Repopulation of the gut microbiota after a screening colonoscopy

Study information

Needs review

study design

prospective cohort

Citation

PMID PubMed identifier for scientific articles.

40938872

DOI Digital object identifier for electronic documents.

https://doi.org/10.1371/journal.pone.0320712

URI Uniform resource identifier for web resources.

Authors

Ghouri Y.A., Ericsson A.C., Anderson J.M., George J.G., Parks E.J., Anguah K.O.B.

Journal

PloS one

Year

2025

OBJECTIVE: Role of microbiome has been highly studied for its association with various medical conditions. After a colonoscopy, repopulation of colonic microbial load is known to occur, however the quality and timing of natural repopulation has not been investigated after a bowel preparation. Further, no study has documented detailed free-living dietary intakes concurrently with gut microbiome repopulation post-colonoscopy. Here we sought to determine the early pattern of repopulation relative to dietary intake. METHODS: Healthy adults (n = 15 [4 female/11 male], BMI = 27.2 ± 3.9 kg/m2, age 51.4 ± 7.2 y) who were scheduled to undergo a screening colonoscopy were recruited from the Gastroenterology Clinic at the University of Missouri. Within two weeks before the colonoscopy (baseline), subjects completed detailed food records for 3 days. Post-colonoscopy, subjects ate their free-living diets and detailed food records were collected on Days 0, 1, 2, 4, 7, 10, and 13. Fecal samples were obtained pre-colonoscopy and on post-colonoscopy Days 3, 5, 8, 11, and 14. Gut microbiome composition was assessed by 16S rRNA amplicon sequencing. RESULTS: Within 5 days after the procedure, subjects reported consuming more total daily energy relative to baseline, presumably to make up for the low energy intake that occurred during the bowel-prep. At baseline, fiber intake (21.0 ± 9.1 g/d) was higher than on the day of the colonoscopy, Day 0 (16.1 ± 11.2, P = 0.0159). Thereafter, daily fiber intake was the same as baseline. Marked intersubject microbiome beta diversity was observed by principal coordinate analysis using weighted and unweighted dissimilarities (P = 0.0001, F = 15.23, one-way PERMANOVA). Select taxa were depleted acutely post-colonoscopy (e.g., within the phylum Bacillota). Specifically, significant effects of time were observed between baseline and Day 3 fecal samples (pairwise P = 0.0013, F = 2.9). These changes tended to return to baseline by Day 5 and with subsequent samples, taxa remained similar to baseline when tested using a weighted dissimilarity analysis (Bray-Curtis). CONCLUSIONS: These results quantitatively demonstrate the magnitude of the significant changes in microbial relative abundance and diversity immediately post-colonoscopy. The timing of repopulation aligned with changes in fiber intake after the procedure. These data highlight the importance of nutrition after a screening colonoscopy in reestablishing a healthy microbiome.

Experiment 1

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Curated date: 2025/10/08

Curator: Jesulolufemi

Revision editor(s): Jesulolufemi

Subjects

Location of subjects: United States of America

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: Colorectal health Colorectal health,colorectal health

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Day 0 (Pre-colonoscopy)

Group 1 name Corresponds to the case (exposed) group for case-control studies: Day 3 (Post-colonoscopy)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Day 3 post-colonoscopy refers to the third day of follow-up after a colorectal cancer screening colonoscopy

Group 0 sample size Number of subjects in the control (unexposed) group: 15

Group 1 sample size Number of subjects in the case (exposed) group: 15

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): 30 days

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