Distinct intestinal microbial signatures linked to accelerated systemic and intestinal biological aging
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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
- United States of America
- 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
- Colon Hindgut,Large bowel,Posterior intestine,Colon,colon
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Controls/ People living without HIV (PLWOH)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- People living with HIV on Antiretroviral Therapy (PLWH on ART)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- People with HIV infection on Anti-Retroviral Therapy(ART)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 23
- Group 1 sample size Number of subjects in the case (exposed) group
- 25
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V1-V2
- 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
- Matched on Factors on which subjects have been matched on in a case-control study
- age, body mass index, ethnic group, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Richness Number of species
- decreased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- decreased
Signature 1
Source: Figure 4D
Description: Log-scale differences in bacterial abundance across colon (triangle), between PLWoH and PLWH on ART.
Abundance in Group 1: increased abundance in People living with HIV on Antiretroviral Therapy (PLWH on ART)
| NCBI | Quality Control | Links |
|---|---|---|
| Alloprevotella | ||
| Catenibacterium | ||
| Enterobacteriaceae | ||
| Prevotella sp. |
Revision editor(s): Imaspecial, Fiddyhamma, WikiWorks
Signature 2
Source: Figure 4D
Description: Log-scale differences in bacterial abundance across colon (triangle), between PLWoH and PLWH on ART.
Abundance in Group 1: decreased abundance in People living with HIV on Antiretroviral Therapy (PLWH on ART)
| NCBI | Quality Control | Links |
|---|---|---|
| Alistipes | ||
| Bacteroidales | ||
| Bacteroides | ||
| Faecalibacterium | ||
| Subdoligranulum | ||
| uncultured Erysipelotrichaceae bacterium | ||
| Coprococcus sp. |
Revision editor(s): Imaspecial, Fiddyhamma, WikiWorks
Experiment 2
Curated date: 2024/03/22
Curator:
Revision editor(s):
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Ileum
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Signature 1
Source: Fig 4D
Description: Log-scale differences in bacterial abundance across ileum (square), between PLWoH and PLWH on ART.
Abundance in Group 1: increased abundance in
| NCBI | Quality Control | Links |
|---|---|---|
| Alloprevotella | ||
| Catenibacterium | ||
| Prevotella sp. | ||
| Prevotella sp. 1-8 |
Revision editor(s): Imaspecial, Fiddyhamma, WikiWorks
Signature 2
Source: Fig 4D
Description: Log-scale differences in bacterial abundance across ileum (square), between PLWOH and PLWH on ART
Abundance in Group 1: decreased abundance in
| NCBI | Quality Control | Links |
|---|---|---|
| Alistipes | ||
| Bacteroides | ||
| Subdoligranulum | ||
| uncultured Erysipelotrichaceae bacterium | ||
| Coprococcus sp. | ||
| Peptostreptococcaceae | ||
| Romboutsia |
Revision editor(s): Imaspecial, Fiddyhamma, WikiWorks
Experiment 3
Curated date: 2024/03/22
Curator:
Revision editor(s):
Subjects
- 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
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Signature 1
Source: Fig 4D
Description: Log-scale differences in bacterial abundance across feces (circle) between PLWOH and PLWH on ART.
Abundance in Group 1: increased abundance in
| NCBI | Quality Control | Links |
|---|---|---|
| Catenibacterium | ||
| Prevotella sp. | ||
| Alloprevotella | ||
| Lachnospiraceae |
Revision editor(s): Imaspecial, Fiddyhamma, WikiWorks
Signature 2
Source: Fig 4D
Description: Log-scale differences in bacterial abundance across feces (circle) between PLWOH and PLWH on ART.
Abundance in Group 1: decreased abundance in
| NCBI | Quality Control | Links |
|---|---|---|
| uncultured Erysipelotrichaceae bacterium | ||
| Alistipes | ||
| Peptostreptococcaceae | ||
| Bacteroides | ||
| Ruminococcus gauvreauii |
Revision editor(s): Imaspecial, Fiddyhamma, WikiWorks
Experiment 4
Curated date: 2024/03/22
Curator:
Revision editor(s):
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Colon , Feces Hindgut,Large bowel,Posterior intestine,Colon,colon,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
- Colon Tissue Sample
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Fecal Sample
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Fecal sample collected from participants
- 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
Lab analysis
Statistical Analysis
Signature 1
Source: Fig 4C
Description: Differential bacterial abundance between tissue and fecal samples on a logarithmic scale. Comparisons include colon vs. feces (red).
