DIET-INFORMED METAGENOMIC CLOCKS FOR AGING IN THE INTEGRATIVE LONGEVITY OMICS STUDY

Sep 28, 2026

Aging differs across individuals and biological systems, motivating aging clocks that estimate biological age from molecular data. While epigenetic, transcriptomic, and proteomic clocks dominate, the microbiome is an underused source of aging biomarkers influenced by diet. Using shotgun metagenomics from 267 participants in the Integrative Longevity Omics cohort, including centenarians and offspring, the study builds taxonomic-composition-based clocks and incorporates caloric intake plus the Nutrient Variety Index (NVI). Diet adjustment significantly improves performance, indicating nutrient composition modulates microbiome aging.

LanguageEnglish

CategoryResearch & Report

FormatPDF

Pages1

Reading Time3 min

AccessFree to download

Abstract

Diet-informed metagenomic clocks

Data and cohort

Dietary adjustment using caloric intake and NVI

1226 Innovation in Aging, 2025, Vol. 9, No. S2 Abstract citation ID: igaf122.4101 DIET-INFORMED METAGENOMIC CLOCKS FOR AGING IN THE INTEGRATIVE LONGEVITY OMICS STUDY Tanya Karagiannis1, Anastasia Leshchyk1, Meghan Short2, Ye Chen1, Sarah Bald3, Stacy Andersen3, Daniel Segrè3, and Paola Sebastiani1, 1. Tufts Medical Center, Boston, Massachusetts, United States, 2. Tufts University School of Medicine, Medford, Massachusetts, United States, 3. Boston University, Boston, Massachusetts, United States Aging is a heterogeneous process that unfolds uniquely across individuals and biological systems. Aging clocks, computational models trained on molecular data to estimate biological age, offera promising framework for investigating aging biology at the individual level. While most clocks rely on epigenetic, transcriptomic, or proteomic data, the human microbiome remains an underutilized source of aging biomarkers despite its central role in host metabolism, immune regulation, and inflammation, all of which are influenced by diet and linked to aging. To explore microbiome-mediated aging, we developed aging clocks using shotgun metagenomics sequencing data from 267 individuals in the Integrative Longevity Omics cohort, including centenariansand their offspring. These clocks estimate biological age based on taxonomic composition across multiple taxonomic levels. To account for dietary influences, we incorporated total caloric intake and a novel metric developed by our group, the Nutrient Variety Index (NVI), which summarizes the distribution of nutrient groups within a diet. Adjusting for caloric intake and NVIs significantly improved clock performance, suggesting that nutrient composition modulates microbiome aging. This integrative approach enhances biological age estimation and has the potential to uncover microbial signatures of healthy aging. Our findings underscore the importance of diet in shaping aging trajectories and highlight the potential of microbiome-based clocks to uncover nutrition-linked aging pathways.

FAQs

What biological age estimation approach does the study use?

It develops aging clocks trained on shotgun metagenomics data that estimate biological age from the taxonomic composition of the gut microbiome.

Why are diet variables incorporated into the metagenomic clocks?

Because the microbiome is shaped by diet and linked to aging through host metabolism, immune regulation, and inflammation; adding diet information helps account for these influences.

What dietary metrics improved the clock performance?

Total caloric intake and the Nutrient Variety Index (NVI), which summarizes the distribution of nutrient groups within a diet.

Sep 28, 2026

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