The Microbiome’s (Contested) Role in Longevity

Written by Emma Loewe: Writer, author, and editor of Cultured. Her writing explores the intersection of nature, climate, and human health. Emma is the author of “Return to Nature” and “The Spirit Almanac.”
Reviewed by Jennie O’Grady: Senior SciComms Specialist at Seed Health

The Seed Digest

• Our gut microbiome seems to lose some beneficial bacteria as we age, which may make us more susceptible to disease.
• Researchers are now exploring whether supporting gut diversity through diet, lifestyle, and targeted interventions like probiotics could help us live longer, healthier lives.

While we tend to obsess over the visible signs of aging, most of its impacts are unseen. Some are downright microscopic. 

“As part of the aging process, we know that there are many things in our body that change—and the microbiome is no different,” says Eran Segal Ph.D, a computational and systems biology researcher at the Weizmann Institute of Science and member of Seed’s Scientific Board. 

Dr. Segal’s Human Phenotype Project studies these changes with unparalleled precision. Over the next 25 years, this large-scale study will track the health data of more than 10,000 individuals (ages 40–70). Dr. Segal and his collaborators take a “multi-omics” approach, meaning they collect participants’ genetic, metabolic, and immune markers and sequence their microbiomes to form a complete picture of how their entire body—down to its resident bacteria, fungi, and other microscopic organisms—ages over time. 

Using this expansive dataset, they can make distinctions between a person’s chronological age (how much time has passed since their birth; how old their body actually is) and their biological age (how much physiological function they have lost; how old their body acts like it is).¹ Fascinatingly enough, the gut microbiome seems to be a key mediator between the two.

How the Gut Microbiome Changes With Age

As our bodies undergo senescence (the biological process that contributes to growing old), our cells accumulate DNA damage, our metabolic rate decreases, our blood vessels lose elasticity, and our immune system weakens.^2,3,4,5

The community of microorganisms in our guts evolves, too. The exact “microbiome signature” of aging is still a mystery, but compared to younger individuals, older adults seem to lose some bacterial diversity or experience shifts in microbiome composition, with certain beneficial species becoming less abundant.^5,6 

Without these beneficial bacteria, the gut has fewer built-in defenses and is more susceptible to being overtaken by harmful species. The ensuing state of imbalance (dysbiosis) is associated with various age-related issues, including increased inflammation, reduced immune function, and higher disease susceptibility.⁵ 

Dr. Segal and his collaborators use this signature of aging to predict a person’s chronological age by looking at the gut microbiome. 

“The predictions are not perfect,” he caveats, “meaning that for some people, the model thinks that their chronological age is older than their real age.” In cases like these, the microbiome is in a sense aging faster than the rest of the body.

Why would this happen? Some older people experience drastic decreases in their appetite and intestinal function, which could be one cause.⁷ This reduces their ability to absorb nutrients from their food and cuts off an essential fuel source for beneficial bacteria in the gut.

Sex differences could also play a role. In one recently published study, Dr. Segal and his team focused on pre-menopausal and post-menopausal women of the same chronological age. Their findings revealed that those who had undergone menopause had a significantly older biological age, suggesting that hormonal shifts may accelerate certain parts of the aging process.⁸

Environment matters too.^5,9 One study found that those who lived in a long-term residential care facility tended to have less microbial diversity than those who resided in a neighborhood community.¹⁰ 

Clearly, no two microbiomes age exactly the same way. Like wrinkles, grey hairs, and laugh lines, microbial shifts are personal and likely caused by many factors. 

This leaves Dr. Segal and other microbiology researchers with a potentially groundbreaking question: Does having a “younger” microbiome increase one’s longevity, and lower their risk of dying from age-related disease?

Inside the Guts of “Super-Agers”

Getting older doesn’t always need to mean getting sicker, as shown by research on “super-agers,” or people who reach old age while remaining physically and mentally fit.

Early research on centenarians shows they may actually have more bacterial diversity in the gut than younger adults, replete with a highly personalized array of species.^11,12 This suggests that the microbiome continues to evolve as we age, ideally becoming more unique to us with each passing decade.

