Effects of Vegetable and Fruit Juicing on Gut and Oral Microbiome Composition

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    • Batch effect issues suspected
    • Uncontrolled confounding suspected
    • Results are suspect (various reasons)
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study design
randomized controlled trial
Citation
PMID PubMed identifier for scientific articles.
39940316
DOI Digital object identifier for electronic documents.
10.3390/nu17030458
URI
Authors
Jennifer Baik, Katherine Ryan Amato, Marco Atallah, Maria Luisa Savo Sardaro, Melinda Ring, Veronika Grote
Journal
MDPI
Year
2025
Pages:
First page:
Keywords:
diet recommendations, fruit juicing, gut microbiome, juice fasts, oral microbiome
Background: In recent years, juicing has often been promoted as a convenient way to increase fruit and vegetable intake, with juice-only diets marketed for digestive cleansing and overall health improvement. However, juicing removes most insoluble fiber, which may diminish the health benefits of whole fruits and vegetables. Lower fiber intake can alter the microbiota, affecting metabolism, immunity, and mental health, though little is known about juicing’s specific effects on the microbiota. This study addresses this gap by exploring how juicing impacts gut and oral microbiome composition in an intervention study. Methods: Fourteen participants followed one of three diets—exclusive juice, juice plus food, or plant-based food—for three days. Microbiota samples (stool, saliva, and inner cheek swabs) were collected at baseline, after a pre-intervention elimination diet, immediately after juice intervention, and 14 days after intervention. Moreover, 16S rRNA gene amplicon sequencing was used to analyze microbiota taxonomic composition. Results: The saliva microbiome differed significantly in response to the elimination diet (unweighted UniFrac: F = 1.72, R = 0.06, p < 0.005; weighted UniFrac: F = 7.62, R = 0.23, p-value = 0.0025) with a significant reduction in Firmicutes (p = 0.004) and a significant increase in Proteobacteria (p = 0.005). The juice intervention diets were also associated with changes in the saliva and cheek microbiota, particularly in the relative abundances of pro-inflammatory bacterial families, potentially due to the high sugar and low fiber intake of the juice-related products. Although no significant shifts in overall gut microbiota composition were observed, with either the elimination diet or the juice intervention diets, bacterial taxa associated with gut permeability, inflammation, and cognitive decline increased in relative abundance. Conclusions: These findings suggest that short-term juice consumption may negatively affect the microbiota.

Experiment 1


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Subjects

Location of subjects
United States of America
Host species Species from which microbiome was sampled. Contact us to have more species added.
Homo sapiens
Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
Internal cheek pouch Internal buccal pouch,Internal cheek pouch,internal cheek pouch
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Health study participation health questionnaire participation,health survey participation,Health study participation,health study participation
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Pre-Intervention for exclusive juice diet
Group 1 name Corresponds to the case (exposed) group for case-control studies
Immediately post-intervention for exclusive juice diet
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Effects of exclusive juice diet immediately after intervention on internal cheek sample.
Group 0 sample size Number of subjects in the control (unexposed) group
5
Group 1 sample size Number of subjects in the case (exposed) group
5

Lab analysis

Sequencing type
16S
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
V4-V5
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Illumina

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
relative abundances
Statistical test
Linear Regression
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

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Richness Number of species
unchanged

Signature 1

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Curated date: 2025/03/03

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Source: Results' Text 3.2.1

Description: Relative abundance of bacterial in cheek samples; pre-intervention vs post-intervention for exclusive juice diet.

Abundance in Group 1: increased abundance in Immediately post-intervention for exclusive juice diet

NCBI Quality ControlLinks
Pseudomonadota   

Revision editor(s): Taofeecoh

Signature 2

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Source: Results' Text 3.2.1

Description: Relative abundance of bacterial in cheek samples; pre-intervention vs post-intervention fo exclusive juice diet.

