Structural changes in gut microbiome after Ramadan fasting: a pilot study
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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
Ozkul C, Yalinay M, Karakan T
Journal
Beneficial microbes
Year
2020
Keywords:
Ramadan fasting, gut microbiota, intermittent fasting, microbiome
It has been largely accepted that dietary changes have an effect on gut microbial composition. In this pilot study we hypothesised that Ramadan fasting, which can be considered as a type of time-restricted feeding may lead to changes in gut microbial composition and diversity. A total of 9 adult subjects were included in the study. Stool samples were collected before (baseline) and at the end of the Ramadan fasting (after 29 days). Following the construction of an 16S rRNA amplicon library, the V4 region was sequenced using the Illumina Miseq platform. Microbial community analysis was performed using the QIIME program. A total of 27,521 operational taxonomic units (OTUs) with a 97% similarity were determined in all of the samples. Microbial richness was significantly increased after Ramadan according to observed OTU results (P=0.016). No significant difference was found in terms of Shannon index or phylogenetic diversity metrics of alpha diversity. Microbial community structure was significantly different between baseline and after Ramadan samples according to unweighted UniFrac analysis (P=0.025). LEfSe analysis revealed that Butyricicoccus, Bacteroides, Faecalibacterium, Roseburia, Allobaculum, Eubacterium, Dialister and Erysipelotrichi were significantly enriched genera after the end of Ramadan fasting. According to random forest analysis, the bacterial species most affected by the Ramadan fasting was Butyricicoccus pullicaecorum. Despite this is a pilot study with a limited sample size; our results clearly revealed that Ramadan fasting, which represents an intermittent fasting regime, leads to compositional changes in the gut microbiota.
Experiment 1
Reviewed Marked as Reviewed by Chloe on 2023-3-20
Subjects
- Location of subjects
- Turkey
- 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
- Fasting Fast,Fasting,fasting
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Adults before fasting
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Adults after fasting
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- healthy adults who were on Ramadan fast with a fasting period of approximately 17H per day for 29 days.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 9
- Group 1 sample size Number of subjects in the case (exposed) group
- 9
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 8 weeks
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- 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)
- 0.05
- 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
- unchanged
- Richness Number of species
- increased
Signature 1
Reviewed Marked as Reviewed by Atrayees on 2023-6-5
Source: Figure S2
Description: LeFSe analysis and Linear discriminant effect size showing the differential abundance of discriminative taxa at the two-time points I.e before and after fasting.
Abundance in Group 1: increased abundance in Adults after fasting
| NCBI | Quality Control | Links |
|---|---|---|
| Akkermansia | ||
| Allobaculum | ||
| Bacteroides | ||
| Butyricicoccus | ||
| Dialister | ||
| Erysipelotrichia | ||
| Eubacterium | ||
| Faecalibacterium | ||
| Megasphaera | ||
| Roseburia | ||
| Verrucomicrobiia | ||
| Erysipelotrichales |
Revision editor(s): Barakat Dindi, Chloe
Signature 2
Reviewed Marked as Reviewed by Atrayees on 2023-6-5
Source: Figure S2
Description: LeFSe analysis and Linear discriminant effect size showing the differential abundance of discriminative taxa at the two-time points I.e before and after fasting.
Abundance in Group 1: decreased abundance in Adults after fasting
Revision editor(s): Barakat Dindi, Chloe
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