Associations between the gut microbiome, inflammation and cardiovascular profiles in people with HIV
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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
- Ireland
- 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
- Human immunodeficiency virus AIDS virus,HIV,Human immunodeficiency virus,human immunodeficiency virus
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- People Without HIV
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- People With HIV
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Individuals who have been diagnosed with HIV (Human Immunodeficiency Virus)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 37
- Group 1 sample size Number of subjects in the case (exposed) group
- 44
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).
- centered log-ratio
- Statistical test
- ANCOM-BC
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.1
- 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, sex, antiretroviral therapy, Confounders controlled for: "comorbidities" 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.comorbidities, Confounders controlled for: "statins" 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.statins
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 2
Source: Fig 2 And Fig-S2
Description: Differential abundance (DA) analysis of species and genus in people with human immunodeficiency virus (HIV) compared to those without HIV.
Abundance in Group 1: increased abundance in People With HIV
Revision editor(s): Aiyshaaaa
Signature 3
Source: Fig 2 And S2
Description: Differential abundance (DA) analysis of species in people with human immunodeficiency virus (HIV) compared to those without HIV.
Abundance in Group 1: decreased abundance in People With HIV
Revision editor(s): Aiyshaaaa
Experiment 3
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Alcohol consumption measurement Alcohol consumption measurement,alcohol consumption measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low Alcohol Intake
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High Alcohol Intake
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Higher alcohol consumption recorded in individuals diagnosed with HIV (Human Immunodeficiency Virus)
- 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: Fig-3
Description: Heatmap showing the correlation of the differentially abundant (DA) species with mean nutrient intake and the Healthy Food Diversity (HFD) index.
Abundance in Group 1: increased abundance in High Alcohol Intake
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides eggerthii |
Revision editor(s): Aiyshaaaa
Signature 2
Source: Fig-3 And S5
Description: Heatmap showing the correlation of the differentially abundant (DA) species and genues level with mean nutrient intake and the Healthy Food Diversity (HFD) index.
Abundance in Group 1: decreased abundance in High Alcohol Intake
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium pseudocatenulatum | ||
| Succinivibrio |
Revision editor(s): Aiyshaaaa
Experiment 4
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Protein intake measurement protein consumption measurement,Protein intake measurement,protein intake measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low Protein Intake
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High Protein Intake
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- High Protein Intake recorded in individuals diagnosed with HIV (Human Immunodeficiency Virus)
Lab analysis
Statistical Analysis
Signature 1
Source: Fig-3
Description: Heatmap showing the correlation of the differentially abundant (DA) species with mean nutrient intake and the Healthy Food Diversity (HFD) index.
Abundance in Group 1: decreased abundance in High Protein Intake
| NCBI | Quality Control | Links |
|---|---|---|
| Dialister succinatiphilus |
Revision editor(s): Aiyshaaaa
Experiment 5
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Diet measurement Diet measurement,diet measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low HFD Index
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High HFD Index
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- High Healthy Food Diversity Index recorded in individuals diagnosed with HIV (Human Immunodeficiency Virus)
Lab analysis
Statistical Analysis
Signature 1
Source: Fig-3
Description: Heatmap showing the correlation of the differentially abundant (DA) species with mean nutrient intake and the Healthy Food Diversity (HFD) index.
Abundance in Group 1: increased abundance in High HFD Index
| NCBI | Quality Control | Links |
|---|---|---|
| Selenomonas ruminantium |
Revision editor(s): Aiyshaaaa
Signature 2
Source: Fig-3
Description: Heatmap showing the correlation of the differentially abundant (DA) species with mean nutrient intake and the Healthy Food Diversity (HFD) index.
