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

From BugSigDB
Needs review
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Koutsos A, Lima M, Conterno L, Gasperotti M, Bianchi M, Fava F, Vrhovsek U, Lovegrove JA, Tuohy KM
Journal
Nutrients
Year
2017
Keywords:
Fluorescence in situ hybridization (FISH), Illumina 16S rRNA gene sequencing, apples, fiber, gut microbiota, in vitro batch culture fermentation, microbial metabolites, pectin, polyphenols, proanthocyanidins
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


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
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

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 Quality ControlLinks
Eubacteriales

Revision editor(s): WikiWorks

Experiment 2


Needs review

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
golden delicious apple - at 10 hr

Lab analysis

Statistical Analysis

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

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 Quality ControlLinks
Eubacteriales

Revision editor(s): WikiWorks

Experiment 3


Needs review

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
pink lady apple - at 10 hr

Lab analysis

Statistical Analysis

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

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 Quality ControlLinks
Eubacteriales

Revision editor(s): WikiWorks