Effects of Commercial Apple Varieties on Human Gut Microbiota Composition and Metabolic Output Using an In Vitro Colonic Model

Study information

Needs review

study design

laboratory experiment

Citation

PMID PubMed identifier for scientific articles.

28538678

DOI Digital object identifier for electronic documents.

10.3390/nu9060533

URI Uniform resource identifier for web resources.

Authors

Koutsos A, Lima M, Conterno L, Gasperotti M, Bianchi M, Fava F, Vrhovsek U, Lovegrove JA, Tuohy KM

Journal

Nutrients

Year

2017

Apples are a rich source of polyphenols and fiber. A major proportion of apple polyphenols escape absorption in the small intestine and together with non-digestible polysaccharides reach the colon, where they can serve as substrates for bacterial fermentation. Animal studies suggest a synergistic interaction between apple polyphenols and the soluble fiber pectin; however, the effects of whole apples on human gut microbiota are less extensively studied. Three commercial apple varieties-Renetta Canada, Golden Delicious and Pink Lady-were digested and fermented in vitro using a batch culture colonic model (pH 5.5-6.0, 37 °C) inoculated with feces from three healthy donors. Inulin and cellulose were used as a readily and a poorly fermentable plant fiber, respectively. Fecal microbiota composition was measured by 16S rRNA gene Illumina MiSeq sequencing (V3-V4 region) and Fluorescence in Situ Hybridization. Short chain fatty acids (SCFAs) and polyphenol microbial metabolites were determined. The three apple varieties significantly changed bacterial diversity, increased Actinobacteria relative abundance, acetate, propionate and total SCFAs (p < 0.05). Renetta Canada and Golden Delicious significantly decreased Bacteroidetes abundance and increased Proteobacteria proportion and bifidobacteria population (p < 0.05). Renetta Canada also increased Faecalibacterium prausnitzii, butyrate levels and polyphenol microbial metabolites (p < 0.05). Together, these data suggest that apples, particularly Renetta Canada, can induce substantial changes in microbiota composition and metabolic activity in vitro, which could be associated with potential benefits to human health. Human intervention studies are necessary to confirm these data and potential beneficial effects.

Experiment 1

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Curated date: 2021/01/10

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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

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Curated date: 2021/01/10

Curator: Lora Kasselman

Revision editor(s): WikiWorks

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	Links
Eubacteriales

Revision editor(s): WikiWorks

Experiment 2

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Mark reviewed

Your review change was submittedDuplicate this Experiment Add a new Signature

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Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks

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: golden delicious 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

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

Edit History Delete

Mark reviewed

Your review change was submitted

Needs review

Curated date: 2021/01/10

Curator: Lora Kasselman

Revision editor(s): WikiWorks

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	Links
Eubacteriales

Revision editor(s): WikiWorks

Experiment 3

Edit History Delete

Mark reviewed

Your review change was submittedDuplicate this Experiment Add a new Signature

Needs review

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks

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: pink lady 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

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

Edit History Delete

Mark reviewed

Your review change was submitted

Needs review

Curated date: 2021/01/10

Curator: Lora Kasselman

Revision editor(s): WikiWorks

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	Links
Eubacteriales

Revision editor(s): WikiWorks