Abundance in Group 1: decreased abundance in High HFD Index
| NCBI | Quality Control | Links |
|---|---|---|
| Eubacterium ventriosum |
Revision editor(s): Aiyshaaaa
Experiment 6
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Fat intake measurement fat consumption measurement,Fat intake measurement,fat intake measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low PUFA Intake (Polyunsaturated Fat Intake)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High PUFA Intake (Polyunsaturated Fat Intake)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- High Polyunsaturated Fat Intake recorded in individuals diagnosed with HIV (Human Immunodeficiency Virus)
Lab analysis
Statistical Analysis
Signature 1
Source: Fig-3
Description: Heatmap showing the correlation of the differentially abundant (DA) species with mean nutrient intake and the Healthy Food Diversity (HFD) index.
Abundance in Group 1: decreased abundance in High PUFA Intake (Polyunsaturated Fat Intake)
| NCBI | Quality Control | Links |
|---|---|---|
| Phocaeicola barnesiae |
Revision editor(s): Aiyshaaaa
Experiment 7
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Cholesterol 7 Alpha-Hydroxy-4-Cholesten-3-One 12-Alpha-Hydroxylase,[H][C@@]1(CC[C@@]2([H])[C@]3([H])CC=C4C[C@@H](O)CC[C@]4(C)[C@@]3([H])CC[C@]12C)[C@H](C)CCCC(C)C,C27H46O,Cholest-5-en-3-ol (3beta)-,Cholest-5-en-3beta-ol,Cholesterin,CYP8B1,CYPVIIIB1,Cytochrome P450 8B1,Cytochrome P450 CYP8B1,Cytochrome P450 Family 8 Subfamily B Polypeptide 1,Cytochrome P450 Subfamily VIIIB (Sterol 12-Alpha-Hydroxylase) Polypeptide 1,Epicholesterol,InChIKey=HVYWMOMLDIMFJA-DPAQBDIFBB,Steroid 12-Alpha-Hydroxylase,Sterol 12 Alpha Hydroxylase,Cholesterol,cholesterol
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low Cholesterol Intake
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High Cholesterol Intake
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- High Cholesterol Intake recorded in individuals diagnosed with HIV (Human Immunodeficiency Virus)
Lab analysis
Statistical Analysis
Signature 1
Source: Fig-3
Description: Heatmap showing the correlation of the differentially abundant (DA) species with mean nutrient intake and the Healthy Food Diversity (HFD) index.
Abundance in Group 1: decreased abundance in High Cholesterol Intake
| NCBI | Quality Control | Links |
|---|---|---|
| Pyramidobacter piscolens |
Revision editor(s): Aiyshaaaa
Experiment 8
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Fat intake measurement fat consumption measurement,Fat intake measurement,fat intake measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low Trans Fat Intake
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High Trans Fat Intake
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- High Trans Fat Intake recorded in individuals diagnosed with HIV (Human Immunodeficiency Virus)
Lab analysis
Statistical Analysis
Signature 1
Source: Fig-3
Description: Heatmap showing the correlation of the differentially abundant (DA) species with mean nutrient intake and the Healthy Food Diversity (HFD) index.
Abundance in Group 1: increased abundance in High Trans Fat Intake
| NCBI | Quality Control | Links |
|---|---|---|
| Ruminococcus bromii |
Revision editor(s): Aiyshaaaa
Signature 2
Source: Fig-3
Description: Heatmap showing the correlation of the differentially abundant (DA) species with mean nutrient intake and the Healthy Food Diversity (HFD) index.
Abundance in Group 1: decreased abundance in High Trans Fat Intake
| NCBI | Quality Control | Links |
|---|---|---|
| Alistipes putredinis | ||
| Bacteroides ovatus | ||
| Bacteroides thetaiotaomicron | ||
| Megamonas hypermegale | ||
| Phocaeicola barnesiae | ||
| Pyramidobacter piscolens | ||
| Segatella albensis |
Revision editor(s): Aiyshaaaa
Experiment 9
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Energy intake Caloric Intake,Energy intake,energy intake
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low Energy Intake
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High Energy Intake
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- High Energy Intake recorded in individuals diagnosed with HIV (Human Immunodeficiency Virus)
Lab analysis
Statistical Analysis
Signature 1
Source: Fig-3 and S5
Description: Heatmap showing the correlation of the differentially abundant (DA) species and genus level with mean nutrient intake and the Healthy Food Diversity (HFD) index.