Abundance in Group 1: decreased abundance in Immediately post-intervention for exclusive juice diet

NCBI Quality ControlLinks
Bacillota   

Revision editor(s): Taofeecoh

Experiment 2


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Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Pre-Intervention for plant-based food diet
Group 1 name Corresponds to the case (exposed) group for case-control studies
Immediately post-intervention for plant-based food diet
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Effects of plant-based food diet immediately after intervention on internal cheek sample.

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Richness Number of species
unchanged

Signature 1

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Curated date: 2025/03/03

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Source: Results' Text 3.2.1

Description: Relative abundance of bacterial in cheek samples; pre-intervention vs post-intervention for plant-based diet.

Abundance in Group 1: increased abundance in Immediately post-intervention for plant-based food diet

NCBI Quality ControlLinks
Fusobacteriota   
Pseudomonadota   

Revision editor(s): Taofeecoh

Signature 2

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Source: Result Text

Description: Relative abundance of bacterial in cheek samples; pre-intervention vs post-intervention for plant-based diet.

Abundance in Group 1: decreased abundance in Immediately post-intervention for plant-based food diet

NCBI Quality ControlLinks
Bacillota   
Bacteroidota   

Revision editor(s): Taofeecoh

Experiment 3


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Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Pre-Intervention for Juice plus food diet
Group 1 name Corresponds to the case (exposed) group for case-control studies
Immediately post-intervention for Juice plus food diet
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Effects of exclusive juice diet immediately after intervention on internal cheek sample.
Group 0 sample size Number of subjects in the control (unexposed) group
4
Group 1 sample size Number of subjects in the case (exposed) group
4

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Richness Number of species
unchanged

Signature 1

EditHistoryDelete
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Curated date: 2025/03/03

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Source: Results' Text 3.2.1

Description: Relative abundance of bacterial in cheek samples; pre-intervention vs post-intervention for juice plus food diet.

Abundance in Group 1: decreased abundance in Immediately post-intervention for Juice plus food diet

NCBI Quality ControlLinks
Bacillota   

Revision editor(s): Taofeecoh

Experiment 4


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Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Pre-Intervention for exclusive Juice diet
Group 1 name Corresponds to the case (exposed) group for case-control studies
Immediately post-intervention for exclusive juice diet
Group 0 sample size Number of subjects in the control (unexposed) group
5
Group 1 sample size Number of subjects in the case (exposed) group
5

Lab analysis

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
centered log-ratio
Statistical test
ANCOM-BC
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
Richness Number of species
unchanged

Signature 1

EditHistoryDelete
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Curated date: 2025/03/03

Curator: Taofeecoh

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Source: Results' Text 3.2.1

Description: Relative abundance of bacterial in cheek samples; pre-intervention vs post-intervention for exclusive juice diet.

Abundance in Group 1: increased abundance in Immediately post-intervention for exclusive juice diet

NCBI Quality ControlLinks
Aerococcaceae   
Burkholderiaceae   
Cardiobacteriaceae   
Comamonadaceae   
Flavobacteriaceae   
Fusobacteriaceae   
Neisseriaceae   
Spirochaetaceae   

Revision editor(s): Taofeecoh

Signature 2

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Source: Results' Text 3.2.1

Description: Relative abundance of bacterial in cheek samples; pre-intervention vs post-intervention for exclusive juice diet.

Abundance in Group 1: decreased abundance in Immediately post-intervention for exclusive juice diet

NCBI Quality ControlLinks
Veillonellaceae   

Revision editor(s): Taofeecoh

Experiment 5


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Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Pre-Intervention for plant-based food diet
Group 1 name Corresponds to the case (exposed) group for case-control studies
Immediately post-intervention for plant-based food diet
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Effects of plant-based food diet immediately after intervention on internal cheek sample.

