Metatranscriptomic analysis to define the Secrebiome, and 16S rRNA profiling of the gut microbiome in obesity and metabolic syndrome of Mexican children
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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
- Mexico
- 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
- obesity Adiposis,Adiposity,Obese,Obese (finding),obesity,Obesity (disorder),Obesity [Ambiguous],obesity disease,obesity disorder,Obesity NOS,Obesity, unspecified,Overweight and obesity
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- normal weight
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- obese
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- children aged 7-10 years old
- 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
- 10
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 3 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
- 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)?
- No
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 1
- Matched on Factors on which subjects have been matched on in a case-control study
- age, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- increased
Signature 1
Source: Figure 2
Description: Differentially abundant taxa in association with groups and their distribution in the samples.
Abundance in Group 1: increased abundance in obese
NCBI | Quality Control | Links |
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Bifidobacterium adolescentis | ||
Porphyromonas | ||
Faecalibacterium | ||
Faecalibacterium prausnitzii |
Revision editor(s): WikiWorks
Signature 2
Source: Figure 2
Description: Differentially abundant taxa in association with groups and their distribution in the samples.
Abundance in Group 1: decreased abundance in obese
NCBI | Quality Control | Links |
---|---|---|
Phascolarctobacterium |
Revision editor(s): WikiWorks
Experiment 2
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- obesity with metabolic syndrome
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- increased
Signature 1
Source: Figure 2
Description: Differentially abundant taxa in association with groups and their distribution in the samples.
Abundance in Group 1: increased abundance in obesity with metabolic syndrome
Revision editor(s): WikiWorks
Signature 2
Source: Figure 2
Description: Differentially abundant taxa in association with groups and their distribution in the samples.
Abundance in Group 1: decreased abundance in obesity with metabolic syndrome
NCBI | Quality Control | Links |
---|---|---|
Bacteroidota | ||
Bacteroidales | ||
Bacteroidia |
Revision editor(s): WikiWorks