High-level adherence to a Mediterranean diet beneficially impacts the gut microbiota and associated metabolome
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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
Authors
De Filippis F, Pellegrini N, Vannini L, Jeffery IB, La Storia A, Laghi L, Serrazanetti DI, Di Cagno R, Ferrocino I, Lazzi C, Turroni S, Cocolin L, Brigidi P, Neviani E, Gobbetti M, O'Toole PW, Ercolini D
Journal
Gut
Year
2016
Keywords:
DIET, DIETARY FIBRE, ENTERIC BACTERIAL MICROFLORA, INTESTINAL BACTERIA, SHORT CHAIN FATTY ACIDS
OBJECTIVES: Habitual diet plays a major role in shaping the composition of the gut microbiota, and also determines the repertoire of microbial metabolites that can influence the host. The typical Western diet corresponds to that of an omnivore; however, the Mediterranean diet (MD), common in the Western Mediterranean culture, is to date a nutritionally recommended dietary pattern that includes high-level consumption of cereals, fruit, vegetables and legumes. To investigate the potential benefits of the MD in this cross-sectional survey, we assessed the gut microbiota and metabolome in a cohort of Italian individuals in relation to their habitual diets. DESIGN AND RESULTS: We retrieved daily dietary information and assessed gut microbiota and metabolome in 153 individuals habitually following omnivore, vegetarian or vegan diets. The majority of vegan and vegetarian subjects and 30% of omnivore subjects had a high adherence to the MD. We were able to stratify individuals according to both diet type and adherence to the MD on the basis of their dietary patterns and associated microbiota. We detected significant associations between consumption of vegetable-based diets and increased levels of faecal short-chain fatty acids, Prevotella and some fibre-degrading Firmicutes, whose role in human gut warrants further research. Conversely, we detected higher urinary trimethylamine oxide levels in individuals with lower adherence to the MD. CONCLUSIONS: High-level consumption of plant foodstuffs consistent with an MD is associated with beneficial microbiome-related metabolomic profiles in subjects ostensibly consuming a Western diet. TRIAL REGISTRATION NUMBER: This study was registered at clinical trials.gov as NCT02118857.
Experiment 1
Needs review
Curated date: 2021/02/11
Curator: Lorakasselman
Revision editor(s): Lorakasselman, Claregrieve1, WikiWorks, Peace Sandy
Subjects
- Location of subjects
- Italy
- 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
- 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
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Diet Dietary,Diets,Diet,diet
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- vegetarians
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- omnivores
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- individuals who eat animal products in addition to other foods (plants, grains, etc)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 51
- Group 1 sample size Number of subjects in the case (exposed) group
- 51
- 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
- V1-V3
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Roche454
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- raw counts
- 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
Alpha Diversity
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/1
Source: Table S2
Description: Differential microbial abundance between omnivores and vegetarians
Abundance in Group 1: decreased abundance in omnivores
| NCBI | Quality Control | Links |
|---|---|---|
| Lachnospira |
Revision editor(s): Lorakasselman, Claregrieve1
Signature 2
Needs review
Source: Table S2
Description: Differential microbial abundance between omnivores and vegetarians
Abundance in Group 1: increased abundance in omnivores
| NCBI | Quality Control | Links |
|---|---|---|
| Ruminococcus | ||
| Veillonellaceae |
Revision editor(s): Claregrieve1
Experiment 2
Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/1
Curated date: 2021/02/11
Curator: Lorakasselman
Revision editor(s): Lorakasselman, Claregrieve1, WikiWorks
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- vegans
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- Not specified
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/1
Source: Table S2
Description: Differential microbial abundance between omnivores and vegans
Abundance in Group 1: decreased abundance in omnivores
| NCBI | Quality Control | Links |
|---|---|---|
| Roseburia | ||
| Lachnospira | ||
| Prevotella |
Revision editor(s): Lorakasselman, Claregrieve1
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/1
Source: Table S2
Description: Differential microbial abundance between omnivores and vegans
Abundance in Group 1: increased abundance in omnivores
| NCBI | Quality Control | Links |
|---|---|---|
| Ruminococcus | ||
| Oscillospira |
Revision editor(s): Claregrieve1
Experiment 3
Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/1
Curated date: 2021/02/11
Curator: Lorakasselman
Revision editor(s): Fatima, Lorakasselman, Claregrieve1, WikiWorks
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- vegetarians
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- individuals who do not eat meat but do eat other animal products
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/1
Source: Table S2
Description: Differential microbial abundance between vegetarians and vegans
Abundance in Group 1: increased abundance in vegetarians
| NCBI | Quality Control | Links |
|---|---|---|
| Oscillospira |
Revision editor(s): Claregrieve1
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