Human gut microbiota adaptation to high-altitude exposure: longitudinal analysis over acute and prolonged periods
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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
- High altitude adaptation High altitude adaptation,high altitude adaptation
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- G-II + G-III (Group 2 and 3)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- G-I (Group 1 at 800 m)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Group of healthy adult males at the baseline at 800 m altitude.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 592
- Group 1 sample size Number of subjects in the case (exposed) group
- 406
- 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
Signature 1
Source: Figure 5C
Description: LEfSe differential analysis comparing the baseline group at 800 m. of altitude vs. acute high-altitude group and prolonged high-altitude group after a 2 week return from 3 months at 4500 m).
Abundance in Group 1: increased abundance in G-I (Group 1 at 800 m)
Revision editor(s): YokoC
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- G-I + G-III (Group and 3)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- G-2 (Group 2 acute altitude at 4500 m)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Group of healthy adult males seven days after ascending to 4,500 m.
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 5C
Description: LEfSe differential analysis comparing the acute high-altitude group at 4500 m vs. the baseline group at 800 m. of altitude and prolonged high-altitude group (after a two week return from 3 months at 4500 m).
Abundance in Group 1: increased abundance in G-2 (Group 2 acute altitude at 4500 m)
Revision editor(s): YokoC
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- G-I + G-II (Group 1 and 2)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- G-3 (Group 3 after prolonged altitude at 800 m)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Group of healthy adult males two weeks post-return to 800 m following 3 months at high altitude
- Group 0 sample size Number of subjects in the control (unexposed) group
- 812
- Group 1 sample size Number of subjects in the case (exposed) group
- 186
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 5C
Description: LEfSe differential analysis comparing the prolonged high-altitude group (after a two week return from 3 months at 4500 m) vs. the baseline group at 800 m. of altitude and acute high-altitude group at 4500 m.
Abundance in Group 1: increased abundance in G-3 (Group 3 after prolonged altitude at 800 m)
Revision editor(s): YokoC
Experiment 4
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- G-I (Group 1 baseline)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- G-2 (Group 2 acute altitude exposure at 4500 m)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Group of healthy adult males seven days after ascending to 4,500 m.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 406
- Group 1 sample size Number of subjects in the case (exposed) group
- 406
Lab analysis
Statistical Analysis
- Statistical test
- Mann-Whitney (Wilcoxon)
- 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
- 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 5A. Within text, Results under "Unique microflora characteristics" section.
Description: Box plots for differential analysis of gut microbiota at the genus level between the acute high-altitude exposure group at 4500 m. vs. the baseline group at 800 m.
Abundance in Group 1: increased abundance in G-2 (Group 2 acute altitude exposure at 4500 m)
| NCBI | Quality Control | Links |
|---|---|---|
| Alistipes | ||
| Gemmiger | ||
| Oscillibacter | ||
| Parabacteroides | ||
| Ruminococcus | ||
| Escherichia/Shigella sp. |
Revision editor(s): YokoC
Signature 2
Source: Figure 5A. Within text, Results under "Unique microflora characteristics" section.
Description: Box plots for differential analysis of gut microbiota at the genus level between the acute high-altitude exposure group at 4500 m. vs. the baseline group at 800 m.
Abundance in Group 1: decreased abundance in G-2 (Group 2 acute altitude exposure at 4500 m)
| NCBI | Quality Control | Links |
|---|---|---|
| Alloprevotella | ||
| Faecalibacterium | ||
| Megamonas | ||
| Roseburia |
Revision editor(s): YokoC
Experiment 5
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- G-3(Group 3 prolonged altitude exposure at 4500 m.)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 186
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 5A, Within text, Results under "Unique microflora characteristics" section.
Description: Box plots for differential analysis of gut microbiota at the genus level between the acute high-altitude exposure group at 4500 m. and the prolonged high-altitude exposure group, two weeks post-return to 800 m following 3 months at high altitude.
Abundance in Group 1: increased abundance in G-2 (Group 2 acute altitude exposure at 4500 m)
| NCBI | Quality Control | Links |
|---|---|---|
| Alistipes | ||
| Gemmiger | ||
| Oscillibacter | ||
| Parabacteroides | ||
| Ruminococcus | ||
| Escherichia/Shigella sp. |
Revision editor(s): YokoC
Signature 2
Source: Figure 5A, Within text, Results under "Unique microflora characteristics" section.
Description: Box plots for differential analysis of gut microbiota at the genus level between the acute high-altitude exposure group at 4500 m. and the prolonged high-altitude exposure group, two weeks post-return to 800 m following 3 months at high altitude.