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Richness Number of species
unchanged

Signature 1

EditHistoryDelete
Mark reviewed
Your review change was submitted
Needs review

Curated date: 2025/03/03

Curator: Taofeecoh

Revision editor(s): Taofeecoh

Source: Results' Text 3.2.1

Description: Relative abundance of bacterial in cheek samples; pre-intervention vs post-intervention for plant-based diet.

Abundance in Group 1: increased abundance in Immediately post-intervention for plant-based food diet

NCBI Quality ControlLinks
Burkholderiaceae   
Cardiobacteriaceae   
Fusobacteriaceae   
Neisseriaceae   

Revision editor(s): Taofeecoh

Signature 2

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Curated date: 2025/03/03

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Source: Results' Text 3.2.1

Description: Relative abundance of bacterial in cheek samples; pre-intervention vs post-intervention for plant-based diet.

Abundance in Group 1: decreased abundance in Immediately post-intervention for plant-based food diet

NCBI Quality ControlLinks
Veillonellaceae   

Revision editor(s): Taofeecoh

Experiment 6


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Curated date: 2025/03/03

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Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Pre-Intervention for Juice plus food diet
Group 1 name Corresponds to the case (exposed) group for case-control studies
Immediately post-intervention for Juice plus food diet
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Effects of exclusive juice diet immediately after intervention on internal cheek sample.
Group 0 sample size Number of subjects in the control (unexposed) group
4
Group 1 sample size Number of subjects in the case (exposed) group
4

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Richness Number of species
unchanged

Signature 1

EditHistoryDelete
Mark reviewed
Your review change was submitted
Needs review

Curated date: 2025/03/04

Curator: Taofeecoh

Revision editor(s): Taofeecoh

Source: Results' Text 3.2.1

Description: Relative abundance of bacterial in cheek samples; pre-intervention vs post-intervention for juice plus food diet.

Abundance in Group 1: increased abundance in Immediately post-intervention for Juice plus food diet

NCBI Quality ControlLinks
Aerococcaceae   
Burkholderiaceae   
Cardiobacteriaceae   
Comamonadaceae   
Flavobacteriaceae   
Fusobacteriaceae   
Neisseriaceae   
Spirochaetaceae   
Tissierellaceae   

Revision editor(s): Taofeecoh

Signature 2

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Your review change was submitted
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Curated date: 2025/03/04

Curator: Taofeecoh

Revision editor(s): Taofeecoh

Source: Results' Text 3.2.1

Description: Relative abundance of bacterial in cheek samples; pre-intervention vs post-intervention for juice plus food diet.

Abundance in Group 1: decreased abundance in Immediately post-intervention for Juice plus food diet

NCBI Quality ControlLinks
Veillonellaceae   

Revision editor(s): Taofeecoh

Experiment 7


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Differences from previous experiment shown

Subjects

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
Saliva Sailva normalis,Saliva atomaris,Saliva molecularis,Salivary gland secretion,Saliva,saliva
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Pre-Intervention for Juice diet
Group 1 name Corresponds to the case (exposed) group for case-control studies
Immediately post-intervention for exclusive juice diet
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Effects of exclusive juice diet immediately after intervention on saliva sample.
Group 0 sample size Number of subjects in the control (unexposed) group
5
Group 1 sample size Number of subjects in the case (exposed) group
5

Lab analysis

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
relative abundances
Statistical test
Linear Regression
MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
No

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Richness Number of species
unchanged

Signature 1

EditHistoryDelete
Mark reviewed
Your review change was submitted
Needs review

Curated date: 2025/03/04

Curator: Taofeecoh

Revision editor(s): Taofeecoh

Source: Results' Text 3.2.1

Description: Relative abundance of bacterial in saliva samples; pre-intervention vs post-intervention for exclusive juice diet.

Abundance in Group 1: increased abundance in Immediately post-intervention for exclusive juice diet

NCBI Quality ControlLinks
Pseudomonadota   

Revision editor(s): Taofeecoh

Signature 2

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Curated date: 2025/03/04

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Source: Results' Text 3.2.1

Description: Relative abundance of bacterial in saliva samples; pre-intervention vs post-intervention fo exclusive juice diet.

