Can Your Gut Microbiome Help You Age Slower?

Can Your Gut Microbiome Help You Age Slower?

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Killifish are small creatures with hundreds of species found in streams, ponds, and rivers across the globe. They’re beautiful fish, ranging in color from a flashy Amazon green to violet gray. At just an inch or two long, they’re often sold in pet stores as easy-to-handle algae eaters. 

These little critters live just a handful of years, though some species, like the African turquoise killifish, live only three-quarters of a year. They reach sexual maturity at a few weeks old. 

Their relatively short lifespan makes them the perfect subjects for life-extension studies. And they—or more specifically, their microbiome—might be a part of the answer to human life extension.

Can Your Gut Microbiome Help You Age Slower? Longevity Advice Header

In 2017, a group of German researchers wanted to see if the microbiome might hold some secrets to longevity. The experiment was simple: collect African turquoise killifish and “swap” the microbiome of younger fish with older ones. I say “swap,” because what these scientists really did was drain the middle-age fish of their own microbiome and then drop fishy guts from younger fish into sterilized water for the middle-age fish to digest. They then repeated the process vice-versa for older fish guts and young fish.

The killifish didn’t exactly delight in innards floating in their tank, but they did taste it to see whether or not it was food and spit it back out. That process was enough.

Strangely, there were no noticeable effects from young killifish nibbling on the microbiome of middle-aged killifish. 

But after six weeks, the middle-aged fish’s microbiome matched that of the younger fish. Incredibly, they also lived 37% longer than the control group. And they started acting like they had more time to live, exerting energy just as a young fish would. 

In human years, a finding like that would change the average age of death in the United States from about 80-years-old to 110. 

Of course, humans aren’t killifish. But this study, along with several others tying the microbiome to Alzheimer’s, certain cancers, and immune system degeneration in other animal studies, shows that microbiome research may hold an important key to living much longer than humans already do.

So what should you know about it?

What is the microbiome?

A image of a gut microbiome sample. Source:
Gut flora image from Wikipedia

There’s you, and then there’s all the stuff inside of you. 

By “stuff,” I mean your body’s resident viruses, bacteria, protists, fungi, parasites, archaea, and other little living creatures—the mix of harmless and harmful “microbiota” that colonize you entirety, from your mouth to your skin to your stomach to your lungs. There are a lot of these microorganisms in every human. Estimates range from a 10:1 to 1:1 ratio between your microbiota and your own human cells. 

The microbiome is the aggregate of all these microbiotas. It can weigh as much as five pounds. There is controversy over whether or not the microbiome should be considered a human organ

The gut has the largest concentration of these microorganisms, and the gut microbiome is the center of most microbiome research (though the skin microbiome has a good amount of interest as well). This article will focus on the gut microbiome. 

What does the gut microbiome do?

In healthy people, the gut microbiome is a colony of microorganisms that works as a part of your immune system, shields you from toxic food, and synthesizes some vitamins

The immune system is made up of lymphocytes, neutrophils, monocytes/macrophages, and molecules that all protect us from disease. It’s designed to respond to and ward off threats—particularly microbes. Our immune system doesn’t do that work alone. It evolved a symbiotic relationship with our gut microbiome, allowing “good” microbes to live peacefully in our digestive system. This mutualistic relationship is underscored by the fact that up to 80% of the body’s immune cells can be found in the gut

The exchange between immune system and microbiome is this: the immune system provides a stable environment for “good” microbes to flourish. In return, the microbiome supports immune cell development and helps coordinate immune responses. 

Its role in digestion can’t be understated either. Harvard’s School of Public Health provides a good example: 

Sugars like table sugar and lactose (milk sugar) are quickly absorbed in the upper part of the small intestine, but more complex carbohydrates like starches and fibers are not as easily digested and may travel lower to the large intestine. There, the microbiota help to break down these compounds with their digestive enzymes. The fermentation of indigestible fibers causes the production of short chain fatty acids (SCFA) that can be used by the body as a nutrient source but also play an important role in muscle function and possibly the prevention of chronic diseases, including certain cancers and bowel disorders. Clinical studies have shown that SCFA may be useful in the treatment of ulcerative colitis, Crohn’s disease, and antibiotic-associated diarrhea.

Of course, there can be problems with the gut microbiome being a determining variable in our digestion. 

For example, one study, published in Nature in 2019, found that the gut microbiome can affect how we digest a host of medications, including common treatments like Cardizem and Prozac. In other words, responsiveness to drugs that may be trying to help us can be hindered or rendered useless depending on our gut microbiome variability. Using this study, an article in Forbes argues, for example, that the differences in individuals’ microbiome may explain why some are far more responsive to some anti-depressants than others. 

