Gut metagenomes of Asian octogenarians reveal metabolic potential expansion and distinct microbial species associated with aging phenotypes
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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
- 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
- Aging ageing,AGING BIOL,Aging, Biological,BIOL AGING,Biological Aging,Senescence,Aging,aging
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- 61-70 years (Younger Age Group)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- 71-80 years (Older Age Group)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants aged 71-80 years, representing an older age group used to assess age-related changes in the gut microbiome compared to the younger group.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 57
- Group 1 sample size Number of subjects in the case (exposed) group
- 33
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
- Linear Regression
- 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
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- increased
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
- Richness Number of species
- decreased
Signature 1
Source: Figure 1E
Description: Microbial taxa Significantly associated with age in 61-70 and 71-80 age groups
Abundance in Group 1: increased abundance in 71-80 years (Older Age Group)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Phocaeicola dorei |
Revision editor(s): MaryAgekameh, MyleeeA, WikiWorks
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Singapore Platinum Metagenomes Project (SPMP)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- SG90
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Dataset of Octogenarians community-living participants (not living in a nursing home, no diagnosis of dementia and not physically unfit) who consented to providing their stool and blood samples (SG90).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 50
- Group 1 sample size Number of subjects in the case (exposed) group
- 213
Lab analysis
Statistical Analysis
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- Not specified
Signature 1
Source: Supplementary Figure 4
Description: Significantly increased in the SG90 group compared to Singapore Platinum Metagenomes Project (SPMP).
Abundance in Group 1: increased abundance in SG90
| NCBI | Quality Control | Links |
|---|---|---|
| Alistipes onderdonkii | ||
| Alistipes shahii | ||
| Bacteroides xylanisolvens | ||
| Escherichia coli | ||
| Parabacteroides merdae | ||
| unclassified Alistipes | ||
| unclassified Escherichia |
Revision editor(s): MaryAgekameh, MyleeeA, WikiWorks
Signature 2
Source: Supplementary Figure 4
Description: Significantly associated with age in the SG90 group compared to Singapore Platinum Metagenomes Project (SPMP)
Abundance in Group 1: decreased abundance in SG90
Revision editor(s): MaryAgekameh, MyleeeA, WikiWorks
Experiment 3
Subjects
- Location of subjects
- Singapore
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- T2D
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Dataset of Octogenarians community-living participants (not living in a nursing home, no diagnosis of dementia and not physically unfit) who consented to providing their stool and blood samples (SG90).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 171
Lab analysis
Statistical Analysis
Signature 1
Source: Supplementary Figure 4
Description: Significantly associated with age in the SG90 group compared to T2D
Abundance in Group 1: increased abundance in SG90
Signature 2
Source: Supplementary Figure 4
Description: Significantly associated with age in the SG90 group compared to T2D
Abundance in Group 1: decreased abundance in SG90
Experiment 4
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- All Cohorts (Decreased age group)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- All Cohorts (Increased age group)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- All cohorts (SG90, T2D, SPMP and CPE) in the older age group i.e 71-80, 81-90 and 91-100.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 288
- Group 1 sample size Number of subjects in the case (exposed) group
- 228
Lab analysis
Statistical Analysis
Signature 1
Source: Supplementary Data File 3
Description: Phylum, Genus and species Significantly associated with age in All cohort groups.
