The small bowel microbiome changes significantly with age and aspects of the ageing process
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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, Mathur R
Journal
Microbial cell (Graz, Austria)
Year
2022
Keywords:
age, aging, coliforms, concomitant diseases, medication use, proteobacteria, small intestinal microbiome
Gut microbiome changes have been associated with human ageing and implicated in age-related diseases including Alzheimer's disease and Parkinson's disease. However, studies to date have used stool samples, which do not represent the entire gut. Although more challenging to access, the small intestine plays critical roles in host metabolism and immune function. In this paper (Leite et al. (2021), Cell Reports, doi: 10.1016/j.celrep.2021.109765), we demonstrate significant differences in the small intestinal microbiome in older subjects, using duodenal aspirates from 251 subjects aged 18-80 years. Differences included significantly decreased microbial diversity in older subjects, driven by increased relative abundance of phylum Proteobacteria, particularly family Enterobacteriaceae and coliform genera Escherichia and Klebsiella. Moreover, while this decreased diversity was associated with the 'ageing process' (comprising chronologic age, number of medications, and number of concomitant diseases), changes in certain taxa were found to be associated with number of medications alone (Klebsiella), number of diseases alone (Clostridium, Bilophila), or chronologic age alone (Escherichia, Lactobacillus, Enterococcus). Lastly, many taxa associated with increasing chronologic age were anaerobes. These changes may contribute to changes in human health that occur during the ageing process.
Experiment 1
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-30
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
- Small intestine Anterior intestine,Intestinum tenue,Mid intestine,Small bowel,Small intestine,small intestine
- 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- youngest age group (18 to 35 years old)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Group 4- oldest age group (66 to 80 years old. elderly people)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This is the oldest age advanced group from the study
- 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
- 82
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- None.
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
- PLS-DA (Partial least square discriminant analysis)
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.0001
- 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
- Richness Number of species
- decreased
Signature 1
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-30
Source: Figure S6 + Results (text): Page 6, under sub-heading "Microbiome differences are most pronounced between younger (group 1) and elderly (group 4) adults."
Description: Variable importance in projection (VIP) selected during PLS-DA analysis of families in the duodenal microbiome of subjects in Groups 4 compared to Group 1.
Abundance in Group 1: increased abundance in Group 4- oldest age group (66 to 80 years old. elderly people)
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridiaceae | ||
| Desulfovibrionaceae | ||
| Enterobacteriaceae | ||
| Enterococcaceae | ||
| Klebsiella | ||
| Lactobacillus | ||
| Lactobacillaceae | ||
| Escherichia |
Revision editor(s): Davvve, ChiomaBlessing
Signature 2
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-30
Source: Figure S6
Description: Variable importance in projection (VIP) selected during PLS-DA analysis of families in the duodenal microbiome of subjects in Groups 4 compared to Group 1.
Abundance in Group 1: decreased abundance in Group 4- oldest age group (66 to 80 years old. elderly people)
Revision editor(s): ChiomaBlessing
Experiment 2
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-30
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Group 2, 3 and 4 - older age groups (36 to 50 years old; 51 to 65 years old and 66 to 80 years old.)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- These are the remaining 3 groups of subjects grouped according to advancing chronological age (N= 41, 36 to 50 years old; N= 96, 51 to 65 years old and N= 82, 66 to 80 years old).
- Group 1 sample size Number of subjects in the case (exposed) group
- 219
Lab analysis
Statistical Analysis
- 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)?
- No
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- Confounders controlled for: "number of medications used" 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.number of medications used, Confounders controlled for: "number of concomitant diseases" 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.number of concomitant diseases
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
- Richness Number of species
- decreased
Signature 1
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-30
Source: Table S2
Description: Facultative and strict anaerobic genera in the duodenal microbiome of older subjects from groups 2, 3, and 4, when compared to group 1
Abundance in Group 1: increased abundance in Group 2, 3 and 4 - older age groups (36 to 50 years old; 51 to 65 years old and 66 to 80 years old.)
| NCBI | Quality Control | Links |
|---|---|---|
| Actinobacillus | ||
| Bacteroides | ||
| Escherichia | ||
| Lactobacillus |
Revision editor(s): ChiomaBlessing
Signature 2
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-30
Source: Table S2
Description: Facultative and strict anaerobic genera in the duodenal microbiome of older subjects from groups 2, 3, and 4, when compared to group 1
Abundance in Group 1: decreased abundance in Group 2, 3 and 4 - older age groups (36 to 50 years old; 51 to 65 years old and 66 to 80 years old.)
| NCBI | Quality Control | Links |
|---|---|---|
| Lysobacteraceae |
Revision editor(s): ChiomaBlessing
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