Abundance in Group 1: decreased abundance in Immediately post-intervention for exclusive juice diet

NCBI Quality ControlLinks
Bacillota   

Revision editor(s): Taofeecoh

Experiment 8


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Curated date: 2025/03/04

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Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Pre-Intervention for plant-based food diet
Group 1 name Corresponds to the case (exposed) group for case-control studies
Immediately post-intervention for plant-based food diet
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Effects of plant-based food diet immediately after intervention on saliva sample.

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Richness Number of species
unchanged

Signature 1

EditHistoryDelete
Mark reviewed
Your review change was submitted
Needs review

Curated date: 2025/03/04

Curator: Taofeecoh

Revision editor(s): Taofeecoh

Source: Results' Text 3.2.1

Description: Relative abundance of bacterial in saliva samples; pre-intervention vs post-intervention for plant-based diet.

Abundance in Group 1: increased abundance in Immediately post-intervention for plant-based food diet

NCBI Quality ControlLinks
Pseudomonadota   

Revision editor(s): Taofeecoh

Signature 2

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Curated date: 2025/03/04

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Source: Results' Text 3.2.1

Description: Relative abundance of bacterial in saliva samples; pre-intervention vs post-intervention for plant-based diet.

Abundance in Group 1: decreased abundance in Immediately post-intervention for plant-based food diet

NCBI Quality ControlLinks
Bacillota   

Revision editor(s): Taofeecoh

Experiment 9


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Curated date: 2025/03/04

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Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Pre-Intervention for Juice plus food diet
Group 1 name Corresponds to the case (exposed) group for case-control studies
Immediately post-intervention for Juice plus food diet
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Effects of exclusive juice diet immediately after intervention on saliva sample.
Group 0 sample size Number of subjects in the control (unexposed) group
4
Group 1 sample size Number of subjects in the case (exposed) group
4

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Richness Number of species
unchanged

Signature 1

EditHistoryDelete
Mark reviewed
Your review change was submitted
Needs review

Curated date: 2025/03/04

Curator: Taofeecoh

Revision editor(s): Taofeecoh

Source: Results' Text 3.2.1

Description: Relative abundance of bacterial in saliva samples; pre-intervention vs post-intervention for juice plus food diet.

Abundance in Group 1: increased abundance in Immediately post-intervention for Juice plus food diet

NCBI Quality ControlLinks
Pseudomonadota   

Revision editor(s): Taofeecoh

Signature 2

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Curated date: 2025/03/04

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Source: Results' Text 3.2.1

Description: Relative abundance of bacterial in saliva samples; pre-intervention vs post-intervention for juice plus food diet.

Abundance in Group 1: decreased abundance in Immediately post-intervention for Juice plus food diet

NCBI Quality ControlLinks
Actinomycetota   
Bacillota   

Revision editor(s): Taofeecoh

Experiment 10


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Curated date: 2025/03/04

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Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Pre-Intervention for exclusive juice diet
Group 1 name Corresponds to the case (exposed) group for case-control studies
Immediately post-intervention for exclusive juice diet
Group 0 sample size Number of subjects in the control (unexposed) group
5
Group 1 sample size Number of subjects in the case (exposed) group
5

Lab analysis

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
centered log-ratio
Statistical test
ANCOM-BC
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
Richness Number of species
unchanged

Signature 1

EditHistoryDelete
Mark reviewed
Your review change was submitted
Needs review

Curated date: 2025/03/04

Curator: Taofeecoh

Revision editor(s): Taofeecoh

Source: Results' Text 3.2.1

Description: Relative abundance of bacterial in saliva samples; pre-intervention vs post-intervention for exclusive juice diet.