Abundance in Group 1: increased abundance in All Cohorts (Increased age group)
Signature 2
Source: Supplementary Data File 3
Description: Phylum, Genus and species Significantly associated with age in All cohort groups
Abundance in Group 1: decreased abundance in All Cohorts (Increased age group)
Experiment 5
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Fasting Blood glucose Decreased age group(Age Corrected)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Fasting Blood glucose increased age group(Age corrected)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Asian octogenarians in the older age group i.e 71-80, 81-90 and 91-100 with age correction. Clinical phenotype associated with age (Fasting Blood glucose)
Lab analysis
Statistical Analysis
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age
Signature 1
Source: Supplementary Data File 6
Description: Microbial Species Significantly associated with Fasting Blood glucose after age correction
Abundance in Group 1: increased abundance in Fasting Blood glucose increased age group(Age corrected)
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium adolescentis | ||
| Parabacteroides goldsteinii | ||
| Limosilactobacillus mucosae |
Experiment 6
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Triglycerides Decreased age group(Age Corrected)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Triglycerides Increased age group(Age Corrected)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Asian octogenarians in the older age group i.e 71-80, 81-90 and 91-100 with age correction. Clinical phenotype associated with age (Triglycirides)
Lab analysis
Statistical Analysis
Signature 1
Source: Supplementary Data File 6
Description: Microbial Species Significantly associated with Triglycerides after age correction
Abundance in Group 1: increased abundance in Triglycerides Increased age group(Age Corrected)
| NCBI | Quality Control | Links |
|---|---|---|
| Haemophilus parainfluenzae |
Experiment 7
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Total cholesterol Decreased age group(Age Corrected)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Total cholesterol Increased age group(Age Corrected)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Asian octogenarians in the older age group i.e 71-80, 81-90 and 91-100 with age correction. Clinical phenotype associated with age (Total cholesterol).
Lab analysis
Statistical Analysis
Signature 1
Source: Supplementary Data File 6
Description: Microbial Species Significantly associated with Total Cholesterol after age correction
Abundance in Group 1: increased abundance in Total cholesterol Increased age group(Age Corrected)
| NCBI | Quality Control | Links |
|---|---|---|
| Lachnospiraceae bacterium 1 4 56FAA |
Signature 2
Source: Supplementary Data File 6
Description: Microbial Species Significantly associated with Total Cholesterol after age correction
Abundance in Group 1: decreased abundance in Total cholesterol Increased age group(Age Corrected)
| NCBI | Quality Control | Links |
|---|---|---|
| Haemophilus parainfluenzae |
Experiment 8
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- LDL Decreased age group(Age Corrected)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- LDL Increased age group(Age Corrected)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Asian octogenarians in the older age group i.e 71-80, 81-90 and 91-100 with age correction. Clinical phenotype associated with age (Low-Density Lipoprotein (LDL) Levels)
Lab analysis
Statistical Analysis
Signature 1
Source: Supplementary Data File 6
Description: Microbial Species Significantly associated with Low-Density Lipoprotein (LDL) Levels after age correction
Abundance in Group 1: increased abundance in LDL Increased age group(Age Corrected)
| NCBI | Quality Control | Links |
|---|---|---|
| Haemophilus parainfluenzae |
Signature 2
Source: Supplementary Data File 6
Description: Microbial Species Significantly associated with Low-Density Lipoprotein (LDL) Levels after age correction
Abundance in Group 1: decreased abundance in LDL Increased age group(Age Corrected)
| NCBI | Quality Control | Links |
|---|---|---|
| Lachnospiraceae bacterium 1 4 56FAA |
Experiment 9
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- hs-CRP Decreased age group(Age Corrected)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- hs-CRP Increased age group(Age Corrected)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Asian octogenarians in the older age group i.e 71-80, 81-90 and 91-100 with age correction. Clinical phenotype associated with age (high-sensitivity C-Reactive Protein {hs-CRP})
Lab analysis
Statistical Analysis
Signature 1
Source: Supplementary Data File 6
Description: Microbial Species Significantly associated with high-sensitivity C-Reactive Protein {hs-CRP} after age correction
Abundance in Group 1: increased abundance in hs-CRP Increased age group(Age Corrected)
| NCBI | Quality Control | Links |
|---|---|---|
| Escherichia coli | ||
| unclassified Eggerthella | ||
| Streptococcus salivarius |
Experiment 10
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- AST Decreased age group(Age Corrected)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- AST Increased age group(Age Corrected)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Asian octogenarians in the older age group i.e 71-80, 81-90 and 91-100 with age correction. Clinical phenotype associated with age (Aspartate Aminotransferase {AST})
Lab analysis
Statistical Analysis
Signature 1
Source: Supplementary Data File 6
Description: Microbial Species Significantly associated with Aspartate Aminotransferase {AST} after age correction
Abundance in Group 1: increased abundance in AST Increased age group(Age Corrected)
| NCBI | Quality Control | Links |
|---|---|---|
| Klebsiella pneumoniae |
Experiment 11
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Vitamin B12 Decreased age group(Age Corrected)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Vitamin B12 Increased age group(Age corrected)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Asian octogenarians in the older age group i.e 71-80, 81-90 and 91-100 with age correction. Clinical phenotype associated with age (Vitamin B12).
