Researchers here report on their assessment of age-related changes in human skin, oral, and gut microbiomes. They find that the skin microbiome is a better marker of chronological age, which might also be taken as indicating that it is a worse tool for measuring biological age. That adherence to chronological age is, after all, observed despite differences in the pace of aging that exist between individuals. A good biomarker of aging is one that reflects the burden of damage and consequent mortality, and therefore will measure a higher age in someone more burdened, rather than only correlating with the chronological progression of time.

Human gut microbiomes are known to change with age, yet the relative value of human microbiomes across the body as predictors of age, and prediction robustness across populations is unknown. In this study, we tested the ability of the oral, gut, and skin (hand and forehead) microbiomes to predict age in adults using data combined from multiple publicly available studies, evaluating the models in each cohort individually.

Intriguingly, the skin microbiome provides the best prediction of age (mean ± standard deviation, 3.8 ± 0.45 years, versus 4.5 ± 0.14 years for the oral microbiome and 11.5 ± 0.12 years for the gut microbiome). This also agrees with forensic studies showing that the skin microbiome predicts postmortem interval better than microbiomes from other body sites. Age prediction models constructed from the hand microbiome generalized to the forehead and vice versa, across cohorts, and results from the gut microbiome generalized across multiple cohorts (United States, United Kingdom, and China).

Interestingly, microbial taxa enriched in young individuals (18 to 30 years) tend to be more abundant and more prevalent than taxa enriched in elderly individuals (older than 60 yrs), suggesting a model in which physiological aging occurs concomitantly with the loss of key taxa over a lifetime, enabling potential microbiome-targeted therapeutic strategies to prevent aging.