Gut microbiota response to in vitro transit time variation is mediated by microbial growth rates, nutrient use efficiency and adaptation to in vivo transit time
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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
Minnebo Y, Delbaere K, Goethals V, Raes J, Van de Wiele T, De Paepe K
Journal
Microbiome
Year
2023
Keywords:
Gastrointestinal transit, Gut microbial ecology, Gut residence time, Gut retention time, Personalised gut microbiome research, Quantitative microbiome profiling, SHIME in vitro gut simulator
BACKGROUND: Transit time is an important modulator of the human gut microbiome. The inability to modify transit time as the sole variable hampers mechanistic in vivo microbiome research. We singled out gut transit time in an unprecedented in vitro approach by subjecting faecal microbial communities from six individuals with either short, medium or long in vivo transit times, to three different colonic transit times of 21, 32 and 63 h in the validated human gut in vitro model, SHIME. RESULTS: Transit time was identified as the single most important driver of microbial cell concentrations (52%), metabolic activity (45%) and quantitative (24%) and proportional (22%) community composition. Deceleration of transit was characterised by a significant decrease of specific Bifidobacterium and Veillonella spp. and increase of specific fibre degrading bacteria and nutrient specialists, such as Bacteroides, Prevotella, Ruminococcus, Bilophila and Akkermansia spp. These microbial communities reached a higher population density and net carbohydrate fermentation, leading to an increased SCFA production at longer transit times. In contrast, the carbohydrate-to-biomass production efficiency was increased at shorter transits, particularly in well-adapted faecal microbiomes from donors with short in vivo transit. Said adaptation was also reflected in the carbohydrate-to-SCFA conversion efficiency which varied with donor, but also colon region and SCFA chain length. A long transit time promoted propionate production, whereas butyrate production and butyrate producers were selectively enriched in the proximal colon at medium transit time. CONCLUSION: Microbial growth rates and nutrient utilisation efficiency mediate the species-specific gut microbiota response to in vitro transit time variation, which is the main driver of in vitro microbial load, metabolism and community composition. Given the in vivo transit time variation within and between individuals, the personalisation of in vitro transit time based on in vivo data is required to accurately study intra- and inter-individual differences in gut microbiome structure, functionality and interactions with host and environmental modulators. Video Abstract.
Experiment 1
Reviewed Marked as Reviewed by KateRasheed on 2025-7-17
Subjects
- Location of subjects
- Belgium
- 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
- Short Transit Time (Proximal colon)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Long Transit Time (Proximal colon)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Proximal colon sample from SHIME model simulating long transit time (24hours)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 6
- Group 1 sample size Number of subjects in the case (exposed) group
- 6
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 6 months
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
- Mann-Whitney (Wilcoxon)
- 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
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, body mass index, diet, physical activity, life style, sex, health, Confounders controlled for: "colonic anatomy" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.colonic anatomy, Confounders controlled for: "pH" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.pH, Confounders controlled for: "gut hormones" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.gut hormones, Confounders controlled for: "bile acid metabolism" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.bile acid metabolism, Confounders controlled for: "genetics" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.genetics
Signature 1
Reviewed Marked as Reviewed by KateRasheed on 2025-7-17
Source: Table S10
Description: Significant differences of bacterial taxa between transit times in proximal colon
Abundance in Group 1: increased abundance in Long Transit Time (Proximal colon)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Dialister | ||
| Eubacteriales | ||
| Parabacteroides | ||
| Prevotella | ||
| Clostridium_XIVaClostridium_XIVa |
Revision editor(s): Vanisha1606, Anne-mariesharp
Signature 2
Reviewed Marked as Reviewed by KateRasheed on 2025-7-17
Source: Table S10
Description: Significant differences of bacterial taxa between transit times in proximal colon
Abundance in Group 1: decreased abundance in Long Transit Time (Proximal colon)
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium | ||
| Collinsella | ||
| Faecalibacterium | ||
| Oscillospiraceae | ||
| Roseburia | ||
| Stenotrophomonas | ||
| Veillonella |
Revision editor(s): Vanisha1606, Anne-mariesharp
Experiment 2
Reviewed Marked as Reviewed by KateRasheed on 2025-7-17
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Medium Transit Time (Proximal colon)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Proximal colon sample from SHIME model simulating medium transit time (16hours)
Lab analysis
Statistical Analysis
Signature 1
Reviewed Marked as Reviewed by KateRasheed on 2025-7-17
Source: Table S10
Description: Significant differences of bacterial taxa between transit times in proximal colon
Abundance in Group 1: increased abundance in Medium Transit Time (Proximal colon)
| NCBI | Quality Control | Links |
|---|---|---|
| Anaeroglobus | ||
| Bacteroides | ||
| Blautia | ||
