The small bowel microbiome changes significantly with age and aspects of the ageing process

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study design
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
Leite G, Pimentel M, Barlow GM, Mathur R
Microbial cell (Graz, Austria)
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

Needs review

Curated date: 2023/10/18

Curator: Davvve

Revision editor(s): Davvve


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
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
aging ageing,AGING BIOL,Aging, Biological,BIOL AGING,Biological Aging,Senescence,aging
Group 0 name Corresponds to the control (unexposed) group for case-control studies
group 1 ( 18 to 35 years old. young adults)
Group 1 name Corresponds to the case (exposed) group for case-control studies
group 4 ( 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 most age advanced group from the study
Group 0 sample size Number of subjects in the control (unexposed) group
Group 1 sample size Number of subjects in the case (exposed) group

Lab analysis

Sequencing type
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance

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)

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness

Signature 1

Needs review

Curated date: 2023/10/19

Curator: Davvve

Revision editor(s): Davvve

Source: Figure S5


Abundance in Group 1: increased abundance in group 4 ( 66 to 80 years old. elderly people)

NCBI Quality ControlLinks

Revision editor(s): Davvve