Effect of Lactobacillus rhamnosus GG Supplementation on Intestinal Inflammation Assessed by PET/MRI Scans and Gut Microbiota Composition in HIV-Infected Individuals
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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
- Denmark
- 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
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- baseline
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- combination antiretroviral therapy treated individuals after taking LGG probiotic for 8 weeks
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Persons with HIV
- Group 0 sample size Number of subjects in the control (unexposed) group
- 27
- Group 1 sample size Number of subjects in the case (exposed) group
- 27
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 2 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
- Mann-Whitney (Wilcoxon)
- 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
Alpha Diversity
- Richness Number of species
- unchanged
Signature 1
Source: Text, Supplementary Figure 3
Description: Effect of Probiotic LGG on Gut Microbiota Composition
Abundance in Group 1: increased abundance in combination antiretroviral therapy treated individuals after taking LGG probiotic for 8 weeks
NCBI | Quality Control | Links |
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Ruminiclostridium | ||
Lachnospiraceae |
Revision editor(s): WikiWorks
Signature 2
Source: Text, Supplementary Figure 3
Description: Effect of Probiotic LGG on Gut Microbiota Composition
Abundance in Group 1: decreased abundance in combination antiretroviral therapy treated individuals after taking LGG probiotic for 8 weeks
NCBI | Quality Control | Links |
---|---|---|
Enterobacteriaceae | ||
Erysipelotrichaceae |
Revision editor(s): WikiWorks
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- individuals with no change in uptake
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- individuals with decreased F-2-fluoro-2-deoxy-D-glucose (F-FDG) uptake on positron emission tomography (PET)/magnetic resonance imaging (MRI)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 7
- Group 1 sample size Number of subjects in the case (exposed) group
- 5
Lab analysis
Statistical Analysis
Alpha Diversity
- Richness Number of species
- unchanged
Signature 1
Source: Text, Figure 2
Description: Changes in relative abundance of Enterobacteriaceae after LGG supplementation in responders and nonresponders
Abundance in Group 1: decreased abundance in individuals with decreased F-2-fluoro-2-deoxy-D-glucose (F-FDG) uptake on positron emission tomography (PET)/magnetic resonance imaging (MRI)
NCBI | Quality Control | Links |
---|---|---|
Enterobacteriaceae |
Revision editor(s): WikiWorks