Structural changes in gut microbiome after Ramadan fasting: a pilot study

Study information

Reviewed Marked as Reviewed by Chloe on 2023-3-20

study design

time series / longitudinal observational

Citation

PMID PubMed identifier for scientific articles.

32073296

DOI Digital object identifier for electronic documents.

https://doi.org/10.3920/BM2019.0039

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

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Reviewed Marked as Reviewed by Chloe on 2023-3-20

Curated date: 2023/03/12

Curator: Barakat Dindi

Revision editor(s): Barakat Dindi, Chloe, WikiWorks

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

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Curated date: 2023/03/13

Curator: Barakat Dindi

Revision editor(s): Barakat Dindi, Chloe, WikiWorks

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, WikiWorks

Signature 2

Edit History Delete

Mark reviewed

Your review change was submitted

Needs review

Curated date: 2023/03/13

Curator: Barakat Dindi

Revision editor(s): Barakat Dindi, Chloe, WikiWorks

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

NCBI	Quality Control	Links
Bacillota
Elusimicrobia
Elusimicrobiaceae
Elusimicrobiales
Enterobacteriaceae
Enterococcus
Erysipelotrichia
Escherichia
Eubacteriales
Lactobacillales
Mollicutes
Pseudomonadota

Revision editor(s): Barakat Dindi, Chloe, WikiWorks