Age and the aging process significantly alter the small bowel microbiome

From BugSigDB
Reviewed Marked as Reviewed by Folakunmi on 2024-1-4
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

Curated date: 2023/06/01

Curator: Atrayees

Revision editor(s): Atrayees, Folakunmi, Victoria

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).
raw counts
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

Curated date: 2023/06/01

Curator: Atrayees

Revision editor(s): Atrayees, Folakunmi

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 ControlLinks
Actinobacillus
Bacteroides
Escherichia
Lactobacillus

Revision editor(s): Atrayees, Folakunmi

Signature 2

Reviewed Marked as Reviewed by Folakunmi on 2024-1-4

Curated date: 2024/01/02

Curator: Folakunmi

Revision editor(s): Folakunmi

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 ControlLinks
Lysobacteraceae

Revision editor(s): Folakunmi

Experiment 2


Reviewed Marked as Reviewed by Folakunmi on 2024-1-4

Curated date: 2023/06/01

Curator: Atrayees

Revision editor(s): Atrayees, Folakunmi, Victoria

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

Curated date: 2023/06/01

Curator: Atrayees

Revision editor(s): Atrayees, Folakunmi

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 ControlLinks
Actinobacillus
Lactobacillus
Bacteroides
Escherichia

Revision editor(s): Atrayees, Folakunmi

Signature 2

Reviewed Marked as Reviewed by Folakunmi on 2024-1-4

Curated date: 2023/06/01

Curator: Atrayees

Revision editor(s): Atrayees, Folakunmi

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 ControlLinks
Lysobacteraceae

Revision editor(s): Atrayees, Folakunmi

Experiment 3


Reviewed Marked as Reviewed by Folakunmi on 2024-1-4

Curated date: 2023/06/01

Curator: Atrayees

Revision editor(s): Atrayees, Folakunmi, Victoria

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

Curated date: 2023/06/01

Curator: Atrayees

Revision editor(s): Atrayees, Folakunmi

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 ControlLinks
Actinobacillus
Bacteroides
Lactobacillus
Escherichia

Revision editor(s): Atrayees, Folakunmi

Signature 2

Reviewed Marked as Reviewed by Folakunmi on 2024-1-4

Curated date: 2023/06/01

Curator: Atrayees

Revision editor(s): Atrayees, Folakunmi

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 ControlLinks
Lysobacteraceae

Revision editor(s): Atrayees, Folakunmi