Effects of Commercial Apple Varieties on Human Gut Microbiota Composition and Metabolic Output Using an In Vitro Colonic Model
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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 Kingdom
- 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
- diet Dietary,Diets,diet
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- renatta canada apple - at 10 hr
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- cellulose
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- poorly fermentable fiber (cellulose)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 3
- Group 1 sample size Number of subjects in the case (exposed) group
- 3
- 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
- V3-V4
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Statistical test
- ANOVA
- 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
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
- Richness Number of species
- increased
Signature 1
Source: Figure 1, Table 2, and text
Description: Changes in bacterial taxa relative abundance (%) at 10 h and 24 h of in vitro batch culture fermentations inoculated with human feces (n = 3 healthy donors) and administrated with inulin, cellulose, Renetta Canada, Golden Delicious and Pink Lady as the substrates (treatments).
Abundance in Group 1: increased abundance in cellulose
NCBI | Quality Control | Links |
---|---|---|
Eubacteriales |
Revision editor(s): WikiWorks
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- golden delicious apple - at 10 hr
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
- Richness Number of species
- increased
Signature 1
Source: Figure 1, Table 2, and text
Description: Changes in bacterial taxa relative abundance (%) at 10 h and 24 h of in vitro batch culture fermentations inoculated with human feces (n = 3 healthy donors) and administrated with inulin, cellulose, Renetta Canada, Golden Delicious and Pink Lady as the substrates (treatments).
Abundance in Group 1: increased abundance in cellulose
NCBI | Quality Control | Links |
---|---|---|
Eubacteriales |
Revision editor(s): WikiWorks
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- pink lady apple - at 10 hr
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
- Richness Number of species
- increased
Signature 1
Source: Figure 1, Table 2, and text
Description: Changes in bacterial taxa relative abundance (%) at 10 h and 24 h of in vitro batch culture fermentations inoculated with human feces (n = 3 healthy donors) and administrated with inulin, cellulose, Renetta Canada, Golden Delicious and Pink Lady as the substrates (treatments).
Abundance in Group 1: increased abundance in cellulose
NCBI | Quality Control | Links |
---|---|---|
Eubacteriales |
Revision editor(s): WikiWorks