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

From BugSigDB
Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09
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

Curated date: 2021/01/10

Curator: WikiWorks743

Revision editor(s): WikiWorks753, WikiWorks743

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

Curated date: 2019-07-23

Curator: Lora Kasselman

Revision editor(s): WikiWorks743

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

Curated date: 2021/01/10

Curator: WikiWorks743

Revision editor(s): WikiWorks753, WikiWorks743

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

Curated date: 2019-07-23

Curator: Lora Kasselman

Revision editor(s): WikiWorks743

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

Curated date: 2019-07-23

Curator: Lora Kasselman

Revision editor(s): WikiWorks743

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

Curated date: 2019-07-23

Curator: Lora Kasselman

Revision editor(s): WikiWorks743

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

Curated date: 2021/01/10

Curator: WikiWorks743

Revision editor(s): WikiWorks753, WikiWorks743

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

Curated date: 2019-07-23

Curator: Lora Kasselman

Revision editor(s): WikiWorks743

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

Curated date: 2019-07-23

Curator: Lora Kasselman

Revision editor(s): WikiWorks743

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

Curated date: 2021/01/10

Curator: WikiWorks743

Revision editor(s): WikiWorks753, WikiWorks743

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

Curated date: 2019-07-23

Curator: Lora Kasselman

Revision editor(s): WikiWorks743

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

Curated date: 2021/01/10

Curator: WikiWorks743

Revision editor(s): WikiWorks753, WikiWorks743

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

Curated date: 2019-07-23

Curator: Lora Kasselman

Revision editor(s): WikiWorks743

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