Gut microbiota in early pediatric multiple sclerosis: a case-control study
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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 (if applicable)
- 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
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- multiple sclerosis Disseminated Sclerosis,generalized multiple sclerosis,insular sclerosis,MS,MS (Multiple Sclerosis),multiple sclerosis,MULTIPLE SCLEROSIS ACUTE FULMINATING,Multiple Sclerosis, Acute Fulminating,Sclerosis, Disseminated,Sclerosis, Multiple
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- healthy controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- pediatric multiple sclerosis
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- early pediatric multiple sclerosis
- Group 0 sample size Number of subjects in the control (unexposed) group
- 17
- Group 1 sample size Number of subjects in the case (exposed) group
- 18
- 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
- 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
- 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, sex
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, ethnic group, breast feeding, sex
Alpha Diversity
- Richness Number of species
- unchanged
Signature 1
Source: Figure 3a, 3b
Description: Difference between multiple sclerosis and controls in the gut microbial communities
Abundance in Group 1: increased abundance in pediatric multiple sclerosis
NCBI | Links |
---|---|
Bilophila ✕� | |
Bifidobacterium � | |
Eubacteriales | |
Desulfovibrio ✕� | |
Coriobacteriaceae | |
Prevotella copri � | |
Catenibacterium � | |
Christensenellaceae | |
Oscillospiraceae | |
Phascolarctobacterium � |
Revision editor(s): WikiWorks
Signature 2
Source: Figure 3a, 3b
Description: Difference between multiple sclerosis and controls in the gut microbial communities
Abundance in Group 1: decreased abundance in pediatric multiple sclerosis
NCBI | Links |
---|---|
Lachnospira � | |
Oscillospiraceae | |
Paraprevotella � | |
Eubacteriales | |
Prevotella copri � | |
Bacteroides � | |
Oscillospira | |
Peptostreptococcus anaerobius � |
Revision editor(s): WikiWorks
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- IMD naive cases
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- IMD exposure multiple sclerosis cases
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Not specified
- Group 0 sample size Number of subjects in the control (unexposed) group
- 9
- Group 1 sample size Number of subjects in the case (exposed) group
- 9
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- Not specified
- Matched on Factors on which subjects have been matched on in a case-control study
- Not specified
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- Not specified
Alpha Diversity
- Richness Number of species
- unchanged
Signature 1
Source: Figure 2b
Description: Difference between multiple sclerosis and controls influenced by the immunomodulatory drug IMD exposure status of cases
Abundance in Group 1: increased abundance in IMD exposure multiple sclerosis cases
NCBI | Links |
---|---|
Actinomycetota |
Revision editor(s): WikiWorks
Signature 2
Source: Figure 2b
Description: Difference between multiple sclerosis and controls influenced by the immunomodulatory drug IMD exposure status of cases
Abundance in Group 1: decreased abundance in IMD exposure multiple sclerosis cases
NCBI | Links |
---|---|
Mycoplasmatota | |
Cyanobacteriota |
Revision editor(s): WikiWorks
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- healthy controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- IMD naive cases multiple sclerosis
- Group 0 sample size Number of subjects in the control (unexposed) group
- 16
Lab analysis
Statistical Analysis
Alpha Diversity
- Richness Number of species
- unchanged
Signature 1
Source: Supplementary Table 7a, Supp Table 7b
Description: Taxa enriched and depleted in the IMD naive cases vs. controls
Abundance in Group 1: increased abundance in IMD naive cases multiple sclerosis
Signature 2
Source: Supplementary Table 7a, Supp Table 7b
Description: Taxa enriched and depleted in the IMD naive cases vs. controls
Abundance in Group 1: decreased abundance in IMD naive cases multiple sclerosis
Revision editor(s): WikiWorks