| Cloacibacillus | ||
| Clostridium_XIVaClostridium_XIVa | ||
| Dialister | ||
| Lachnospiraceae | ||
| Parabacteroides |
Revision editor(s): Anne-mariesharp
Signature 2
Reviewed Marked as Reviewed by KateRasheed on 2025-7-17
Source: Table S10
Description: Significant differences of bacterial taxa between transit times in proximal colon
Abundance in Group 1: decreased abundance in Medium Transit Time (Proximal colon)
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium | ||
| Collinsella | ||
| Stenotrophomonas | ||
| Veillonella |
Revision editor(s): Anne-mariesharp
Experiment 3
Reviewed Marked as Reviewed by KateRasheed on 2025-7-17
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Medium Transit Time (Proximal colon)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Long Transit Time (Proximal colon)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Proximal colon sample from SHIME model simulating long transit time (24hours)
Lab analysis
Statistical Analysis
Signature 1
Reviewed Marked as Reviewed by KateRasheed on 2025-7-17
Source: Table S10
Description: Significant differences of bacterial taxa between transit times in proximal colon
Abundance in Group 1: increased abundance in Long Transit Time (Proximal colon)
| NCBI | Quality Control | Links |
|---|---|---|
| Dialister | ||
| Parabacteroides | ||
| Prevotella |
Revision editor(s): Anne-mariesharp
Signature 2
Reviewed Marked as Reviewed by KateRasheed on 2025-7-17
Source: Table S10
Description: Significant differences of bacterial taxa between transit times in proximal colon
Abundance in Group 1: decreased abundance in Long Transit Time (Proximal colon)
| NCBI | Quality Control | Links |
|---|---|---|
| Anaeroglobus | ||
| Bifidobacterium | ||
| Blautia | ||
| Eubacteriales | ||
| Clostridium_XIVaClostridium_XIVa | ||
| Collinsella | ||
| Faecalibacterium | ||
| Roseburia | ||
| Oscillospiraceae | ||
| Stenotrophomonas |
Revision editor(s): Anne-mariesharp
Experiment 4
Reviewed Marked as Reviewed by KateRasheed on 2025-7-17
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Short Transit Time (Distal colon)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Long Transit Time (Distal colon)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Distal colon sample from SHIME model simulating long transit time (39hours)
Lab analysis
Statistical Analysis
Signature 1
Reviewed Marked as Reviewed by KateRasheed on 2025-7-17
Source: Table S10
Description: Significant differences of bacterial taxa between transit times in distal colon
Abundance in Group 1: increased abundance in Long Transit Time (Distal colon)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Cloacibacillus | ||
| Dialister | ||
| Parabacteroides | ||
| Pseudomonas | ||
| Sutterella |
Revision editor(s): Anne-mariesharp
Signature 2
Reviewed Marked as Reviewed by KateRasheed on 2025-7-17
Source: Table S10
Description: Significant differences of bacterial taxa between transit times in distal colon
Abundance in Group 1: decreased abundance in Long Transit Time (Distal colon)
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium | ||
| Collinsella | ||
| Enterobacteriaceae | ||
| Eubacteriales | ||
| Faecalibacterium | ||
| Roseburia | ||
| Stenotrophomonas | ||
| Veillonella |
Revision editor(s): Anne-mariesharp
Experiment 5
Reviewed Marked as Reviewed by KateRasheed on 2025-7-17
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Medium Transit Time (Distal colon)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Distal colon sample from SHIME model simulating medium transit time (26hours)
Lab analysis
Statistical Analysis
Signature 1
Reviewed Marked as Reviewed by KateRasheed on 2025-7-17
Source: Table S10
Description: Significant differences of bacterial taxa between transit times in distal colon
Abundance in Group 1: increased abundance in Medium Transit Time (Distal colon)
| NCBI | Quality Control | Links |
|---|---|---|
| Alistipes | ||
| Anaeroglobus | ||
| Bacteroides | ||
| Dialister | ||
| Oscillospiraceae | ||
| Parabacteroides | ||
| Pseudomonas | ||
| Sutterella |
Revision editor(s): Anne-mariesharp
Signature 2
Reviewed Marked as Reviewed by KateRasheed on 2025-7-17
Source: Table S10
Description: Significant differences of bacterial taxa between transit times in distal colon
Abundance in Group 1: decreased abundance in Medium Transit Time (Distal colon)
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium | ||
| Collinsella | ||
| Veillonella |
Revision editor(s): Anne-mariesharp
Experiment 6
Reviewed Marked as Reviewed by KateRasheed on 2025-7-17
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Medium Transit Time (Distal colon)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Long Transit Time (Distal colon)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Distal colon sample from SHIME model simulating long transit time (39hours)
Lab analysis
Statistical Analysis
Signature 1
Reviewed Marked as Reviewed by KateRasheed on 2025-7-17
Source: Table S10
Description: Significant differences of bacterial taxa between transit times in distal colon
Abundance in Group 1: increased abundance in Long Transit Time (Distal colon)
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotella |
Revision editor(s): Anne-mariesharp
Signature 2
Reviewed Marked as Reviewed by KateRasheed on 2025-7-17
Source: Table S10
Description: Significant differences of bacterial taxa between transit times in distal colon
Abundance in Group 1: decreased abundance in Long Transit Time (Distal colon)
| NCBI | Quality Control | Links |
|---|---|---|
| Alistipes | ||
| Anaeroglobus | ||
| Eubacteriales | ||
| Collinsella | ||
| Enterobacteriaceae | ||
| Faecalibacterium | ||
| Roseburia | ||
| Oscillospiraceae | ||
| Stenotrophomonas |
Revision editor(s): Anne-mariesharp
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