Abundance in Group 1: increased abundance in Immediately post-intervention for exclusive juice diet

NCBI Quality ControlLinks
Burkholderiaceae   
Campylobacteraceae   
Flavobacteriaceae   
Fusobacteriaceae   
Neisseriaceae   
Spirochaetaceae   

Revision editor(s): Taofeecoh

Signature 2

EditHistoryDelete
Mark reviewed
Your review change was submitted
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Curated date: 2025/03/04

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Source: Results' Text 3.2.1

Description: Relative abundance of bacterial in saliva samples; pre-intervention vs post-intervention for exclusive juice diet.

Abundance in Group 1: decreased abundance in Immediately post-intervention for exclusive juice diet

NCBI Quality ControlLinks
Coriobacteriaceae   
Lachnospiraceae   
Prevotellaceae   
Streptococcaceae   
Veillonellaceae   

Revision editor(s): Taofeecoh

Experiment 11


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Curated date: 2025/03/04

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Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Pre-Intervention for plant-based food diet
Group 1 name Corresponds to the case (exposed) group for case-control studies
Immediately post-intervention for plant-based food diet
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Effects of plant-based food diet immediately after intervention on saliva sample.

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Richness Number of species
unchanged

Signature 1

EditHistoryDelete
Mark reviewed
Your review change was submitted
Needs review

Curated date: 2025/03/04

Curator: Taofeecoh

Revision editor(s): Taofeecoh

Source: Results' Text 3.2.1

Description: Relative abundance of bacterial in saliva samples; pre-intervention vs post-intervention for plant-based diet.

Abundance in Group 1: increased abundance in Immediately post-intervention for plant-based food diet

NCBI Quality ControlLinks
Fusobacteriaceae   
Neisseriaceae   

Revision editor(s): Taofeecoh

Signature 2

EditHistoryDelete
Mark reviewed
Your review change was submitted
Needs review

Curated date: 2025/03/04

Curator: Taofeecoh

Revision editor(s): Taofeecoh

Source: Results' Text 3.2.1

Description: Relative abundance of bacterial in saliva samples; pre-intervention vs post-intervention for plant-based diet.

Abundance in Group 1: decreased abundance in Immediately post-intervention for plant-based food diet

NCBI Quality ControlLinks
Streptococcaceae   

Revision editor(s): Taofeecoh

Experiment 12


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Curated date: 2025/03/04

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Revision editor(s): Taofeecoh

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Pre-Intervention for Juice plus food diet
Group 1 name Corresponds to the case (exposed) group for case-control studies
Immediately post-intervention for Juice plus food diet
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Effects of exclusive juice diet immediately after intervention on saliva sample.
Group 0 sample size Number of subjects in the control (unexposed) group
4
Group 1 sample size Number of subjects in the case (exposed) group
4

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Richness Number of species
unchanged

Signature 1

EditHistoryDelete
Mark reviewed
Your review change was submitted
Needs review

Curated date: 2025/03/04

Curator: Taofeecoh

Revision editor(s): Taofeecoh

Source: Results' Text 3.2.1

Description: Relative abundance of bacterial in saliva samples; pre-intervention vs post-intervention for juice plus food diet.

Abundance in Group 1: increased abundance in Immediately post-intervention for Juice plus food diet

NCBI Quality ControlLinks
Fusobacteriaceae   
Neisseriaceae   
Spirochaetaceae   
Tissierellaceae   

Revision editor(s): Taofeecoh

Signature 2

EditHistoryDelete
Mark reviewed
Your review change was submitted
Needs review

Curated date: 2025/03/04

Curator: Taofeecoh

Revision editor(s): Taofeecoh

Source: Results' Text 3.2.1

Description: Relative abundance of bacterial in saliva samples; pre-intervention vs post-intervention for juice plus food diet.

