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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Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI Uniform resource identifier for web resources.
Authors
Brasili E, Hassimotto NMA, Del Chierico F, Marini F, Quagliariello A, Sciubba F, Miccheli A, Putignani L, Lajolo F
Journal
Journal of agricultural and food chemistry
Year
2019
We have investigated the effect of intake of two different orange juices from Citrus sinensis cv. "Cara Cara" and cv. "Bahia" on faecal microbiota and metabolome using an integrated meta-omics approach. Following a randomized crossover design, healthy subjects daily consumed 500 mL of orange juice from Cara Cara or Bahia juices or an isocaloric control drink. Stools were collected at baseline (T0) and after a week (T7) of intervention. Operational taxonomic units (OTUs) were pyrosequenced targeting 16S rRNA, and faecal metabolites were analyzed by an untargeted metabolomics approach based on 1H NMR spectroscopy. The major shift observed in microbiota composition after orange juice intake was the increased abundance of a network of Clostridia OTUs from Mogibacteriaceae, Tissierellaceae, Veillonellaceae, Odoribacteraceae, and Ruminococcaceae families, whose members were differently affected by Cara Cara or Bahia juice consumption. A core of six metabolites such as inositol, choline, lysine, arginine, urocanic acid, and formate significantly increased in Cara Cara compared to the Bahia group.
Experiment 1
Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09
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
Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09
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 | Links |
|---|---|
| Oscillospira | |
| Porphyromonadaceae |
Revision editor(s): WikiWorks743
Experiment 2
Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09
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 Cara Cara
- 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
- 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
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09
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 | Links |
|---|---|
| Tissierellaceae | |
| k__Bacteria, p__Firmicutes, c__Clostridia, o__ Clostridiales, f__ Mogibacteriaceaef__ Mogibacteriaceae |
Revision editor(s): WikiWorks743
Signature 2
Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09
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 | Links |
|---|---|
| Odoribacter |
Revision editor(s): WikiWorks743
Experiment 3
Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09
Curated date: 2021/01/10
Curator: WikiWorks743
Revision editor(s): WikiWorks753, WikiWorks743, Aiyshaaaa
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 Bahia
- 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
- 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
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09
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 | Links |
|---|---|
| k__Bacteria, p__Firmicutes, c__Clostridia, o__ Clostridiales, f__ Mogibacteriaceaef__ Mogibacteriaceae | |
| Veillonellaceae |
Revision editor(s): WikiWorks743
Experiment 4
Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09
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
- controls at time 7
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Cara Cara
- 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
- 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
Signature 1
Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09
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 | Links |
|---|---|
| Parabacteroides | |
| Barnesiellaceae | |
| Eubacterium dolichum CAG:375 | |
| Clostridiaceae | |
| Dorea | |
| Oscillospiraceae | |
| Anaerotruncus | |
| Enterobacteriaceae | |
| Butyricimonas |
Revision editor(s): WikiWorks743
Signature 2
Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09
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 | Links |
|---|---|
| Christensenellaceae |
Revision editor(s): WikiWorks743
Experiment 5
Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09
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
- controls at time 7
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Bahia
- 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
- 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
Signature 1
Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09
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 | Links |
|---|---|
| Adlercreutzia | |
| Enterococcus | |
| Clostridiaceae | |
| Clostridium | |
| Oscillospiraceae | |
| Anaerotruncus |
Revision editor(s): WikiWorks743
Experiment 6
Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09
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
- Bahia at time 7
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Cara Cara
- 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
- 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
Signature 1
Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09
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 | Links |
|---|---|
| Eubacterium dolichum CAG:375 |
Revision editor(s): WikiWorks743
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