A gut microbiome signature for HIV and metabolic dysfunction-associated steatotic liver disease
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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
- Spain
- 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
- Non-alcoholic fatty liver disease fatty liver disease, nonalcoholic,fatty liver disease, nonalcoholic, susceptibility to, 1,liver disease, alcoholic, susceptibility to, 1,NAFLD - Nonalcoholic Fatty Liver Disease,NAFLD - nonalcoholic fatty liver disease,NAFLD1,non-alcoholic fatty liver,non-alcoholic fatty liver disease,Nonalcoholic Fatty Liver Disease,nonalcoholic fatty liver disease,Non-alcoholic fatty liver disease
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- HIV- MASLD+
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- HIV+ MASLD+
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants living with HIV (PLWH) and Metabolic dysfunction-associated steatotic liver disease (MASLD).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 20
- Group 1 sample size Number of subjects in the case (exposed) group
- 30
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)?
- Yes
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 4
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Figure S2
Description: LEfSe analysis graph indicating differentially abundant bacterial genera between the different study groups. Only those genus whose LDA score was greater than 4 have been represented.
Abundance in Group 1: increased abundance in HIV+ MASLD+
Revision editor(s): Aleru Divine
Signature 2
Source: Figure S2
Description: LEfSe analysis graph indicating differentially abundant bacterial genera between the different study groups. Only those genus whose LDA score was greater than 4 have been represented.
Abundance in Group 1: decreased abundance in HIV+ MASLD+
Revision editor(s): Aleru Divine
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- HIV+ MASLD-
- Group 0 sample size Number of subjects in the control (unexposed) group
- 30
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Figure S2
Description: LEfSe analysis graph indicating differentially abundant bacterial genera between the different study groups. Only those genus whose LDA score was greater than 4 have been represented.
Abundance in Group 1: increased abundance in HIV+ MASLD+
Revision editor(s): Aleru Divine
Signature 2
Source: Figure S2
Description: LEfSe analysis graph indicating differentially abundant bacterial genera between the different study groups. Only those genus whose LDA score was greater than 4 have been represented.
Abundance in Group 1: decreased abundance in HIV+ MASLD+
Revision editor(s): Aleru Divine
Experiment 3
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- HIV- MASLD+
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants with Metabolic dysfunction-associated steatotic liver disease (MASLD) without HIV infection.
- Group 1 sample size Number of subjects in the case (exposed) group
- 20
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Figure S2
Description: LEfSe analysis graph indicating differentially abundant bacterial genera between the different study groups. Only those genus whose LDA score was greater than 4 have been represented.
Abundance in Group 1: increased abundance in HIV- MASLD+
Revision editor(s): Aleru Divine
Signature 2
Source: Figure S2
Description: LEfSe analysis graph indicating differentially abundant bacterial genera between the different study groups. Only those genus whose LDA score was greater than 4 have been represented.
Abundance in Group 1: decreased abundance in HIV- MASLD+
Revision editor(s): Aleru Divine
