Age and the aging process significantly alter the small bowel microbiome
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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
Leite G, Pimentel M, Barlow GM, Chang C, Hosseini A, Wang J, Parodi G, Sedighi R, Rezaie A, Mathur R
Journal
Cell reports
Year
2021
Keywords:
Escherichia, Lactobacillus, Proteobacteria, age, aging, coliforms, concomitant diseases, duodenal microbiome, medication use, small intestinal microbiome
Gut microbial diversity decreases with aging, but existing studies have used stool samples, which do not represent the entire gut. We analyzed the duodenal microbiome in 251 subjects aged 18-35 (n = 32), 36-50 (n = 41), 51-65 (n = 96), and 66-80 (n = 82). Decreased duodenal microbial diversity in older subjects is associated with combinations of chronological age, number of concomitant diseases, and number of medications used, and also correlated with increasing coliform numbers (p < 0.0001). Relative abundance (RA) of phylum Proteobacteria increases in older subjects, with increased RA of family Enterobacteriaceae and coliform genera Escherichia and Klebsiella, and is associated with alterations in the RA of other duodenal microbial taxa and decreased microbial diversity. Increased RA of specific genera are associated with chronological age only (Escherichia, Lactobacillus, and Enterococcus), number of medications only (Klebsiella), or number of concomitant diseases only (Clostridium and Bilophila). These findings indicate the small intestinal microbiome changes significantly with age and the aging process.
Experiment 1
Reviewed Marked as Reviewed by Folakunmi on 2024-1-4
Subjects
- Location of subjects
- Switzerland
- 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
- Duodenum Proximal intestine,Upper intestine,Duodenum,duodenum
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Aging ageing,AGING BIOL,Aging, Biological,BIOL AGING,Biological Aging,Senescence,Aging,aging
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Group 1 (18–35 years old)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Group 2
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- 36-50 years old
- Group 0 sample size Number of subjects in the control (unexposed) group
- 32
- Group 1 sample size Number of subjects in the case (exposed) group
- 41
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
- Linear Regression
- 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
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2024-1-4
Source: Table S2
Description: Genera solely associated with age after multivariate analysis controlling for the number of medications used and the number of concomitant diseases.
Abundance in Group 1: increased abundance in Group 2
| NCBI | Quality Control | Links |
|---|---|---|
| Actinobacillus | ||
| Bacteroides | ||
| Escherichia | ||
| Lactobacillus |
Signature 2
Reviewed Marked as Reviewed by Folakunmi on 2024-1-4
Source: Table S2
Description: Genera solely associated with age after multivariate analysis controlling for the number of medications used and the number of concomitant diseases.
Abundance in Group 1: decreased abundance in Group 2
| NCBI | Quality Control | Links |
|---|---|---|
| Xanthomonadaceae |
Revision editor(s): Folakunmi
Experiment 2
Reviewed Marked as Reviewed by Folakunmi on 2024-1-4
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Group 3
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- participants aged 51 to 65 years old
- Group 1 sample size Number of subjects in the case (exposed) group
- 96
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2024-1-4
Source: Table S2
Description: Genera solely associated with age after multivariate analysis controlling for the number of medications used and the number of concomitant diseases.
Abundance in Group 1: increased abundance in Group 3
| NCBI | Quality Control | Links |
|---|---|---|
| Actinobacillus | ||
| Lactobacillus | ||
| Bacteroides | ||
| Escherichia |
Signature 2
Reviewed Marked as Reviewed by Folakunmi on 2024-1-4
Source: Table S2
Description: Genera solely associated with age after multivariate analysis controlling for the number of medications used and the number of concomitant diseases.
Abundance in Group 1: decreased abundance in Group 3
| NCBI | Quality Control | Links |
|---|---|---|
| Xanthomonadaceae |
Experiment 3
Reviewed Marked as Reviewed by Folakunmi on 2024-1-4
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Group 4
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- 66 to 80 years old
- Group 1 sample size Number of subjects in the case (exposed) group
- 82
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2024-1-4
Source: Table S2
Description: Genera solely associated with age after multivariate analysis controlling for the number of medications used and the number of concomitant diseases.
Abundance in Group 1: increased abundance in Group 4
| NCBI | Quality Control | Links |
|---|---|---|
| Actinobacillus | ||
| Bacteroides | ||
| Lactobacillus | ||
| Escherichia |
Signature 2
Reviewed Marked as Reviewed by Folakunmi on 2024-1-4
Source: Table S2
Description: Genera solely associated with age after multivariate analysis controlling for the number of medications used and the number of concomitant diseases.
Abundance in Group 1: decreased abundance in Group 4
| NCBI | Quality Control | Links |
|---|---|---|
| Xanthomonadaceae |
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