Blue poo: impact of gut transit time on the gut microbiome using a novel marker
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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
Asnicar F, Leeming ER, Dimidi E, Mazidi M, Franks PW, Al Khatib H, Valdes AM, Davies R, Bakker E, Francis L, Chan A, Gibson R, Hadjigeorgiou G, Wolf J, Spector TD, Segata N, Berry SE
Journal
Gut
Year
2021
Keywords:
gastrointestinal transit, intestinal bacteria
BACKGROUND AND AIMS: Gut transit time is a key modulator of host-microbiome interactions, yet this is often overlooked, partly because reliable methods are typically expensive or burdensome. The aim of this single-arm, single-blinded intervention study is to assess (1) the relationship between gut transit time and the human gut microbiome, and (2) the utility of the 'blue dye' method as an inexpensive and scalable technique to measure transit time. METHODS: We assessed interactions between the taxonomic and functional potential profiles of the gut microbiome (profiled via shotgun metagenomic sequencing), gut transit time (measured via the blue dye method), cardiometabolic health and diet in 863 healthy individuals from the PREDICT 1 study. RESULTS: We found that gut microbiome taxonomic composition can accurately discriminate between gut transit time classes (0.82 area under the receiver operating characteristic curve) and longer gut transit time is linked with specific microbial species such as Akkermansia muciniphila, Bacteroides spp and Alistipes spp (false discovery rate-adjusted p values <0.01). The blue dye measure of gut transit time had the strongest association with the gut microbiome over typical transit time proxies such as stool consistency and frequency. CONCLUSIONS: Gut transit time, measured via the blue dye method, is a more informative marker of gut microbiome function than traditional measures of stool consistency and frequency. The blue dye method can be applied in large-scale epidemiological studies to advance diet-microbiome-health research. Clinical trial registry website https://clinicaltrials.gov/ct2/show/NCT03479866 and trial number NCT03479866.
Experiment 1
Reviewed Marked as Reviewed by Svetlana up on 2025-3-27
Subjects
- Location of subjects
- United Kingdom
- 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
- Increased intestinal transit time Increased intestinal transit time,increased intestinal transit time
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- C1-Fast Gut Transit Time
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- C4-Slow Gut Transit Time
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group consists of participants with the slowest gut transit time, associated with lower microbial diversity and distinct taxonomic composition.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 79
- Group 1 sample size Number of subjects in the case (exposed) group
- 174
- 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
- WMS
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
- 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
- Mann-Whitney (Wilcoxon)
- 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)?
- Yes
Alpha Diversity
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
- Richness Number of species
- increased
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2025-3-27
Source: Fig. 3B
Description: Relative abundances for the four gut transit time classes in PREDICT 1
Abundance in Group 1: increased abundance in C4-Slow Gut Transit Time
| NCBI | Quality Control | Links |
|---|---|---|
| Akkermansia muciniphila | ||
| Alistipes finegoldii | ||
| Alistipes putredinis | ||
| Bacteroides caccae | ||
| Bacteroides uniformis | ||
| Barnesiella intestinihominis | ||
| Parabacteroides distasonis |
Revision editor(s): Joiejoie
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2025-3-27
Source: Fig. 3B
Description: Relative abundances for the four gut transit time classes in PREDICT 1
Abundance in Group 1: decreased abundance in C4-Slow Gut Transit Time
| NCBI | Quality Control | Links |
|---|---|---|
| Agathobacter rectalis |
Revision editor(s): Joiejoie
Experiment 2
Reviewed Marked as Reviewed by Svetlana up on 2025-3-27
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- C2-Normal-Fast Gut Transit Time
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group represents individuals with a gut transit time of 14–38 hours, distinguishing them as the faster segment within the normal range.
