Almond Snacking for 8 wk Increases Alpha-Diversity of the Gastrointestinal Microbiome and Decreases Bacteroides fragilis Abundance Compared with an Isocaloric Snack in College Freshmen
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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
Dhillon J, Li Z, Ortiz RM
Journal
Current developments in nutrition
Year
2019
Keywords:
ANCOM, adolescence, amplicon sequence variants, cardiovascular, functional foods, gut, metabolism, minority, nutrients, nuts
Background: Changes in gut microbiota are associated with cardiometabolic disorders and are influenced by diet. Almonds are a rich source of fiber, unsaturated fats, and polyphenols, all nutrients that can favorably alter the gut microbiome. Objectives: The aim of this study was to examine the effects of 8 wk of almond snacking on the gut (fecal) microbiome diversity and abundance compared with an isocaloric snack of graham crackers in college freshmen. Methods: A randomized, controlled, parallel-arm, 8-wk intervention in 73 college freshmen (age: 18-19 y; 41 women and 32 men; BMI: 18-41 kg/m2) with no cardiometabolic disorders was conducted. Participants were randomly allocated to either an almond snack group (56.7 g/d; 364 kcal; n = 38) or graham cracker control group (77.5 g/d; 338 kcal/d; n = 35). Stool samples were collected at baseline and 8 wk after the intervention to assess primary microbiome outcomes, that is, gut microbiome diversity and abundance. Results: Almond snacking resulted in 3% greater quantitative alpha-diversity (Shannon index) and 8% greater qualitative alpha-diversity (Chao1 index) than the cracker group after the intervention (P < 0.05). Moreover, almond snacking for 8 wk decreased the abundance of the pathogenic bacterium Bacteroides fragilis by 48% (overall relative abundance, P < 0.05). Permutational multivariate ANOVA showed significant time effects for the unweighted UniFrac distance and Bray-Curtis beta-diversity methods (P < 0.05; R2 ≤ 3.1%). The dietary and clinical variables that best correlated with the underlying bacterial community structure at week 8 of the intervention included dietary carbohydrate (percentage energy), dietary fiber (g), and fasting total and HDL cholesterol (model Spearman rho = 0.16; P = 0.01). Conclusions: Almond snacking for 8 wk improved alpha-diversity compared with cracker snacking. Incorporating a morning snack in the dietary regimen of predominantly breakfast-skipping college freshmen improved the diversity and composition of the gut microbiome. This trial was registered at clinicaltrials.gov as NCT03084003.
Experiment 1
Reviewed Marked as Reviewed by Atrayees on 2023-6-26
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
- higher fiber (almonds) - at baseline
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- lower fiber (cracker), at baseline
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- students eating crackers
- Group 0 sample size Number of subjects in the control (unexposed) group
- 38
- Group 1 sample size Number of subjects in the case (exposed) group
- 35
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V4-V5
- 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
- ANCOM
- 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
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- decreased
Signature 1
Needs review
Source: Table 1
Description: ANCOM results of selected taxa prevalent in at least 25% of the samples obtained from college freshmen in the almond and cracker groups at baseline
Abundance in Group 1: increased abundance in lower fiber (cracker), at baseline
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides fragilis |
Experiment 2
Reviewed Marked as Reviewed by Atrayees on 2023-6-26
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- higher fiber (almonds) - 8 wk after intervention
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- lower fiber (cracker) - 8 wk after intervention
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- decreased
Signature 1
Needs review
Source: Table 1
Description: ANCOM results of selected taxa prevalent in at least 25% of the samples obtained from college freshmen in the almond and cracker groups 8 wk after the intervention
Abundance in Group 1: increased abundance in lower fiber (cracker) - 8 wk after intervention
| NCBI | Quality Control | Links |
|---|---|---|
| Lachnospira | ||
| unclassified Mollicutes |
Signature 2
Needs review
Source: Table 1
Description: ANCOM results of selected taxa prevalent in at least 25% of the samples obtained from college freshmen in the almond and cracker groups 8 wk after the intervention
Abundance in Group 1: decreased abundance in lower fiber (cracker) - 8 wk after intervention
| NCBI | Quality Control | Links |
|---|---|---|
| Alistipes | ||
| Butyricimonas | ||
| Odoribacter | ||
| Muribaculaceae |
Experiment 3
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- higher fiber (almonds)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- lower fiber (cracker)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 35
- Group 1 sample size Number of subjects in the case (exposed) group
- 38
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- Not specified
Signature 1
Needs review
Source: Table 1
Description: ANCOM results of selected taxa prevalent in at least 25% of the samples obtained from college freshmen in the almond and cracker groups at baseline and 8 wk after the intervention
Abundance in Group 1: decreased abundance in lower fiber (cracker)
| NCBI | Quality Control | Links |
|---|---|---|
| Sutterella |
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