Scientists are currently exploring the potential relationships between the microbiome and other bodily activities. For example, there may be ties between the microbiome and mental health, autism, and polycystic ovary syndrome (PCOS).

What determines what’s in our gut microbiome? 

Each individual’s DNA determines some of their gut microbiome—but only about 2%. That may be because humans get exposed to environmental factors pretty darned quickly. From the mother’s birth canal to her breast milk, infants start to develop the blueprint of their adult microbiome. The microbiome development process has been well documented from birth to age three and in adults, but there’s still a lot to learn about microbiome development in children.

Lifestyle and environmental factors account for the vast majority of microbiome differences. These factors include (but are not limited to):

The more diverse your microbiome, the healthier you are. While diet is often presented to be the deciding factor in your microbiome diversity, the story isn’t so simple. Studies show that nutrition can determine 5%-20% of your gut microbiome, which is enough to concern yourself with, but not enough to rely on as the sole determinant of your microbiome’s health. 

Notably—and one of the reasons we, as spanners, are talking about this—your chronological age significantly correlates with your microbiome’s diversity.

The gut microbiome and aging cycle
Aging and gut dysbiosis (a lack of microbe diversity) have a strong correlation. Source: Nutrition and healthy aging

So what can you do to monitor your microbiome to make sure it stays healthy and diverse? 

Gut health tracking companies: the microbiome and aging

There aren’t that many companies that offer gut health tracking. While looking at which businesses to recommend for this piece, I looked for companies that provide quantifiable ways of tracking microbiome health (not just “sensitivity” information), CLIA lab certification, and a sample report to analyze. Those search requirements led me to find just two companies offering actionable data: Psomagen and Viome.

1. Psomagen

Gut microbiome tracking company Psomagen
Psomagen Gutbiome+
  • Price: $129

Psomagen collects a DNA sample (from your spit) and a stool sample to determine your microbiome’s diversity. Using that information, the company generates a 50+ page report on both your DNA (check out our review of the best DNA tests if that’s what you’re more interested in) and your microbiome. 

Psomagen gives you a “diversity score” that ranges from 0-100, which is meant to represent how diverse your microbiome is. All scores benchmark you against other users. They split out further scores for things like “Your Mood & Bacteria” (strains that may affect your mental health), “Your Weight & Bacteria,” and “Starch Breakdown.” 

At the end of every section, Psomagen suggests adding or removing items from your diet to improve your score.

2. Viome

Viome Gut Microbiome Test
  • Price: $179

Viome collects a stool sample to analyze its users’ microbiome. That information feeds into a series of reports and an app (iOS/Android) to go with it. Viome sequences your microbes’ RNA to produce its findings. Viome claims to be “the only company that can identify and quantify the living microorganisms in your gut including bacteria, viruses, eukaryotes, archaea, and more at the species and strain level,” and I haven’t found any competitor able to challenge that assertion.

Viome gives you a score based on your performance compared to other users. Instead of a specific number, Viome only offers three possible outputs: “Needs Improvement,” “Average,” and “Good.” The company gives you this feedback in several categories like “Inflammatory Activity,” “Methane Gas Production Pathways,” and “Metabolic Fitness.” The results also include an extensive list of every active microbe Viome found in its analysis.

Viome also provides an extensive report on foods you should and shouldn’t eat based on your microbiome profile.

What other gut microbiome companies are worth considering?

Beyond Psomagen and Viome, I took a look at the following companies.

  • BIOHM (not included because their lab isn’t CLIA certified)
  • Thryve (not included because their lab isn’t CLIA certified)
  • Wellnicity (not included because they don’t offer a sample report)

Should you test your microbiome? 

I’m dubious that spanners can learn a whole lot from these tests.

There’s no “ideal” microbiome. We don’t even know what a “good” microbiome is. So I’m not convinced that trying to nudge your scores on Psomagen or Viome higher will necessarily mean that you’re healthier. 

Plus, the recommendations that they give you—like “eat more vegetables”—border on the obvious. Viome even writes,

“You may notice some foods that you are allergic or sensitive to in your recommended food lists. Err on the side of caution. If you know you have a reaction or dislike to a recommended food, please do not consume it. Foods are specifically chosen based on your unique microbiome rather than on allergies.”

You don’t need to spend hundreds of dollars to know not to eat food you’re allergic to… even if your microbiome might like it. 

Finally, and most aggravatingly, we’re not entirely sure how to change the microbiome or even how much we can change it. While fecal microbiota transplants (FMTs) show some promise in changing the microbiome, there’s not enough research on long-term impacts

And as for probiotics? The National Institutes of Health writes

A great deal of research has been done on probiotics, but much remains to be learned about whether they’re helpful and safe for various health conditions.