Bacteria that often decrease in the elderly, such as strains of Christensenella (associated with metabolic health) have been found in higher amounts in semi-supercentenarians (105–109-year-olds). Bifidobacterium (important for digestion and immune support) and Akkermansia (linked to gut barrier health and lower inflammation) also seem to be relatively abundant in those who reach very old age.^5,13,14

These shared bacterial fingerprints suggest that specific microbes, or the balance of specific microbes, might have anti-aging properties. But we need more research to be sure.¹³

What This Means for Your Longevity

To recap, we know that the gut microbiome changes as we age. Some of these changes are associated with health and longevity; others with disease.

However, it’s not clear whether microbial shifts are causes of age-related declines or merely consequences of them.

“I think the key question is between correlation and causality,” Dr. Segal says. “The fact that we see changes… a skeptic could say ‘Sure—but those are a byproduct of the aging process and if you were to alter the microbiome it would not have an effect.’ I think it’s a fair criticism.”

To untangle cause and effect, researchers like Dr. Segal are starting to adjust participants’ microbiomes to take on “younger” qualities and then studying how these changes impact their risk of developing age-related issues. 

“It still remains to be seen and proven that such an intervention will also improve overall health,” Dr. Segal says. However, decades of work in the microbiology field make him suspect it will. 

He points to the fact that certain bacteria in the gut make metabolites (such as short-chain fatty acids) that get circulated in the bloodstream and help regulate inflammation.¹⁵ It stands to reason, then, that adjusting the production of these metabolites would also impact the inflammatory response—a key pacemaker of aging. 

“By altering the microbiome and making it ‘younger,’ we can probably affect the circulating metabolites of people to more resemble somebody who’s younger—and that might have health benefits,” Dr. Segal says. 

This could have massive implications for human health and longevity. “In the future, we may be able to ‘treat’ our microbiomes in a personalized, targeted way to promote healthier aging and potentially extend lifespan,” says Jennie O’Grady, a Senior SciComms Specialist at Seed.

Such treatments could include diet modifications, fecal transplants, and probiotic supplements that contain bacteria that typically decline with age, such as Bifidobacteria.

Your Healthy Aging Gameplan

In the not-too-distant future, you may be able to pop into your GP for an influx of anti-aging bacteria. In the meantime, the National Institutes of Health (NIH) has found that the following five key habits can add healthy years to one’s life.¹⁶ It’s no surprise that many of them are also known to promote a more diverse and resilient gut microbiome too:

1. Maintain a healthy diet: Get the daily recommended amounts of vegetables, fruit, nuts, whole grains, polyunsaturated fatty acids, and omega-3 fatty acids. Limit red and processed meats, beverages with added sugar, trans fat, and sodium. 
2. Get regular physical activity: The NIH recommends at least 30 minutes of moderate to vigorous physical activity a day, or 3.5 hours a week.
3. Watch your alcohol consumption: Low-risk alcohol consumption is typically defined as one drink or less per day for women or two drinks or less per day for men.¹⁶
4. Don’t smoke: That encompasses cigarettes, pipes, and cigars.
5. Maintain a healthy body weight:  The NIH defines “low-risk” body weight as a BMI in the 18.5 to 24.9 kg/m2 range.

Each one of these five healthy lifestyle factors significantly lowers the risk of total death, death from cancer, and death from heart disease according to NIH research. 

Naturally, some aspects of lifespan are beyond our control. Genetics play a role in how long we live (but research suggests they account for only about 25% of the equation), as does the environment we reside in and the healthcare we have access to.¹⁷ 

Frequently Asked Questions (FAQs)

How does the gut microbiome change with age?

The latest microbiome sequencing research tells us that as we get older, our gut microbiomes may become less diverse and less abundant in certain beneficial bacteria. But this isn’t the case for everyone: Some centenarians have more bacterial diversity in the gut than younger adults. 

How does the microbiome affect aging? 

Researchers are still trying to figure that out. It’s possible that maintaining a more diverse microbiome high in certain species can actively reduce the risk of age-related issues and diseases, but they can’t say that for certain just yet.

What gut bacteria is associated with longevity? 

The longest-lived people among us tend to have diverse microbiomes that are high in bacteria such as Akkermansia, Bifidobacterium, and Christensenella. It’s unclear if these microbes are a driver of longevity or a result of it. 

The Key Insight

Aging may be inevitable, but how we age could be more flexible than we think. The gut microbiome is emerging as a potential player in longevity—one we can nurture through diet, lifestyle, and targeted interventions like supplements.

While researchers work to untangle correlation from causation, one thing is clear: caring for the microbiome might just be one of the most promising ways to care for our future selves.