed) group
- 138
- Group 1 sample size Number of subjects in the case (exposed) group
- 139
- 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
- T-Test
- 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 4
Description: Significantly different genera of gut microbiota between male and female subjects
Abundance in Group 1: increased abundance in Female
Revision editor(s): Anne-mariesharp, Montana-D
Signature 2
Source: Figure 4
Description: Significantly different genera of gut microbiota between male and female subjects.
Abundance in Group 1: decreased abundance in Female
Revision editor(s): Montana-D, Anne-mariesharp
Experiment 2
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Abnormal stool composition Abnormal faeces composition,Abnormal feces composition,Abnormal stool composition,abnormal stool composition
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Loose (stool in males)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Intermediate (stool in males)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Stool consistency (in males) classified as Intermediate using the Bristol stool scale (BSS)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 43
- Group 1 sample size Number of subjects in the case (exposed) group
- 86
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 8A
Description: Significantly different genera of microbial communities among each stool consistency group for males according to the BSS (Bristol Stool Scale)
Abundance in Group 1: increased abundance in Intermediate (stool in males)
| NCBI | Quality Control | Links |
|---|---|---|
| Oscillospira | ||
| unclassified Oscillospiraceae |
Revision editor(s): Anne-mariesharp
Signature 2
Source: Figure 8A
Description: Significantly different genera of microbial communities among each stool consistency group for males according to the BSS (Bristol Stool Scale)
Abundance in Group 1: decreased abundance in Intermediate (stool in males)
| NCBI | Quality Control | Links |
|---|---|---|
| Fusobacterium | ||
| Bilophila |
Revision editor(s): Anne-mariesharp
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Loose (stool in Males)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Hard (stool in Males)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Stool consistency (in males) classified as Hard using the Bristol stool scale (BSS)
- 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
- Chao1 Abundance-based estimator of species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Figure 8A
Description: Significantly different genera of microbial communities among each stool consistency group for males according to their BSS (Bristol Scale Score)
Abundance in Group 1: increased abundance in Hard (stool in Males)
| NCBI | Quality Control | Links |
|---|---|---|
| Oscillospira | ||
| unclassified Oscillospiraceae |
Revision editor(s): Montana-D, Anne-mariesharp
Experiment 4
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Intermediate (stool in Males)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 86
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 8A
Description: Significantly different genera of microbial communities among each stool consistency group for males according to their BSS (Bristol Scale Score)
Abundance in Group 1: increased abundance in Hard (stool in Males)
| NCBI | Quality Control | Links |
|---|---|---|
| Oscillospira |
Revision editor(s): Montana-D, Anne-mariesharp
Experiment 5
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Loose (stool in Females)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Intermediate (stool in Females)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Stool consistency (in females) classified as intermediate using the Bristol stool scale (BSS)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 32
- Group 1 sample size Number of subjects in the case (exposed) group
- 80
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
Signature 2
Source: Figure 8B
Description: Significantly different genera of microbial communities among each stool consistency group for females according to the BSS (Bristol Scale Score)
Abundance in Group 1: decreased abundance in Intermediate (stool in Females)
| NCBI | Quality Control | Links |
|---|---|---|
| Haemophilus | ||
| Serratia |
Revision editor(s): Montana-D
Experiment 6
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Loose (stool in females)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Hard (stool in females)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Stool consistency (in females) classified as hard using the Bristol stool scale (BSS)
- Group 1 sample size Number of subjects in the case (exposed) group
- 27
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 8B
Description: Significantly different genera of microbial communities among each stool consistency group for females according to the BSS (Bristol Stool Scale)
Abundance in Group 1: increased abundance in Hard (stool in females)
| NCBI | Quality Control | Links |
|---|---|---|
| Campylobacter | ||
| Turicibacter | ||
| SMB53SMB53 |
Revision editor(s): Anne-mariesharp
Experiment 7
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Intermediate (stool in Females)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Hard (stool in Females)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Stool consistency (in females) classified as Hard using the Bristol stool scale (BSS)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 80
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 8B
Description: Significantly different genera of microbial communities among each stool consistency group for females according to the BSS (Bristol Stool Scale)
Abundance in Group 1: increased abundance in Hard (stool in Females)
| NCBI | Quality Control | Links |
|---|---|---|
| Adlercreutzia | ||
| Campylobacter | ||
| Turicibacter | ||
| SMB53SMB53 |
Revision editor(s): Anne-mariesharp
Experiment 8
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Biological sex Biological sex,biological sex
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Male (20 - 39years)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Female (20 - 39years)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Female subjects within the age group of 20 - 39years
- Group 0 sample size Number of subjects in the control (unexposed) group
- 19
- Group 1 sample size Number of subjects in the case (exposed) group
- 28
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: Supplementary Figure 4a
Description: Significantly differential taxa between males and females within the age range (20-39)
Abundance in Group 1: increased abundance in Female (20 - 39years)
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerofustis | ||
| Bifidobacterium | ||
| Campylobacter | ||
| Ruminococcus | ||
| Pseudoramibacter_EubacteriumPseudoramibacter_Eubacterium |
Revision editor(s): Montana-D, Anne-mariesharp
Signature 2
Source: Supplementary Figure 4a
Description: Significantly differential taxa between males and females within the age range (20-39)
Abundance in Group 1: decreased abundance in Female (20 - 39years)
| NCBI | Quality Control | Links |
|---|---|---|
| Escherichia | ||
| Oribacterium |
Revision editor(s): Montana-D, Anne-mariesharp
Experiment 9
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Male (40 - 59years)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Female (40 - 59years)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Female subjects within the age group of 40 - 59years
- Group 0 sample size Number of subjects in the control (unexposed) group
- 51
- Group 1 sample size Number of subjects in the case (exposed) group
- 49
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: Supplementary Figure 4b
Description: Significant differential taxa between males and females of age range (40 - 59 years)
Abundance in Group 1: increased abundance in Female (40 - 59years)
Revision editor(s): Anne-mariesharp
Signature 2
Source: Supplementary Figure 4b
Description: Significant differential taxa between males and females of age range (40 - 59 years)
Abundance in Group 1: decreased abundance in Female (40 - 59years)
| NCBI | Quality Control | Links |
|---|---|---|
| Megamonas | ||
| Prevotella | ||
| unclassified Gemellaceaeunclassified Gemellaceae |
Revision editor(s): Anne-mariesharp, Montana-D
Experiment 10
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Male (60 years or above)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Female (60 years or above)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Female subjects that are 60 years or above
- Group 0 sample size Number of subjects in the control (unexposed) group
- 69
- Group 1 sample size Number of subjects in the case (exposed) group
- 61
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
- decreased
- Richness Number of species
- decreased
Signature 1
Source: Supplementary Figure 4C
Description: Significantly abundant taxa between males and females of age range (60 or above)
Abundance in Group 1: increased abundance in Female (60 years or above)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Eggerthella | ||
| Holdemania | ||
| Turicibacter |
Revision editor(s): Montana-D, Anne-mariesharp
Signature 2
Source: Supplementary Figure 4C
Description: Significantly abundant taxa between males and females of age range (60 or above)
Abundance in Group 1: decreased abundance in Female (60 years or above)
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomyces | ||
| Desulfovibrio | ||
| Megasphaera | ||
| Moryella | ||
| Paraprevotella | ||
| Prevotella | ||
| Slackia | ||
| unclassified Bacteroidota | ||
| unclassified S24-7unclassified S24-7 |
Revision editor(s): Montana-D, Anne-mariesharp
