The microbiome is associated with obesity-related metabolome signature in the process of aging

Study information

Needs review

study design

cross-sectional observational, not case-control

Citation

PMID PubMed identifier for scientific articles.

40851038

DOI Digital object identifier for electronic documents.

https://doi.org/10.1038/s41522-025-00811-w

URI Uniform resource identifier for web resources.

Authors

Binyamin D., Turjeman S., Asulin N., Schweitzer R., Koren O.

Journal

NPJ biofilms and microbiomes

Year

2025

Aging involves changes in the gut microbiome impacting health and longevity; however, the roles of specific microbial metabolites remain understudied. Here, we examine the microbial contribution to the metabolic profile in aged mice. Fecal samples were collected from female Swiss-Webster mice raised conventionally (Conv) or germ free (GF), at 8 weeks (young) and 18 (aged) months of age, and the microbiome and metabolome were characterized. Significant differences were observed in bacterial composition and its predicted functional activity between young and aged mice. Interestingly, we found more age-related differences in metabolite abundances among Conv mice than GF mice, highlighting the contribution of the microbiome to aging. Moreover, microbiome-associated metabolites, predominantly lipids, were higher in aged mice, with linoleic acid metabolism enriched in this group. Our study underscores a microbiome-dependent component to age-related metabolic changes in mice, particularly in lipid-associated pathways, and contributes to the growing body of literature linking gut microbiota to host metabolism in aging.

Experiment 1

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Curated date: 2025/10/17

Curator: Jesulolufemi

Revision editor(s): Jesulolufemi

Subjects

Location of subjects: Israel

Host species Species from which microbiome was sampled. Contact us to have more species added.: Mus musculus

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Young mice (8 weeks old)

Group 1 name Corresponds to the case (exposed) group for case-control studies: Aged mice (18 months old)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Stool microbiome composition of aged (18 months) conventional mice compared with young (8 weeks) conventional mice

Group 0 sample size Number of subjects in the control (unexposed) group: 30

Group 1 sample size Number of subjects in the case (exposed) group: 30

Lab analysis

Sequencing type: 16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: 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: ANCOM-BC

Significance threshold p-value or FDR threshold used for differential abundance testing (if any): 0.001

MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?: Yes

Alpha Diversity

Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample: increased

Signature 1

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Curated date: 2025/10/17

Curator: Jesulolufemi

Revision editor(s): Jesulolufemi

Source: Figure 2D/ Supplementary Table 2

Description:

Abundance in Group 1: increased abundance in Aged mice (18 months old)

NCBI	Quality Control	Links
Bifidobacterium
Bilophila
Butyricicoccus
Clostridium
Coprococcus
Lactobacillus
Oscillospira
Roseburia
Turicibacter
unclassified Lachnospiraceae
unclassified Peptococcaceae
Unclassified RF39Unclassified RF39
Unclassified ClostridialesUnclassified Clostridiales
Unclassified RuminococcaceaeUnclassified Ruminococcaceae
Clostridium 1Clostridium 1

Revision editor(s): Jesulolufemi

Signature 2

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Mark reviewed

Your review change was submitted

Needs review

Curated date: 2025/10/17

Curator: Jesulolufemi

Revision editor(s): Jesulolufemi

Source: Figure 2D/ Supplementary Table 2

Description:

Abundance in Group 1: decreased abundance in Aged mice (18 months old)

NCBI	Quality Control	Links
Parabacteroides
Akkermansia
Prevotella
unclassified Rikenellaceae
Alistipes
unclassified Bacteroidales
Odoribacter
unclassified Bacteria
Unclassified S24-7Unclassified S24-7

Revision editor(s): Jesulolufemi

Experiment 2

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Your review change was submittedDuplicate this Experiment Add a new Signature

Needs review

Curated date: 2025/10/17

Curator: Jesulolufemi

Revision editor(s): Jesulolufemi

Differences from previous experiment shown

Subjects

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: Microbiome Microbiome,microbiome

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Germ-free (GF, aged)

Group 1 name Corresponds to the case (exposed) group for case-control studies: Conventional (Conv, aged)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Aged mice with normal microbiota compared to germ-free aged mice