There are many ways to measure age. Chronological age—how long one has been alive—is the most straightforward. But this doesn’t account for factors such as diet, genetics, physical health, or lifestyle. This is why many researchers turn to biological age as a better predictor to the state of the body. One approach involves looking at the trillions of microbes residing in the gut.
In 2015, Mauna Dasari, then a microbial ecology graduate student at the University of Notre Dame, applied this approach to baboons. Because baboons have similar development patterns to humans, they are a good model for understanding microbiome age in people. Dasari sifted through thousands of fecal samples from wild baboons looking for gut microbiome patterns that could be used as a predictor for age. Dasari and her team used this data to build a microbiome clock that predicted baboon age with a median error of about two years, which outperformed the median error of six to 11 years of existing microbiome clocks based on human data.1–3 Insights from this work, reported in eLife, can help researchers find new ways to promote healthy aging and extend both lifespan and healthspan.
For this study, Dasari extracted DNA from nearly 14,000 samples collected from 479 wild baboons from the Amboseli Baboon Research Project, a long-term study of wild baboons in East Africa. She called this work “a happy accident” since these fecal samples were initially collected over 14 years for a hormone project that the lab was involved in. The team analyzed the microbes using computational and machine learning algorithms. To estimate chronological age, this microbiome clock simultaneously analyzed 1,440 microbiome features. The researchers observed shifts in microbial abundance across life stages. For example, certain microbes became more prevalent with age while others were abundant at early or late stages of life. In addition, microbiomes in early life and in old age were more diverse than during early adulthood.
Because Dasari’s samples came from the same baboons tracked over a long time period, she had data points covering developmental milestones and environmental conditions, such as drought, that fluctuated over the seasons. Using their tool, Dasari and her colleagues looked into how these demographic and socio-environmental factors affected age predictions. They found that specific factors could cause the microbiome age to deviate from the chronological age. For example, baboons with microbiomes that appeared older than expected tended to be male, correlating with the trend that male mammals age faster than female mammals.4 Higher ranking baboons also appeared old for their age, while lower ranking baboons had younger microbiomes, possibly due to differences in access to food. Female baboons showed signs of accelerated microbiome aging during the dry season compared to the wet season, likely due to nutritional stress.
Dasari, now a grants officer at California Academy of Sciences, found that socio-environmental factors, such as rank and sex, skew microbiome age in wild baboons.
Mauna Dasari
Lastly, the researchers found that microbiome age did not predict maturation milestones or survival. Because of the transient nature of gut microbes, the microbiome age only reflected current, and not past, conditions. In the future, the team hopes to correlate microbiome age with other features of biological aging and see how gut microbes could predict the total lifespan and survival of an individual.
“I think it’s a very impressive endeavor,” said Baptiste Sadoughi, a primatologist at Arizona State University who was not involved in the study. “The amount of work, both lab work and then analysis, that went into this paper is actually quite unique for a wild animal system.” Sadoughi noted that most wildlife research includes 1,000 to 2,000 samples at most.
Since gut microbiomes differ between species, this microbiome clock may not be translated directly to humans. To create a more universal microbiome clock, the team would need to identify consistent microbiome features across species. Despite this limitation, Dasari said these studies can help researchers understand how microbiomes change as organisms age. “There are a lot of different ways that our body shows age,” said Dasari. “Having a diverse diet and interacting with people and other things are helpful for lessening those effects of aging.” She remarked that a diverse microbiome helps one’s body adapt to whatever is coming.
Due to shifts in the microbiome during aging, manipulating the microbial community could promote healthy aging. Dasari believes fecal transplants would be a better way than transient probiotics to influence the gut microbiome more broadly. Previous studies have found that fecal transplants from young mice into older mice reversed signs of aging.5
“The fact that we can go back in our freezers and use 14 years’ worth of baboon poop that we had collected to understand a whole new aspect of aging, or something that could eventually be clinically relevant, is really amazing,” Dasari said.
- Dasari MR, et al. Social and environmental predictors of gut microbiome age in wild baboons. eLife. 2025;13:RP102166.
- Galkin F, et al. Human gut microbiome aging clock based on taxonomic profiling and deep learning. iScience. 2020;23(6):101199.
- Huang S, et al. Human skin, oral, and gut microbiomes predict chronological age. mSystems. 2020;5(1):e00630-19.
- Lemaître JF, et al. Sex differences in adult lifespan and aging rates of mortality across wild mammals. Proc Natl Acad Sci U S A. 2020;117(15):8546-8553.
- Parker A, et al. Fecal microbiota transfer between young and aged mice reverses hallmarks of the aging gut, eye, and brain. Microbiome. 2022;10(1):68.
