Influence of dietary components on the gut microbiota of middle-aged adults: the gut-Mediterranean connection
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Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
Experiment 1
Subjects
- Location of subjects
- Canada
- 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
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- (Q1) low level of diet
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- (Q4) High level of diet
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- To delve deeper into the differential microbial composition driving the changes in diversity between Q1 and Q4, a Linear Discriminant Analysis Effect Size (LEfSe) analysis was conducted
- 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
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- LEfSe
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.25
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 3
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, Confounders controlled for: "bmi" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.bmi, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
Signature 1
Source: Figure 3A
Description: Result with higher adherence to MedD patterns indicating distinct microbial profiles between participants with the lowest (Q1) and highest (Q4) adherence to the diet (p < 0.01).
Abundance in Group 1: increased abundance in (Q4) High level of diet
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillales | ||
| Bacillales incertae sedis | ||
| Coriobacteriaceae | ||
| Coriobacteriales | ||
| Lactobacillales | ||
| Prevotellaceae | ||
| Sutterellaceae |
Revision editor(s): SheikhAlMamun
Signature 2
Source: Figure 3A
Description: Result with higher adherence to MedD patterns indicating distinct microbial profiles between participants with the lowest (Q1) and highest (Q4) adherence to the diet (p < 0.01).
Abundance in Group 1: decreased abundance in (Q4) High level of diet
| NCBI | Quality Control | Links |
|---|---|---|
| Gemella | ||
| Gemella sanguinis | ||
| Prevotella corporis | ||
| ActinobacteriaActinobacteria | ||
| Blautia obeum | ||
| Blautia hansenii |
Revision editor(s): SheikhAlMamun
Experiment 2
Subjects
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Differential microbial taxa and their association with diet between Q1 vs. Q4 study groups. A Cladogram diagram showing the microbial taxa with significant differences between the study groups. Microbial classification, from the level of phylum to species, is shown from the inside to the outside.
Lab analysis
Statistical Analysis
- Statistical test
- MaAsLin2
- 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
- increased
Signature 1
Source: Figure 3B
Description: This field would detail the nature of the signature, for example, which microbial taxa are increased, and under what conditions (e.g., higher adherence to the Mediterranean diet).
Abundance in Group 1: increased abundance in (Q4) High level of diet
| NCBI | Quality Control | Links |
|---|---|---|
| Coprobacter | ||
| Fusobacterium | ||
| Prevotella | ||
| Turicibacter |
Revision editor(s): SheikhAlMamun
Signature 2
Source: Figure 3B
Description: This field would detail the nature of the signature, for example, which microbial taxa are decreased and under what conditions (e.g., higher adherence to the Mediterranean diet).
Abundance in Group 1: decreased abundance in (Q4) High level of diet
| NCBI | Quality Control | Links |
|---|---|---|
| Holdemanella | ||
| Clostrdium X1VAClostrdium X1VA | ||
| Clostridium X1VBClostridium X1VB | ||
| AnaevoraxAnaevorax | ||
| ParabacteroidsParabacteroids |
Revision editor(s): SheikhAlMamun
Experiment 3
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Diet measurement Diet measurement,diet measurement
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Association between Mediterranean food components and gut microbiome. A Spearman correlation analysis between the modified Mediterranean diet score (mMDS) and its dietary components.
Lab analysis
Statistical Analysis
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.01
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Not specified
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- Not specified
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- Not specified
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
Signature 1
Source: Figure 2C & 2D
Description: Similarly, no notable differences were found in the relative abundance between the four quartiles at either the phylum or family level (p > 0.05)
Abundance in Group 1: increased abundance in (Q4) High level of diet
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidaceae | ||
| Coriobacteriaceae | ||
| Erysipelotrichaceae | ||
| Lachnospiraceae | ||
| Porphyromonadaceae | ||
| Rikenellaceae | ||
| Sutterellaceae | ||
| Veillonellaceae | ||
| Verrucomicrobiaceae |
Revision editor(s): SheikhAlMamun
Signature 2
Source: Figure 2C & 2D
Description: Similarly, no notable differences were found in the relative abundance between the four quartiles at either the phylum or family level (p > 0.05)
Abundance in Group 1: decreased abundance in (Q4) High level of diet
| NCBI | Quality Control | Links |
|---|---|---|
| BacteroidsBacteroids | ||
| FirmicutesFirmicutes | ||
| ProteobacteriaProteobacteria | ||
| ActinobacteriaActinobacteria | ||
| RuminococcaceaeRuminococcaceae | ||
| VerrucomicrobiaVerrucomicrobia |
Revision editor(s): SheikhAlMamun
Experiment 4
Subjects
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- centered log-ratio
Signature 1
Source: Figure 2E & 2F
Description: Linear regression of diet score and genera identified using Microbiome Multivariable Association with Linear Models (MaAsLin2) analysis
Abundance in Group 1: increased abundance in (Q4) High level of diet
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotella | ||
| Turicibacter |
Revision editor(s): SheikhAlMamun
Signature 2
Source: Figure 2E & 2F
Description: Linear regression of diet score and genera identified using Microbiome Multivariable Association with Linear Models (MaAsLin2) analysis
Abundance in Group 1: decreased abundance in (Q4) High level of diet
| NCBI | Quality Control | Links |
|---|---|---|
| Blautia | ||
| Coprococcus |
Revision editor(s): SheikhAlMamun
