Daily Consumption of Orange Juice from Citrus sinensis L. Osbeck cv. Cara Cara and cv. Bahia Differently Affects Gut Microbiota Profiling as Unveiled by an Integrated Meta-Omics Approach
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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
- Brazil
- 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
- Time 0 days controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Time 7 days
- Group 0 sample size Number of subjects in the control (unexposed) group
- 21
- Group 1 sample size Number of subjects in the case (exposed) group
- 21
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- current
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V1-V3
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Roche454
Statistical Analysis
- 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)?
- Yes
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Table 1, Table 2, Table S2
Description: Relative Abundance of Significant Gut Microbiota OTUs at T7 in Cara Cara (Brazilian orange juice), Bahia (Brazilian orange juice) and CTRLs groups
Abundance in Group 1: decreased abundance in Time 7 days
| NCBI | Quality Control | Links |
|---|---|---|
| Oscillospira | ||
| Porphyromonadaceae |
Revision editor(s): WikiWorks
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Time 0 days Cara Cara
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Table 1, Table 2, Table S3
Description: Relative Abundance of Significant Gut Microbiota OTUs at T7 in Cara Cara (Brazilian orange juice), Bahia (Brazilian orange juice) and CTRLs groups
Abundance in Group 1: increased abundance in Time 7 days
| NCBI | Quality Control | Links |
|---|---|---|
| Tissierellaceae | ||
| Clostridia | ||
| Veillonellaceae | ||
| Odoribacteraceae | ||
| Clostridiaceae |
Signature 2
Source: Table 1, Table 2, Table S4
Description: Relative Abundance of Significant Gut Microbiota OTUs at T7 in Cara Cara (Brazilian orange juice), Bahia (Brazilian orange juice) and CTRLs groups
Abundance in Group 1: decreased abundance in Time 7 days
| NCBI | Quality Control | Links |
|---|---|---|
| Odoribacter |
Revision editor(s): WikiWorks
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Time 0 days Bahia
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Source: Table 1, Table 2, Table S5
Description: Relative Abundance of Significant Gut Microbiota OTUs at T7 in Cara Cara (Brazilian orange juice), Bahia (Brazilian orange juice) and CTRLs groups
Abundance in Group 1: increased abundance in Time 7 days
| NCBI | Quality Control | Links |
|---|---|---|
| Veillonellaceae | ||
| Clostridia | ||
| Clostridiaceae | ||
| Tissierellaceae | ||
| Odoribacteraceae |
Experiment 4
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- controls at time 7
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Cara Cara
Lab analysis
Statistical Analysis
Signature 1
Source: Table 1, Table 2, Table S7
Description: Relative Abundance of Significant Gut Microbiota OTUs at T7 in Cara Cara (Brazilian orange juice), Bahia (Brazilian orange juice) and CTRLs groups
Abundance in Group 1: increased abundance in Cara Cara
| NCBI | Quality Control | Links |
|---|---|---|
| Parabacteroides | ||
| Barnesiellaceae | ||
| Amedibacillus dolichus CAG:375 | ||
| Clostridiaceae | ||
| Dorea | ||
| Oscillospiraceae | ||
| Anaerotruncus | ||
| Enterobacteriaceae | ||
| Butyricimonas |
Revision editor(s): WikiWorks
Signature 2
Source: Table 1, Table 2, Table S8
Description: Relative Abundance of Significant Gut Microbiota OTUs at T7 in Cara Cara (Brazilian orange juice), Bahia (Brazilian orange juice) and CTRLs groups
Abundance in Group 1: decreased abundance in Cara Cara
| NCBI | Quality Control | Links |
|---|---|---|
| Christensenellaceae |
Revision editor(s): WikiWorks
Experiment 5
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Bahia
Lab analysis
Statistical Analysis
Signature 1
Source: Table 1, Table 2, Table S9
Description: Relative Abundance of Significant Gut Microbiota OTUs at T7 in Cara Cara (Brazilian orange juice), Bahia (Brazilian orange juice) and CTRLs groups
Abundance in Group 1: increased abundance in Bahia
| NCBI | Quality Control | Links |
|---|---|---|
| Adlercreutzia | ||
| Enterococcus | ||
| Clostridiaceae | ||
| Clostridium | ||
| Oscillospiraceae | ||
| Anaerotruncus |
Revision editor(s): WikiWorks
Experiment 6
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Bahia at time 7
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Cara Cara
Lab analysis
Statistical Analysis
Signature 1
Source: Table 1, Table 2, Table S11
Description: Relative Abundance of Significant Gut Microbiota OTUs at T7 in Cara Cara (Brazilian orange juice), Bahia (Brazilian orange juice) and CTRLs groups
Abundance in Group 1: increased abundance in Cara Cara
| NCBI | Quality Control | Links |
|---|---|---|
| Amedibacillus dolichus CAG:375 |
Revision editor(s): WikiWorks