Lab analysis
Statistical Analysis
Signature 1
Source: Supplementary Data File 6
Description: Microbial Species Significantly associated with Vitamin B12 after age correction
Abundance in Group 1: increased abundance in Vitamin B12 Increased age group(Age corrected)
| NCBI | Quality Control | Links |
|---|---|---|
| Streptococcus parasanguinis | ||
| Phocaeicola coprocola |
Experiment 12
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- All cohorts (Decreased age group)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- All cohorts (Increased age group)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- All cohorts (SG90, T2D, SPMP and CPE) in the older age group i.e 71-80, 81-90 and 91-100.
Lab analysis
Statistical Analysis
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- Not specified
Signature 1
Source: Supplementary Figure 3
Description: Microbial abundance enriched in All cohorts (SG90, T2D, SPMP and CPE) with decease in Age. Using TSS Normalization and Linear model.
Abundance in Group 1: increased abundance in All cohorts (Increased age group)
Revision editor(s): MaryAgekameh, MyleeeA, WikiWorks
Signature 2
Source: Supplementary Figure 3
Description: Microbial abundance enriched in All cohorts (SG90, T2D, SPMP and CPE) with decease in Age. Using TSS Normalization and Linear model.
Abundance in Group 1: decreased abundance in All cohorts (Increased age group)
Revision editor(s): MaryAgekameh, MyleeeA, WikiWorks
Experiment 13
Subjects
Lab analysis
Statistical Analysis
Signature 1
Source: Supplementary Figure 3
Description: Microbial abundance enriched in All cohorts (SG90, T2D, SPMP and CPE) with increase in Age. Using CSS Normalization and Linear model.
Abundance in Group 1: increased abundance in All cohorts (Increased age group)
Revision editor(s): MaryAgekameh, MyleeeA, WikiWorks
Signature 2
Source: Supplementary Figure 3
Description: Microbial abundance enriched in All cohorts (SG90, T2D, SPMP and CPE) with decrease in Age. Using TSS Normalization and Linear model.
Abundance in Group 1: decreased abundance in All cohorts (Increased age group)
Revision editor(s): MaryAgekameh, MyleeeA, WikiWorks
Experiment 14
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- All Cohorts (Decreasing age group)
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- centered log-ratio
- Statistical test
- ANCOM
Signature 1
Source: Supplementary Figure 3
Description: Microbial abundance enriched in All cohorts (SG90, T2D, SPMP and CPE) with increase in Age. Using ANCOM and Centered Log Ratio.
Abundance in Group 1: increased abundance in All cohorts (Increased age group)
Revision editor(s): MaryAgekameh, MyleeeA, WikiWorks
Signature 2
Source: Supplementary Figure 3
Description: Microbial abundance enriched in All cohorts (SG90, T2D, SPMP and CPE) with decrease in Age. Using ANCOM and Centered Log Ratio.
Abundance in Group 1: decreased abundance in All cohorts (Increased age group)
Revision editor(s): MaryAgekameh, MyleeeA, WikiWorks
Experiment 15
Subjects
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- MaAsLin2
Signature 1
Source: Supplementary Figure 3
Description: Microbial abundance enriched in All cohorts (SG90, T2D, SPMP and CPE) with increase in Age. Using TSS Normalization and MaAslin2.
Abundance in Group 1: increased abundance in All cohorts (Increased age group)
Revision editor(s): MaryAgekameh, MyleeeA, WikiWorks
Signature 2
Source: Supplementary Figure 3
Description: Microbial abundance enriched in All cohorts (SG90, T2D, SPMP and CPE) with decrease in Age. Using TSS Normalization and MaAslin2.