Abundance in Group 1: increased abundance in
Revision editor(s): Imaspecial, Fiddyhamma, WikiWorks
Signature 2
Source: Fig 4C
Description: Differential bacterial abundance between tissue and fecal samples on a logarithmic scale. Comparisons include colon vs. feces (red).
Abundance in Group 1: decreased abundance in
Revision editor(s): Imaspecial, Fiddyhamma, WikiWorks
Experiment 5
Curated date: 2024/03/22
Curator:
Revision editor(s):
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Ileum, 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
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Ileum Tissue Sample
Lab analysis
Statistical Analysis
Signature 1
Source: Fig 4C
Description: Differential bacterial abundance between tissue and fecal samples on a logarithmic scale. Comparisons include Ileum vs. feces (blue).
Abundance in Group 1: increased abundance in
Revision editor(s): Imaspecial, Fiddyhamma, WikiWorks
Signature 2
Source: Fig 4C
Description: Differential bacterial abundance between tissue and fecal samples on a logarithmic scale. Comparisons include Ileum vs. feces (blue).
Abundance in Group 1: decreased abundance in
Revision editor(s): Imaspecial, Fiddyhamma, WikiWorks
Experiment 6
Curated date: 2024/11/13
Curator:
Revision editor(s):
Subjects
- 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
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Controls/ People living without HIV (PLWOH)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- People living with HIV on Antiretroviral Therapy (PLWH on ART)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- People with HIV infection on Anti-Retroviral Therapy(ART)
Lab analysis
Statistical Analysis
Alpha Diversity
- Richness Number of species
- decreased
Signature 1
Source: Additional figure 10E
Description: Estimated log difference between heterosexual PLWH on ART and heterosexual PLWoH
Abundance in Group 1: decreased abundance in
| NCBI | Quality Control | Links |
|---|---|---|
| Ruminococcus sp. | ||
| unclassified Oscillospiraceae | ||
| Bacteroides |
Revision editor(s): Fiddyhamma, WikiWorks
Experiment 7
Curated date: 2024/11/13
Curator:
Revision editor(s):
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Ileum
Lab analysis
Statistical Analysis
Alpha Diversity
- Richness Number of species
- decreased
Signature 1
Source: Additional figure 10E
Description: Estimated log difference between heterosexual PLWH on ART and heterosexual PLWoH
Abundance in Group 1: increased abundance in
| NCBI | Quality Control | Links |
|---|---|---|
| Enterobacteriaceae |
Revision editor(s): Fiddyhamma, WikiWorks
Signature 2
Source: Additional figure 10E
Description: Estimated log difference between heterosexual PLWH on ART and heterosexual PLWoH
Abundance in Group 1: decreased abundance in
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Coprococcus sp. | ||
| Ruminococcus sp. | ||
| Christensenellaceae R7Christensenellaceae R7 |
Revision editor(s): Fiddyhamma, WikiWorks
Experiment 8
Curated date: 2024/11/13
Curator:
Revision editor(s):
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Colon Hindgut,Large bowel,Posterior intestine,Colon,colon
Lab analysis
Statistical Analysis
Alpha Diversity
- Richness Number of species
- decreased
Signature 1
Source: Additional figure 10E
Description: Estimated log difference between heterosexual PLWH on ART and heterosexual PLWoH
Abundance in Group 1: increased abundance in
| NCBI | Quality Control | Links |
|---|---|---|
| Enterobacteriaceae |
Revision editor(s): Fiddyhamma, WikiWorks
Signature 2
Source: Additional figure 10E
Description: Estimated log difference between heterosexual PLWH on ART and heterosexual PLWoH
Abundance in Group 1: decreased abundance in
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Coprococcus sp. | ||
| Ruminococcus sp. | ||
| Christensenellaceae R7Christensenellaceae R7 |
Revision editor(s): Fiddyhamma, WikiWorks
