Gut microbiome composition is linked to whole grain-induced immunological improvements
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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
Martínez I, Lattimer JM, Hubach KL, Case JA, Yang J, Weber CG, Louk JA, Rose DJ, Kyureghian G, Peterson DA, Haub MD, Walter J
Journal
The ISME journal
Year
2013
The involvement of the gut microbiota in metabolic disorders, and the ability of whole grains to affect both host metabolism and gut microbial ecology, suggest that some benefits of whole grains are mediated through their effects on the gut microbiome. Nutritional studies that assess the effect of whole grains on both the gut microbiome and human physiology are needed. We conducted a randomized cross-over trial with four-week treatments in which 28 healthy humans consumed a daily dose of 60 g of whole-grain barley (WGB), brown rice (BR), or an equal mixture of the two (BR+WGB), and characterized their impact on fecal microbial ecology and blood markers of inflammation, glucose and lipid metabolism. All treatments increased microbial diversity, the Firmicutes/Bacteroidetes ratio, and the abundance of the genus Blautia in fecal samples. The inclusion of WGB enriched the genera Roseburia, Bifidobacterium and Dialister, and the species Eubacterium rectale, Roseburia faecis and Roseburia intestinalis. Whole grains, and especially the BR+WGB treatment, reduced plasma interleukin-6 (IL-6) and peak postprandial glucose. Shifts in the abundance of Eubacterium rectale were associated with changes in the glucose and insulin postprandial response. Interestingly, subjects with greater improvements in IL-6 levels harbored significantly higher proportions of Dialister and lower abundance of Coriobacteriaceae. In conclusion, this study revealed that a short-term intake of whole grains induced compositional alterations of the gut microbiota that coincided with improvements in host physiological measures related to metabolic dysfunctions in humans.
Experiment 1
Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/12
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
- Diet Dietary,Diets,Diet,diet
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- baseline
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- barley (WGB)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- subjects who took a daily 60g dose of barley
- Group 0 sample size Number of subjects in the control (unexposed) group
- 28
- Group 1 sample size Number of subjects in the case (exposed) group
- 28
- 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
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V1-V3
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Roche454
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- ANOVA
- 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
- increased
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/13
Curated date: 2021/01/10
Curator: Lora Kasselman
Revision editor(s): Fatima, Claregrieve1, WikiWorks
Source: Table 2, text
Description: Differential microbial abundance between baseline and end of study for barley study group
Abundance in Group 1: increased abundance in barley (WGB)
| NCBI | Quality Control | Links |
|---|---|---|
| Blautia | ||
| Blautia wexlerae | ||
| Bacillota | ||
| Roseburia faecis | ||
| Roseburia intestinalis | ||
| Agathobacter rectalis |
Revision editor(s): Fatima, Claregrieve1, WikiWorks
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/13
Source: Table 2, text
Description: Differential microbial abundance between baseline and end of study for barley study group
Abundance in Group 1: decreased abundance in barley (WGB)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidota | ||
| Odoribacter | ||
| Odoribacter splanchnicus | ||
| Porphyromonadaceae | ||
| unclassified Bacteroidota | ||
| Bacteroidaceae | ||
| Roseburia | ||
| Dialister |
Revision editor(s): Claregrieve1, WikiWorks
Experiment 2
Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/13
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- brown rice (BR)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- subjects who took a daily 60g dose of brown rice fiber
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/13
Source: Table 2, text
Description: Differential microbial abundance between baseline and end of study for brown rice study group
Abundance in Group 1: increased abundance in brown rice (BR)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillota |
Revision editor(s): Claregrieve1, WikiWorks
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/13
Source: Table 2, text
Description: Differential microbial abundance between baseline and end of study for brown rice study group
Abundance in Group 1: decreased abundance in brown rice (BR)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidota |
Revision editor(s): Claregrieve1, WikiWorks
Experiment 3
Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/13
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- brown rice + barley (BR + WGB)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- subjects who took a daily dose of 30g barley + 30g brown rice
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/13
Source: Table 2, text
Description: Differential microbial abundance between baseline and end of study for barley+brown rice study group
Abundance in Group 1: increased abundance in brown rice + barley (BR + WGB)
| NCBI | Quality Control | Links |
|---|---|---|
| Blautia | ||
| Bacillota |
Revision editor(s): Claregrieve1, WikiWorks
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/13
Source: Table 2, text
Description: Differential microbial abundance between baseline and end of study for barley+brown rice study group
Abundance in Group 1: decreased abundance in brown rice + barley (BR + WGB)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidaceae | ||
| Bacteroides | ||
| Bacteroidota |
Revision editor(s): Claregrieve1, WikiWorks
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