Abundance in Group 1: decreased abundance in High Energy Intake
| NCBI | Quality Control | Links |
|---|---|---|
| Alistipes putredinis | ||
| Bacteroides | ||
| Bacteroides thetaiotaomicron | ||
| Phocaeicola plebeius | ||
| Phocaeicola barnesiae |
Revision editor(s): Aiyshaaaa
Experiment 10
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Carbohydrate intake measurement carbohydrate consumption measurement,Carbohydrate intake measurement,carbohydrate intake measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low Carbohydrate Intake
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High Carbohydrate Intake
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- High Carbohydrate Intake recorded in individuals diagnosed with HIV (Human Immunodeficiency Virus)
Lab analysis
Statistical Analysis
Signature 1
Source: Fig-3
Description: Heatmap showing the correlation of the differentially abundant (DA) species with mean nutrient intake and the Healthy Food Diversity (HFD) index.
Abundance in Group 1: decreased abundance in High Carbohydrate Intake
| NCBI | Quality Control | Links |
|---|---|---|
| Alistipes putredinis | ||
| Bacteroides eggerthii | ||
| Bacteroides thetaiotaomicron | ||
| Barnesiella intestinihominis | ||
| Phocaeicola barnesiae | ||
| Phocaeicola plebeius |
Revision editor(s): Aiyshaaaa
Experiment 11
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Fat intake measurement fat consumption measurement,Fat intake measurement,fat intake measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low Saturated Fat Intake
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High Saturated Fat Intake
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- High Saturated Fat Intake recorded in individuals diagnosed with HIV (Human Immunodeficiency Virus)
Lab analysis
Statistical Analysis
Signature 1
Source: Fig-3
Description: Heatmap showing the correlation of the differentially abundant (DA) species with mean nutrient intake and the Healthy Food Diversity (HFD) index.
Abundance in Group 1: increased abundance in High Saturated Fat Intake
| NCBI | Quality Control | Links |
|---|---|---|
| Ruminococcus bromii |
Revision editor(s): Aiyshaaaa
Signature 2
Source: Fig-3
Description: Heatmap showing the correlation of the differentially abundant (DA) species with mean nutrient intake and the Healthy Food Diversity (HFD) index.
Abundance in Group 1: decreased abundance in High Saturated Fat Intake
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides ovatus | ||
| Megamonas hypermegale | ||
| Phocaeicola barnesiae | ||
| Phocaeicola plebeius | ||
| Pyramidobacter piscolens |
Revision editor(s): Aiyshaaaa
Experiment 12
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Sugar consumption measurement sugar intake measurement,Sugar consumption measurement,sugar consumption measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low Sugar Intake
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High Sugar Intake
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- High Sugar Intake recorded in individuals diagnosed with HIV (Human Immunodeficiency Virus)
Lab analysis
Statistical Analysis
Signature 1
Source: Fig-3 and S5
Description: Heatmap showing the correlation of the differentially abundant (DA) species and genus level with mean nutrient intake and the Healthy Food Diversity (HFD) index.
Abundance in Group 1: decreased abundance in High Sugar Intake
Revision editor(s): Aiyshaaaa
Experiment 13
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Diet measurement Diet measurement,diet measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low Fiber Intake
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High Fiber Intake
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- High Fiber Intake recorded in individuals diagnosed with HIV (Human Immunodeficiency Virus)
Lab analysis
Statistical Analysis
Signature 1
Source: Fig-3
Description: Heatmap showing the correlation of the differentially abundant (DA) species with mean nutrient intake and the Healthy Food Diversity (HFD) index.
Abundance in Group 1: decreased abundance in High Fiber Intake
| NCBI | Quality Control | Links |
|---|---|---|
| Alistipes putredinis |
Revision editor(s): Aiyshaaaa