Abundance in Group 1: decreased abundance in Immediately post-intervention for Juice plus food diet

NCBI Quality ControlLinks
Coriobacteriaceae   
Lachnospiraceae   
Prevotellaceae   
Streptococcaceae   
Veillonellaceae   

Revision editor(s): Taofeecoh

Experiment 13


EditHistoryDelete
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Curated date: 2025/03/04

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Differences from previous experiment shown

Subjects

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,feces
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Pre-Intervention for exclusive juice diet
Group 1 name Corresponds to the case (exposed) group for case-control studies
Immediately post-intervention for exclusive juice diet
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Effects of exclusive juice diet immediately after intervention on fecal sample.
Group 0 sample size Number of subjects in the control (unexposed) group
5
Group 1 sample size Number of subjects in the case (exposed) group
5

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Richness Number of species
unchanged

Signature 1

EditHistoryDelete
Mark reviewed
Your review change was submitted
Needs review

Curated date: 2025/03/04

Curator: Taofeecoh

Revision editor(s): Taofeecoh

Source: Results' Text 3.2.2

Description: Relative abundance of bacterial in fecal samples; pre-intervention vs post-intervention for exclusive juice diet.

Abundance in Group 1: increased abundance in Immediately post-intervention for exclusive juice diet

NCBI Quality ControlLinks
Alcaligenaceae   
Coriobacteriaceae   
Corynebacteriaceae   
Erysipelotrichaceae   
Odoribacteraceae   
Porphyromonadaceae   
Rikenellaceae   
Tissierellaceae   

Revision editor(s): Taofeecoh

Experiment 14


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Curated date: 2025/03/04

Curator: Taofeecoh

Revision editor(s): Taofeecoh

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Pre-Intervention for Juice plus food diet
Group 1 name Corresponds to the case (exposed) group for case-control studies
Immediately post-intervention for Juice plus food diet
Group 0 sample size Number of subjects in the control (unexposed) group
4
Group 1 sample size Number of subjects in the case (exposed) group
4

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Richness Number of species
unchanged

Signature 1

EditHistoryDelete
Mark reviewed
Your review change was submitted
Needs review

Curated date: 2025/03/04

Curator: Taofeecoh

Revision editor(s): Taofeecoh

Source: Results' Text 3.2.2

Description: Relative abundance of bacterial in fecal samples; pre-intervention vs post-intervention for juice plus food diet.

Abundance in Group 1: increased abundance in Immediately post-intervention for Juice plus food diet

NCBI Quality ControlLinks
Coriobacteriaceae   
Enterobacteriaceae   
Erysipelotrichaceae   
Porphyromonadaceae   

Revision editor(s): Taofeecoh

Experiment 15


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Curated date: 2025/03/04

Curator: Taofeecoh

Revision editor(s): Taofeecoh

Differences from previous experiment shown

Subjects

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
Internal cheek pouch Internal buccal pouch,Internal cheek pouch,internal cheek pouch
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Baseline
Group 1 name Corresponds to the case (exposed) group for case-control studies
Pre-intervention
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Effects of elimination diet on internal cheek sample.
Group 0 sample size Number of subjects in the control (unexposed) group
14
Group 1 sample size Number of subjects in the case (exposed) group
14

Lab analysis

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
relative abundances
Statistical test
Linear Regression
MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
No

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Richness Number of species
unchanged

Signature 1

EditHistoryDelete
Mark reviewed
Your review change was submitted
Needs review

Curated date: 2025/03/04

Curator: Taofeecoh

Revision editor(s): Taofeecoh

Source: Results' Text 3.1.1

Description: Relative abundance of bacterial in internal cheek samples after elimination diet; baseline vs pre-intervention.

Abundance in Group 1: increased abundance in Pre-intervention

NCBI Quality ControlLinks
Pseudomonadota   

Revision editor(s): Taofeecoh

Signature 2

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Curated date: 2025/03/04

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Revision editor(s): Taofeecoh

Source: Results' Text 3.1.1

Description: Relative abundance of bacterial in internal cheek samples after elimination diet; baseline vs pre-intervention.