Abundance in Group 1: decreased abundance in G-2 (Group 2 acute altitude exposure at 4500 m)
| NCBI | Quality Control | Links |
|---|---|---|
| Faecalibacterium | ||
| Roseburia | ||
| Megamonas | ||
| Alloprevotella |
Revision editor(s): YokoC
Experiment 6
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Smoking behavior smoking,Smoking behavior,smoking behavior
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Non-Smokers
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Smokers
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Group of healthy adult males who smoke.
- Group 0 sample size Number of subjects in the control (unexposed) group
- Not specified
- Group 1 sample size Number of subjects in the case (exposed) group
- Not specified
Signature 1
Source: Figure 7
Description: Heatmap of a Spearman correlation analysis of genera with lifestyle factors (smoking).
Abundance in Group 1: increased abundance in Smokers
| NCBI | Quality Control | Links |
|---|---|---|
| Roseburia |
Revision editor(s): YokoC
Signature 2
Source: Figure 7
Description: Heatmap of a Spearman correlation analysis of genera with lifestyle factors (smoking).
Abundance in Group 1: decreased abundance in Smokers
| NCBI | Quality Control | Links |
|---|---|---|
| Odoribacter | ||
| Butyricimonas | ||
| Parabacteroides | ||
| Alloprevotella | ||
| Bilophila | ||
| Dialister | ||
| Clostridium IVClostridium IV | ||
| Oscillibacter |
Revision editor(s): YokoC
Experiment 7
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Alcohol drinking alcohol consumption,Alcohol drinking,alcohol drinking
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- No alcohol use
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Alcohol use
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Group of healthy adult males who use alcohol.
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 7
Description: Heatmap of a Spearman correlation analysis of genera with lifestyle factors (alcohol use).
Abundance in Group 1: increased abundance in Alcohol use
| NCBI | Quality Control | Links |
|---|---|---|
| Roseburia |
Revision editor(s): YokoC
Signature 2
Source: Figure 7
Description: Heatmap of a Spearman correlation analysis of genera with lifestyle factors (alcohol use).
Abundance in Group 1: decreased abundance in Alcohol use
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium | ||
| Butyricicoccus | ||
| Dorea | ||
| Clostridium XIVaClostridium XIVa |
Revision editor(s): YokoC
Experiment 8
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Age Age,age
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Lower age
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Higher age
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Group of healthy adult males between the ages of 18 - 25.
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 7
Description: Heatmap of a Spearman correlation analysis of genera with lifestyle factors (age).
Abundance in Group 1: increased abundance in Higher age
| NCBI | Quality Control | Links |
|---|---|---|
| Blautia | ||
| Fusicatenibacter | ||
| Roseburia |
Revision editor(s): YokoC
Signature 2
Source: Figure 7
Description: Heatmap of a Spearman correlation analysis of genera with lifestyle factors (age).
Abundance in Group 1: decreased abundance in Higher age
| NCBI | Quality Control | Links |
|---|---|---|
| Methanobrevibacter | ||
| Collinsella | ||
| Bifidobacterium | ||
| Oscillibacter |
Revision editor(s): YokoC
Experiment 9
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Body mass index BMI,Quetelet's Index,Body mass index,body mass index
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Lower BMI (Body Mass Index)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Higher BMI (Body Mass Index)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Group of healthy adult males with a higher Body Mass Index (BMI).
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 7
Description: Heatmap of a Spearman correlation analysis of genera with lifestyle factors (BMI).
Abundance in Group 1: increased abundance in Higher BMI (Body Mass Index)
| NCBI | Quality Control | Links |
|---|---|---|
| Collinsella |
Revision editor(s): YokoC
Signature 2
Source: Figure 7
Description: Heatmap of a Spearman correlation analysis of genera with lifestyle factors (BMI).
Abundance in Group 1: decreased abundance in Higher BMI (Body Mass Index)
| NCBI | Quality Control | Links |
|---|---|---|
| Dialister |
Revision editor(s): YokoC
Experiment 10
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Tea consumption measurement Tea consumption measurement,tea consumption measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Lower tea consumption
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Higher tea consumption
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 7
Description: Heatmap of a Spearman correlation analysis of genera with lifestyle factors (tea consumption).
Abundance in Group 1: increased abundance in Higher tea consumption
| NCBI | Quality Control | Links |
|---|---|---|
| Methanobrevibacter |
Revision editor(s): YokoC