- Group 1 sample size Number of subjects in the case (exposed) group
- 424
Lab analysis
Statistical Analysis
Alpha Diversity
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
- Richness Number of species
- increased
Signature 1
Source: Fig. 3B
Description: Relative abundances for the four gut transit time classes in PREDICT 1
Abundance in Group 1: increased abundance in C2-Normal-Fast Gut Transit Time
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides uniformis |
Revision editor(s): Joiejoie
Experiment 3
Reviewed Marked as Reviewed by Svetlana up on 2025-3-27
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- C2-Normal-Fast Gut Transit Time
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- C4-Slow Gut Transit Time
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group consists of participants with the slowest gut transit time, associated with lower microbial diversity and distinct taxonomic composition.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 424
- Group 1 sample size Number of subjects in the case (exposed) group
- 174
Lab analysis
Statistical Analysis
Alpha Diversity
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
- Richness Number of species
- increased
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2025-3-27
Source: Fig. 3B
Description: The relative abundances of specific gut microbiome species across four gut transit time classes, highlighting species with significant differences and average relative abundances exceeding 1% in the PREDICT 1 study.
Abundance in Group 1: increased abundance in C4-Slow Gut Transit Time
| NCBI | Quality Control | Links |
|---|---|---|
| Akkermansia muciniphila | ||
| Alistipes finegoldii | ||
| Alistipes putredinis | ||
| Bacteroides caccae | ||
| Barnesiella intestinihominis |
Revision editor(s): Joiejoie
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2025-3-27
Source: Fig. 3B
Description: The relative abundances of specific gut microbiome species across four gut transit time classes, highlighting species with significant differences and average relative abundances exceeding 1% in the PREDICT 1 study.
Abundance in Group 1: decreased abundance in C4-Slow Gut Transit Time
| NCBI | Quality Control | Links |
|---|---|---|
| Agathobacter rectalis |
Revision editor(s): Joiejoie
Experiment 4
Reviewed Marked as Reviewed by Svetlana up on 2025-3-27
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- C3 - Normal Gut Transit Time
- Group 0 sample size Number of subjects in the control (unexposed) group
- 186
Lab analysis
Statistical Analysis
Alpha Diversity
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
- Richness Number of species
- increased
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2025-3-27
Source: Fig. 3B
Description: Relative abundances for the four gut transit time classes in PREDICT 1
Abundance in Group 1: increased abundance in C4-Slow Gut Transit Time
| NCBI | Quality Control | Links |
|---|---|---|
| Akkermansia muciniphila | ||
| Alistipes finegoldii | ||
| Alistipes putredinis | ||
| Barnesiella intestinihominis | ||
| Parabacteroides distasonis |
Revision editor(s): Joiejoie
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2025-3-27
Source: Fig. 3B
Description: Relative abundances for the four gut transit time classes in PREDICT 1
Abundance in Group 1: decreased abundance in C4-Slow Gut Transit Time
| NCBI | Quality Control | Links |
|---|---|---|
| Agathobacter rectalis |
Revision editor(s): Joiejoie
Experiment 5
Reviewed Marked as Reviewed by Svetlana up on 2025-3-27
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- C1-Fast Gut Transit Time
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- C3 - Normal Gut Transit Time
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group represents individuals with a gut transit time of 38–58 hours, distinguishing them as the slower segment within the normal range.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 79
- Group 1 sample size Number of subjects in the case (exposed) group
- 186
Lab analysis
Statistical Analysis
Alpha Diversity
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
- Richness Number of species
- increased
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2025-3-27
Source: Fig. 3B
Description: Relative abundances for the four gut transit time classes in PREDICT 1
Abundance in Group 1: increased abundance in C3 - Normal Gut Transit Time
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides uniformis |
Revision editor(s): Joiejoie
Experiment 6
Reviewed Marked as Reviewed by Svetlana up on 2025-3-27
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- C2-Normal-Fast Gut Transit Time
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- C3-Normal Gut Transit Time
- Group 0 sample size Number of subjects in the control (unexposed) group
- 424
Lab analysis
Statistical Analysis
Alpha Diversity
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
- Richness Number of species
- increased
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2025-3-27
Source: Fig. 3B
Description: Relative abundances for the four gut transit time classes in PREDICT 1
Abundance in Group 1: increased abundance in C3-Normal Gut Transit Time
| NCBI | Quality Control | Links |
|---|---|---|
| Akkermansia muciniphila |
Revision editor(s): Joiejoie
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