Abundance in Group 1: decreased abundance in Pre-intervention

NCBI Quality ControlLinks
Bacillota   

Revision editor(s): Taofeecoh

Experiment 16


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Curated date: 2025/03/04

Curator: Taofeecoh

Revision editor(s): Taofeecoh

Differences from previous experiment shown

Subjects

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
Saliva Sailva normalis,Saliva atomaris,Saliva molecularis,Salivary gland secretion,Saliva,saliva
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Effects of elimination diet on saliva sample.

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Richness Number of species
unchanged

Signature 1

EditHistoryDelete
Mark reviewed
Your review change was submitted
Needs review

Curated date: 2025/03/04

Curator: Taofeecoh

Revision editor(s): Taofeecoh

Source: Results' Text 3.1.1

Description: Relative abundance of bacterial in saliva samples after elimination diet; baseline vs pre-intervention.

Abundance in Group 1: increased abundance in Pre-intervention

NCBI Quality ControlLinks
Pseudomonadota   

Revision editor(s): Taofeecoh

Signature 2

EditHistoryDelete
Mark reviewed
Your review change was submitted
Needs review

Curated date: 2025/03/04

Curator: Taofeecoh

Revision editor(s): Taofeecoh

Source: Results' Text 3.1.1

Description: Relative abundance of bacterial in saliva samples after elimination diet; baseline vs pre-intervention.

Abundance in Group 1: decreased abundance in Pre-intervention

NCBI Quality ControlLinks
Bacillota   

Revision editor(s): Taofeecoh

Experiment 17


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Needs review

Curated date: 2025/03/04

Curator: Taofeecoh

Revision editor(s): Taofeecoh

Differences from previous experiment shown

Subjects

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,feces
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Effects of elimination diet on fecal sample.

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Richness Number of species
unchanged

Signature 1

EditHistoryDelete
Mark reviewed
Your review change was submitted
Needs review

Curated date: 2025/03/04

Curator: Taofeecoh

Revision editor(s): Taofeecoh

Source: Results' Text 3.1.2

Description: Relative abundance of bacterial in fecal samples after elimination diet; baseline vs pre-intervention.

Abundance in Group 1: increased abundance in

NCBI Quality ControlLinks
Bacillota   

Revision editor(s): Taofeecoh

Experiment 18


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Curated date: 2025/03/04

Curator: Taofeecoh

Revision editor(s): Taofeecoh

Differences from previous experiment shown

Subjects

Lab analysis

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
centered log-ratio
Statistical test
ANCOM-BC
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
Richness Number of species
unchanged

Signature 1

EditHistoryDelete
Mark reviewed
Your review change was submitted
Needs review

Curated date: 2025/03/04

Curator: Taofeecoh

Revision editor(s): Taofeecoh

Source: Results' Text 3.1.2

Description: Relative abundance of bacterial in fecal samples after elimination diet; baseline vs pre-intervention.

Abundance in Group 1: increased abundance in Pre-intervention

NCBI Quality ControlLinks
Faecalibacterium prausnitzii   
Blautia obeum   
Blautia producta   
Dorea longicatena   
Roseburia sp.   
Coprococcus sp.   
Bacteroides uniformis   

Revision editor(s): Taofeecoh

Signature 2

EditHistoryDelete
Mark reviewed
Your review change was submitted
Needs review

Curated date: 2025/03/04

Curator: Taofeecoh

Revision editor(s): Taofeecoh

Source: Results' Text 3.1.2

Description: Relative abundance of bacterial in fecal samples after elimination diet; baseline vs pre-intervention.

Abundance in Group 1: decreased abundance in Pre-intervention

NCBI Quality ControlLinks
Enterobacteriaceae spp.Enterobacteriaceae spp.
Bacteroides fragilis   
Bacteroides caccae   
Corynebacterium aurimucosum   

Revision editor(s): Taofeecoh

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