Increased dietary protein stimulates amino acid catabolism via the gut microbiota and secondary bile acid production
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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.
Authors
Tobón-Cornejo S, Sanchez-Tapia M, Guizar-Heredia R, Velázquez Villegas L, Noriega LG, Furuzawa-Carballeda J, Hernández-Pando R, Vázquez-Manjarrez N, Granados-Portillo O, López-Barradas A, Rebollar-Vega R, Maya O, Miller AW, Serralde A, Guevara-Cruz M, Torres N, Tovar AR
Journal
Gut microbes
Year
2025
Keywords:
Gut microbiota, amino acid catabolism, glucagon, high-protein diet, secondary bile acids
Excess amino acids from a protein-rich diet are mainly catabolized in the liver. However, it is still unclear to what extent the gut microbiota may be involved in the mechanisms governing this catabolism. Therefore, the aim of this study was to investigate whether consumption of different dietary protein concentrations induces changes in the taxonomy of the gut microbiota, which may contribute to the regulation of hepatic amino acid catabolism. Consumption of a high-protein diet caused overexpression of HIF-1α in the colon and increase in mitochondrial activity, creating a more anaerobic environment that was associated with changes in the taxonomy of the gut microbiota promoting an increase in the synthesis of secondary bile acids, increased secretion of pancreatic glucagon. This effect was demonstrated in pancreatic islets, where secondary bile acids stimulated the expression of the PC2 enzyme that promotes glucagon formation. The increase in circulating glucagon was associated with an induction of the expression of hepatic amino acid-degrading enzymes, an effect attenuated by antibiotics. Thus, high protein intake in mice and humans induced the increase of different species in the gut microbiota with the capacity to produce secondary bile acids leading to an increase in secondary bile acids and glucagon levels, promoting amino acid catabolism.
Experiment 1
Reviewed Marked as Reviewed by Svetlana up on 2025-4-4
Subjects
- Location of subjects
- United States of America
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Mus musculus
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Colon Hindgut,Large bowel,Posterior intestine,Colon,colon
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Response to diet Response to diet,response to diet
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low protein group- LP
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High protein group- HP
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Dietary regimen constituting of 50% protein for 10 days.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 20
- Group 1 sample size Number of subjects in the case (exposed) group
- 20
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-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
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2025-4-4
Source: Figure 4E
Description: Linear discriminant analysis (LDA) shows significant differences in the relative abundance of bacterial species in mice fed different protein concentrations.
Abundance in Group 1: increased abundance in High protein group- HP
| NCBI | Quality Control | Links |
|---|---|---|
| Escherichia coli | ||
| Thomasclavelia cocleata | ||
| Parabacteroides distasonis | ||
| Mucispirillum schaedleri |
Revision editor(s): Miss Lulu
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2025-4-4
Source: Figure 4E
Description: Linear discriminant analysis (LDA) shows significant differences in the relative abundance of bacterial species in mice fed different protein concentrations.
Abundance in Group 1: decreased abundance in High protein group- HP
| NCBI | Quality Control | Links |
|---|---|---|
| Akkermansia muciniphila |
Revision editor(s): Miss Lulu
Experiment 2
Reviewed Marked as Reviewed by Svetlana up on 2025-4-4
Differences from previous experiment shown
Subjects
- 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
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Baseline Participants
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- End of study Participants
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Effect of high protein diet on humans after clinical trial was conducted.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 19
- Group 1 sample size Number of subjects in the case (exposed) group
- 19
- 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
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2025-4-4
Source: Figure 10D
Description: Linear discriminant analysis (LDA) of the gut microbiota at the species level. Concentration of fecal secondary bile acids
Abundance in Group 1: increased abundance in End of study Participants
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerorhabdus furcosa | ||
| Gemmiger formicilis | ||
| Parabacteroides distasonis | ||
| [Clostridium] fimetarium | ||
| Paraeggerthella hongkongensis | ||
| Solobacterium moorei |
Revision editor(s): Miss Lulu
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2025-4-4
Source: Figure 10D
Description: Linear discriminant analysis (LDA) of the gut microbiota at the species level. Concentration of fecal secondary bile acids
Abundance in Group 1: decreased abundance in End of study Participants
Revision editor(s): Miss Lulu
Experiment 3
Reviewed Marked as Reviewed by Svetlana up on 2025-4-4
Differences from previous experiment shown
Subjects
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Mus musculus
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Colon Hindgut,Large bowel,Posterior intestine,Colon,colon
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Normal protein group- NP
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High protein group- HP
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Dietary regimen constituting of 50% protein for 10 days.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 20
- Group 1 sample size Number of subjects in the case (exposed) group
- 20
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Not specified
Lab analysis
Statistical Analysis
- Statistical test
- ANOVA
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- Not specified
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2025-4-4
Source: Figure 4D
Description: Gut microbiota is modified by dietary protein concentration in mice (genus)
Abundance in Group 1: increased abundance in High protein group- HP
| NCBI | Quality Control | Links |
|---|---|---|
| SMB53SMB53 | ||
| Allobaculum | ||
| Sutterella | ||
| Lactobacillus |
Revision editor(s): Miss Lulu
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2025-4-4
Source: Figure 4D
Description: Gut microbiota is modified by dietary protein concentration in mice (genus)
Abundance in Group 1: decreased abundance in High protein group- HP
| NCBI | Quality Control | Links |
|---|---|---|
| AF12AF12 | ||
| Rikenella | ||
| Coprococcus | ||
| Oscillospira |
Revision editor(s): Miss Lulu
Experiment 4
Reviewed Marked as Reviewed by Svetlana up on 2025-4-4
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low protein group- LP
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2025-4-4
Source: Figure 4D
Description: Gut microbiota is modified by dietary protein concentration in mice (genus)
Abundance in Group 1: increased abundance in High protein group- HP
| NCBI | Quality Control | Links |
|---|---|---|
| AF12AF12 | ||
| SMB53SMB53 | ||
| Allobaculum | ||
| Sutterella | ||
| Lactobacillus |
Revision editor(s): Miss Lulu
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2025-4-4
Source: Figure 4D
Description: Gut microbiota is modified by dietary protein concentration in mice (genus)
Abundance in Group 1: decreased abundance in High protein group- HP
| NCBI | Quality Control | Links |
|---|---|---|
| Rikenella | ||
| Coprococcus | ||
| Oscillospira |
Revision editor(s): Miss Lulu
Experiment 5
Reviewed Marked as Reviewed by Svetlana up on 2025-4-4
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Normal protein group- NP
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Dietary regimen constituting of 20% protein for 10 days.
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2025-4-4
Source: Figure 4D
Description: Gut microbiota is modified by dietary protein concentration in mice (genus)
Abundance in Group 1: increased abundance in Normal protein group- NP
| NCBI | Quality Control | Links |
|---|---|---|
| AF12AF12 | ||
| Coprococcus | ||
| Oscillospira | ||
| Sutterella | ||
| Lactobacillus |
Revision editor(s): Miss Lulu
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2025-4-4
Source: Figure 4D
Description: Gut microbiota is modified by dietary protein concentration in mice.(genus)
Abundance in Group 1: decreased abundance in Normal protein group- NP
| NCBI | Quality Control | Links |
|---|---|---|
| Rikenella | ||
| SMB53SMB53 | ||
| Allobaculum |
Revision editor(s): Miss Lulu
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