Probiotics have shown promise for a variety of health purposes, including prevention of antibiotic-associated diarrhea (including diarrhea caused by Clostridium difficile), prevention of necrotizing enterocolitis and sepsis in premature infants, treatment of infant colic, treatment of periodontal disease, and induction or maintenance of remission in ulcerative colitis.

However, in most instances, we still don’t know which probiotics are helpful and which are not. We also don’t know how much of the probiotic people would have to take or who would be most likely to benefit. Even for the conditions that have been studied the most, researchers are still working toward finding the answers to these questions. [Emphasis added]

In other words, the microbiome may hold some clues to longevity, but we’re unsure of how to quantify and/or manipulate it.

Tell me I’m wrong

In researching this article I found that the microbiome is overwhelmingly complex. Most research on it is recent—from 2015 on—and so is the interest in microbiome health. 

Caption: “Microbiome research” search volume over time

I’d love to learn more about the microbiome and microbiome testing from all of you. Did I miss a company worth reviewing? What else should we cover with the microbiome for longevity? 

Let us know in the comments!


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  2. Deborah

    Thanks for such a thorough study on all the research that is available. If you think about it, our language includes expressions for ‘gut feelings’ and ‘gut reactions’. Our gut may indeed be more in charge than we are truly aware.

    1. Rachel Burger

      Thanks Deborah! I love the analogy about “gut feelings.” There’s been a ton of great research about how the gut can impact your mental health and there’s so much more to be learned.

  3. Rob

    I’ll tell you a funny story on a different approach I took to help my son when his digestion became completely dysregulated.

    Following a long course of tetracycline for acne he started exhibiting anxiety and high sensitivity to environmental inputs and ADD. It was a perfect wave of, puberty, inadequate sleep and other factors. His digestion was screwed up and he lost a scary amount of weight.

    I took him to his PC doctor and then a gastroenterologist and realized they knew nothing. Literally nothing to help him. I was dumbfounded that traditional medicine was useless here. I took matters into my own hands and studied the issue like crazy. This turned me into a functional medicine believer (and, on my own behalf a biohacker).

    So over the course of a year I brought my boy back to good health with heavy diet manipulation (elimination diet), probiotics, numerous supplements and lots of sleep!

    In studies on probiotics I found the ones with the most research for helping the symptoms I was seeing. Most are pretty well known in the US but some were off the beaten path like Eastern European yogurt culture strains.

    His moods improved very quickly from the probiotics and over time his overall health improved from some or all of the other protocols, sleep being the one I believe helped the most.

    Now to the funny part. In my study of probiotics I came to the belief that taking probiotics as a pill was far from well understood and, in fact, a poor substitute for closer interaction with nature. Meaning, if you lived and worked on a farm I sincerely doubt you would need probiotics!

    Now, my kid is not a roll in the dirt kind of kid. He, like all his buddies, are computer game kids. He built his own powerful game computer and spends most of his time with that.

    But, he loves animals!

    So we decided to raise some ducks! Ordered the eggs, incubated them and ended up with two wonderful little ducks who live in our backyard.

    Ducks favorite thing to do is muck around in the dirt. And my son loves them and holds them and pets them and even kisses them on their beaks.

    I call them our duckbiotics.

    My boy stopped taking probiotics and has been very healthy now for years. He hardly ever gets colds any more either. Our secret weapon is duckbiotics.

    The moral of this story is go outside in nature. Dig in the soil, pick some plants, touch lots of stuff – then eat lunch without washing your hands.

    Or kiss a duck.

    1. Rachel Burger

      As someone who was raised with chickens and would much rather be romping in muck than stuck inside, this story absolutely delights me. My mother insists that eating a bit of dirt is great for kids. I’m inclined to agree with you entirely!

  4. Kirsi

    Great article! I live in Europe and was looking forward to find a company here. I came across a startup in Germany – Biomes ( Now waiting for my results! Can you check them out as well?

    1. Rachel Burger

      Hey Kirsi,

      Thanks for the recommendation! I hadn’t come across this company in my search but, at a glance, they look like they have some interesting stuff going on. Let me know what you think about their feedback on your microbiome! The more actionable, the better.

      I plan to do an update of this article and when I do I’ll see if I can verify their lab and take a close look at their sample report ?.

      1. Kirsi

        Hi Rachel,
        sorry for the delay in getting back. I finally got the report. It is easy to read and very broad. It is also actionable. They have recommendations what to do different or more/less. My results were actually very good, so no lot of recommendations. I still plan to repeat the test later to see if any changes!

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