Abundance in Group 1: decreased abundance in All cohorts (Increased age group)
Revision editor(s): MaryAgekameh, MyleeeA, WikiWorks
Experiment 16
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- SG90+CPE (Decreasing age group)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- SG90+CPE (Increased age group)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Dataset of Octogenarians community-living participants (not living in a nursing home, no diagnosis of dementia and not physically unfit) who consented to providing their stool and blood samples (SG90) and CPE-colonized subjects and their healthy family members (21–80 years old) with Chinese ethnicity.
- 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
- 226
Signature 1
Source: Supplementary Figure 3
Description: Microbial abundance in the SG90+CPE datasets significantly enriched with increase in Age. Using TSS Normalization and Linear model.
Abundance in Group 1: increased abundance in SG90+CPE (Increased age group)
| NCBI | Quality Control | Links |
|---|---|---|
| Alistipes indistinctus | ||
| Alistipes shahii | ||
| Bacteroides xylanisolvens | ||
| Parabacteroides merdae | ||
| Phocaeicola dorei | ||
| unclassified Alistipes |
Signature 2
Source: Supplementary File 3
Description: Microbial abundance in the SG90+CPE datasets enriched with decease in Age. Using TSS Normalization and Linear model.
Abundance in Group 1: decreased abundance in SG90+CPE (Increased age group)
Revision editor(s): MyleeeA, MaryAgekameh, WikiWorks
Experiment 17
Subjects
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Dataset of Octogenarians community-living participants (not living in a nursing home, no diagnosis of dementia and not physically unfit) who consented to providing their stool and blood samples (SG90) and CPE-colonized subjects and their healthy family members (21–80 years old) with Chinese ethnicity.
Lab analysis
Statistical Analysis
Signature 1
Source: Supplementary Figure 3
Description: Microbial abundance in the SG90+CPE datasets enriched with increase in Age. Using CSS Normalization and Linear model.
Abundance in Group 1: increased abundance in SG90+CPE (Increased age group)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides xylanisolvens | ||
| Parabacteroides merdae | ||
| Alistipes shahii | ||
| Alistipes indistinctus | ||
| unclassified Alistipes | ||
| Phocaeicola dorei |
Signature 2
Source: Supplementary Figure 3
Description: Microbial abundance in the SG90+CPE datasets enriched with decease in Age. Using CSS Normalization and Linear model.
Abundance in Group 1: decreased abundance in SG90+CPE (Increased age group)
Experiment 18
Subjects
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- centered log-ratio
- Statistical test
- ANCOM
Signature 1
Source: Supplementary Figure 3
Description: Microbial abundance in the SG90+CPE datasets enriched with increase in Age. Using Center log Ratio Normalization and ANCOM BC.
Abundance in Group 1: increased abundance in SG90+CPE (Increased age group)
Signature 2
Source: Supplementary Figure 3
Description: Microbial abundance in the SG90+CPE datasets enriched with decrease in Age. Using Center log Ratio Normalization and ANCOM BC.
Abundance in Group 1: decreased abundance in SG90+CPE (Increased age group)
Experiment 19
Subjects
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- MaAsLin2
Signature 1
Source: Supplementary Figure 3
Description: Microbial abundance in the SG90+CPE datasets enriched with increase in Age.
Abundance in Group 1: increased abundance in SG90+CPE (Increased age group)
| NCBI | Quality Control | Links |
|---|---|---|
| Alistipes indistinctus | ||
| Alistipes shahii | ||
| unclassified Alistipes | ||
| Bacteroides xylanisolvens | ||
| Phocaeicola dorei | ||
| Parabacteroides merdae |
Signature 2
Source: Supplementary Figure 3
Description: Microbial abundance in the SG90+CPE datasets enriched with decease in Age.
Abundance in Group 1: decreased abundance in SG90+CPE (Increased age group)
Contents
- 1 Experiment 1
- 2 Experiment 2
- 3 Experiment 3
- 4 Experiment 4
- 5 Experiment 5
- 6 Experiment 6
- 7 Experiment 7
- 8 Experiment 8
- 9 Experiment 9
- 10 Experiment 10
- 11 Experiment 11
- 12 Experiment 12
- 13 Experiment 13
- 14 Experiment 14
- 15 Experiment 15
- 16 Experiment 16
- 17 Experiment 17
- 18 Experiment 18
- 19 Experiment 19
