Stool microRNA profiles reflect different dietary and gut microbiome patterns in healthy individuals
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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
Tarallo S, Ferrero G, De Filippis F, Francavilla A, Pasolli E, Panero V, Cordero F, Segata N, Grioni S, Pensa RG, Pardini B, Ercolini D, Naccarati A
Journal
Gut
Year
2022
Keywords:
colonic microflora, diet, molecular genetics
OBJECTIVES: MicroRNA (miRNA) profiles have been evaluated in several biospecimens in relation to common diseases for which diet may have a considerable impact. We aimed at characterising how specific diets are associated with the miRNome in stool of vegans, vegetarians and omnivores and how this is reflected in the gut microbial composition, as this is still poorly explored. DESIGN: We performed small RNA and shotgun metagenomic sequencing in faecal samples and dietary recording from 120 healthy volunteers, equally distributed for the different diets and matched for sex and age. RESULTS: We found 49 miRNAs differentially expressed among vegans, vegetarians and omnivores (adj. p <0.05) and confirmed trends of expression levels of such miRNAs in vegans and vegetarians compared with an independent cohort of 45 omnivores. Two miRNAs related to lipid metabolism, miR-636 and miR-4739, were inversely correlated to the non-omnivorous diet duration, independently of subject age. Seventeen miRNAs correlated (
Experiment 1
Reviewed Marked as Reviewed by KateRasheed on 2025-7-2
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 measurement Diet measurement,diet measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Omnivores (O)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Vegans(VN)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Healthy individuals following a vegan diet (excludes all animal-derived foods) for at least 1 year
- Group 0 sample size Number of subjects in the control (unexposed) group
- 40
- Group 1 sample size Number of subjects in the case (exposed) group
- 40
- 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-V5
- 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).
- 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
- Matched on Factors on which subjects have been matched on in a case-control study
- age, sex
Signature 1
Reviewed Marked as Reviewed by KateRasheed on 2025-7-2
Source: Figure 3A
Description: Differentially abundant bacterial taxa in Vegans(VN) compared to Omnivores(O)
Abundance in Group 1: increased abundance in Vegans(VN)
| NCBI | Quality Control | Links |
|---|---|---|
| Roseburia sp. CAG:182 | ||
| Segatella copri |
Revision editor(s): Ese
Signature 2
Reviewed Marked as Reviewed by KateRasheed on 2025-7-2
Source: Figure 3A
Description: Differentially abundant bacterial taxa in Vegans(VN) compared to Omnivores(O)
Abundance in Group 1: decreased abundance in Vegans(VN)
| NCBI | Quality Control | Links |
|---|---|---|
| Phocaeicola dorei |
Revision editor(s): Ese
Experiment 2
Reviewed Marked as Reviewed by KateRasheed on 2025-7-2
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Omnivores(O)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Vegetarians(VT)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Healthy individuals following a vegetarian diet (excludes all meat and fish, but may include dairy and eggs) for at least 1 year
Lab analysis
Statistical Analysis
Signature 1
Reviewed Marked as Reviewed by KateRasheed on 2025-7-2
Source: Figure 3A
Description: Differentially abundant bacterial taxa in Vegetarians(VT) compared to Omnivores(O)
Abundance in Group 1: increased abundance in Vegetarians(VT)
| NCBI | Quality Control | Links |
|---|---|---|
| Segatella copri |
Revision editor(s): Ese
Experiment 3
Reviewed Marked as Reviewed by KateRasheed on 2025-7-2
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Gene expression protocol Gene expression protocol,gene expression protocol
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low miR-425-3p
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High miR-425-3p
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Healthy individuals with high stool expression levels of microRNA-425-3p
- Group 0 sample size Number of subjects in the control (unexposed) group
- Not specified
- Group 1 sample size Number of subjects in the case (exposed) group
- Not specified
Lab analysis
Statistical Analysis
Signature 1
Reviewed Marked as Reviewed by KateRasheed on 2025-7-2
Source: Figure 3F, Figure S4, Result Text
Description: Taxonomy of bacterial taxa among individuals with high stool expression levels of microRNA-425-3p
Abundance in Group 1: increased abundance in High miR-425-3p
| NCBI | Quality Control | Links |
|---|---|---|
| Akkermansia muciniphila | ||
| Oscillibacter sp. 57_20 | ||
| Oscillibacter sp. CAG:241 | ||
| Roseburia hominis | ||
| Ruminococcaceae bacterium D5 | ||
| Roseburia sp. CAG:182 |
Revision editor(s): Ese
Signature 2
Reviewed Marked as Reviewed by KateRasheed on 2025-7-2
Source: Figure 3F, Figure S4, Result Text
Description: Taxonomy of bacterial taxa among individuals with high stool expression levels of microRNA-425-3p
Abundance in Group 1: decreased abundance in High miR-425-3p
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerotruncus colihominis | ||
| Flavonifractor plautii |
Revision editor(s): Ese
Experiment 4
Reviewed Marked as Reviewed by KateRasheed on 2025-7-2
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low miR-638
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High miR-638
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Healthy individuals with high stool expression levels of microRNA-638
Lab analysis
Statistical Analysis
Signature 1
Reviewed Marked as Reviewed by KateRasheed on 2025-7-2
Source: Figure 3F, Figure S4, Result Text
Description: Taxonomy of bacterial taxa among individuals with high stool expression levels of microRNA-638
Abundance in Group 1: increased abundance in High miR-638
| NCBI | Quality Control | Links |
|---|---|---|
| Roseburia sp. CAG:182 | ||
| Ruminococcaceae bacterium D5 | ||
| Firmicutes bacterium CAG:95 |
Revision editor(s): Ese
Signature 2
Reviewed Marked as Reviewed by KateRasheed on 2025-7-2
Source: Figure 3F, Figure S4, Result Text
Description: Taxonomy of bacterial taxa among individuals with high stool expression levels of microRNA-638
Abundance in Group 1: decreased abundance in High miR-638
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerotruncus colihominis | ||
| Firmicutes bacterium CAG:83 | ||
| Flavonifractor plautii |
Revision editor(s): Ese
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