Association of dietary fibre intake and gut microbiota in adults
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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
Lin D, Peters BA, Friedlander C, Freiman HJ, Goedert JJ, Sinha R, Miller G, Bernstein MA, Hayes RB, Ahn J
Journal
The British journal of nutrition
Year
2018
Increasing evidence indicates that gut microbiota may influence colorectal cancer risk. Diet, particularly fibre intake, may modify gut microbiota composition, which may affect cancer risk. We investigated the relationship between dietary fibre intake and gut microbiota in adults. Using 16S rRNA gene sequencing, we assessed gut microbiota in faecal samples from 151 adults in two independent study populations: National Cancer Institute (NCI), n 75, and New York University (NYU), n 76. We calculated energy-adjusted fibre intake based on FFQ. For each study population with adjustment for age, sex, race, BMI and smoking, we evaluated the relationship between fibre intake and gut microbiota community composition and taxon abundance. Total fibre intake was significantly associated with overall microbial community composition in NYU (P=0·008) but not in NCI (P=0·81). In a meta-analysis of both study populations, higher fibre intake tended to be associated with genera of class Clostridia, including higher abundance of SMB53 (fold change (FC)=1·04, P=0·04), Lachnospira (FC=1·03, P=0·05) and Faecalibacterium (FC=1·03, P=0·06), and lower abundance of Actinomyces (FC=0·95, P=0·002), Odoribacter (FC=0·95, P=0·03) and Oscillospira (FC=0·96, P=0·06). A species-level meta-analysis showed that higher fibre intake was marginally associated with greater abundance of Faecalibacterium prausnitzii (FC=1·03, P=0·07) and lower abundance of Eubacterium dolichum (FC=0·96, P=0·04) and Bacteroides uniformis (FC=0·97, P=0·05). Thus, dietary fibre intake may impact gut microbiota composition, particularly class Clostridia, and may favour putatively beneficial bacteria such as F. prausnitzii. These findings warrant further understanding of diet-microbiota relationships for future development of colorectal cancer prevention strategies.
Experiment 1
Subjects
- Location of subjects
- United States of America
- 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
- high fiber (Q3 and Q4)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- low fiber (Q1 and Q2)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- lower quartiles (Q1 and Q2) of fiber intake vs control (Q3 and Q4)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 76
- Group 1 sample size Number of subjects in the case (exposed) group
- 75
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- no "long term" antibiotics use
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
- Roche454, Illumina
Statistical Analysis
- Statistical test
- DESeq2
- 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
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, sex, body height, body weight, race, smoking behavior, body mass index
Signature 1
Needs review
Source: Figure 2.
Description: Figure 2 Forest plot of fold change of select genera (G) and species (S) in both the New York University and National Cancer Institute study populations with a significant or marginally significant association with higher total fibre intake and Table 2
Abundance in Group 1: increased abundance in low fiber (Q1 and Q2)
| NCBI | Links |
|---|---|
| Actinomyces | |
| Bacteroides uniformis | |
| Odoribacter | |
| Amedibacillus dolichus |
Signature 2
Needs review
Source: Figure 2.
Description: Figure 2 Forest plot of fold change of select genera (G) and species (S) in both the New York University and National Cancer Institute study populations with a significant or marginally significant association with higher total fibre intake and Table 2
Abundance in Group 1: decreased abundance in low fiber (Q1 and Q2)
| NCBI | Links |
|---|---|
| Actinomyces | |
| Odoribacter | |
| Oscillospira |
Experiment 2
Subjects
- Location of subjects
- United States of America
- 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
- high fiber from FRUITS/VEGETABLES (Q3 and Q4)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- low fiber from FRUITS/VEGETABLES (Q1 and Q2)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- lower quartiles (Q1 and Q2) of FRUIT/VEGETABLE fiber intake vs control (Q3 and Q4)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 76
- Group 1 sample size Number of subjects in the case (exposed) group
- 75
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- no "long term" antibiotics use
Lab analysis
- Sequencing type
- 16S
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Roche454, Illumina
Statistical Analysis
- Statistical test
- DESeq2
- 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
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, sex, body height, body weight, race, smoking behavior, body mass index
Signature 1
Needs review
Source: Figure 3.
Description: Fig. 3. Heat map representing colour-coded fold changes of select genera (G) and species (S), by total fibre and fibre from specific sources (fruits/vegetables, grains, and beans). * P <0·05 and ** P <0·001 in the meta-analysis of the National Cancer Institute and New York University study populations.
Abundance in Group 1: increased abundance in low fiber from FRUITS/VEGETABLES (Q1 and Q2)
| NCBI | Links |
|---|---|
| Actinomyces | |
| Odoribacter | |
| Bacteroides uniformis |
Revision editor(s): WikiWorks
Experiment 3
Subjects
- Location of subjects
- United States of America
- 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
- high fiber from BEANS (Q3 and Q4)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- low fiber from BEANS (Q1 and Q2)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- lower quartiles (Q1 and Q2) of BEAN fiber intake vs control (Q3 and Q4)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 76
- Group 1 sample size Number of subjects in the case (exposed) group
- 75
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- no "long term" antibiotics use
Lab analysis
- Sequencing type
- 16S
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Roche454, Illumina
Statistical Analysis
- Statistical test
- DESeq2
- 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
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, sex, body height, body weight, race, smoking behavior, body mass index
Signature 1
Needs review
Source: Figure 3.
Description: Fig. 3. Heat map representing colour-coded fold changes of select genera (G) and species (S), by total fibre and fibre from specific sources (fruits/vegetables, grains, and beans). * P <0·05 and ** P <0·001 in the meta-analysis of the National Cancer Institute and New York University study populations.
Abundance in Group 1: increased abundance in low fiber from BEANS (Q1 and Q2)
| NCBI | Links |
|---|---|
| Odoribacter | |
| Amedibacillus dolichus |
Signature 2
Needs review
Source: Figure 3.
Description: Fig. 3. Heat map representing colour-coded fold changes of select genera (G) and species (S), by total fibre and fibre from specific sources (fruits/vegetables, grains, and beans). * P <0·05 and ** P <0·001 in the meta-analysis of the National Cancer Institute and New York University study populations.
Abundance in Group 1: decreased abundance in low fiber from BEANS (Q1 and Q2)
| NCBI | Links |
|---|---|
| Faecalibacterium | |
| Faecalibacterium prausnitzii |
Revision editor(s): WikiWorks
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