New Research: How Our Gut Microbiome Changes as We Age

Sam Westreich, PhD

Loss of stability, greater personalization — and what we can do to stay healthy

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Still captivating on the outside, but how's that microbiome looking?Photo by Ravi Patel on Unsplash

Starting this article off with some bad news for you all: as you get older, you will age. There is no amount of superfood, Manuka honey, exercise, or mystical buy-it-off-the-sketchiest-sites-on-the-internet pill that will keep you from aging.

Until some billionaire-funded startup comes out with the anti-aging pill (and don’t hold your breath), the best thing that we can do is focus on aging gracefully. Yes, there will be some deterioration and breakdown, but wouldn’t you rather be one of the senior citizens running 10k races, rather than one who is confined to a hospice bed?

We can take care of our weight with smart diet choices. We can strengthen our body with regular exercise. But what about our gut microbiome?

A recent paper, focusing on aging microbiomes in rhesus macaque monkeys, gives some insights into how our partner bacteria in our digestive tract will change, as we do.

TL;DR for anyone who is too busy to read the remaining 5 minutes of this article:

  • Over our lifespan, the types of bacteria in our gut do change; we see more rare species appear, and the situation can become less stable.
  • Changes in the microbiome are likely due to aging itself, not due to changes in our lifestyle as we get older.
  • These changes can put us at greater risk of disease, but it’s not a guaranteed thing, and we may want to focus on frailty — but not the level of rare species.

After reading that, you definitely don’t want to stop reading, do you? Me neither — it’s fascinating stuff! Let’s dive in and see what we can learn.

The Leopard Can Change His Shorts, and You Can Change Your Gut Microbiome

We are born with many factors locked, out of our control. We can temporarily change our hair color, but it grows back in that original color. We can’t change our DNA to remove mutations that put us at risk of getting inherited diseases. Even our height potential is mainly due to genetics, and we can’t change it once we’re past puberty.

But our gut microbiome? That’s a lot more malleable, and a lot more in our control.

For those who aren’t familiar, our gut microbiome is the collection of trillions of bacteria, living inside our intestinal tract in (relative) harmony with us. We provide them with food and an environment, and they help break down nutrients, create vitamins, and keep our immune system trained and fit without overreacting to everyday bugs.

Our gut microbiome is made of lots of different species of bacteria, and the blend is unique for each of us, like a messier, smellier version of a fingerprint. And while most of us tend to have fairly stable gut microbiomes day-to-day, that’s because our lives are pretty stable, day-to-day.

Make big changes in your life? Switch to a vegan diet, or decide to move from Moscow to Calcutta? Your gut microbiome is also going to change. Even smaller lifestyle choices, like eating less meat or processed foods, or moving in with a significant other, will alter your gut microbiome.

And so does getting older.

Interestingly, the changes in our microbiome as we get older make us look more different from one another, not more similar. But why? There are a number of possible reasons:

  • When we are young, we are mixing with others more (school, family), keeping our microbiomes more similar. As we get older, we are more on our own, and our microbiome becomes more different.
  • As we age, our lifestyles become more different, which could drive microbiome differences.
  • Older folks tend to be taking more medication, which can impact and alter our gut microbiome.
  • Many diseases will have an impact on the gut, especially if they significantly affect our lifestyle. (Consider a disease that weakens your immune system long-term, or the drugs taken after receiving a transplant, or an injury that prevents you from vigorously exercising.)

All of these are just hypotheses, and it may be next to impossible to truly measure the impact factor of each one on our gut microbiomes (in part because it’s very hard to get an ethics board to sign off on withholding medication from people to study how their gut changes).

But the net result: our microbiome changes as we get older, and it tends to make us more unique and different from the microbiomes of others.

If we kept the same lifestyle, would our microbiome stay the same?

Above, it's noted that there are a number of lifestyle factors that may influence our microbiome as we grow up, leading to changes. We obviously cannot eliminate all changes in our lifestyle; no one lives exactly the same life as an adult as they did when they were a child.

But if we could eliminate lifestyle factors, would that keep our microbiome stable, looking like the bacteria of someone twenty years younger?

The answer, it seems, is no — our microbiome also changes as a direct result of getting older. This is supported by the article linked above, looking at wild rhesus macaques.

Rhesus macaque monkeys, as they grow up, will stay in the same troupe, interact with largely the same individuals, will continue to be in the same environment and exposed to the same bacterial sources. If age-linked microbiome changes were driven by lifestyle changes, we’d see more similarity in monkey microbiomes as they grow up… but their microbiomes also go through changes as they age.

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A part of Figure 3 from a study on baboons, showing that older animals have greater heritability in their microbiomes.Source: NCBI

We also see that, as primates age, their own genetics have a greater and greater impact on their microbiome composition. Evidence suggests that your body has a natural preference towards certain microbes, and moves more strongly in that direction as you get older.

And this may be a good thing! This personalization of our gut microbiomes as we age may help to maintain stability and balance between host and bacteria. Perhaps these bacteria are the ones best suited to supporting an older body.

Furthermore, these patterns seem linked with healthy aging; in a large study of more than 9,000 people, the ones who were the healthiest saw a depletion of core bacteria, and a greater uptick in rarer species.

Microbiome frailty, not rare species, is what we should measure as we age

There are some risks to an increase in rare species as we get older, risks to moving away from the core types of microbes that are present in most younger humans.

Reduced core populations mean that new niches are available in our gut, which could be capitalized on by pathogens. It may be easier for us to get stomach bugs, or we may lose bacteria that provide important healthy functions for us, such as synthesizing short-chain fatty acids (SCFAs).

But as shown by the large human study linked a few paragraphs above, greater diversity does not guarantee that we’re at a greater risk of disease. The presence of these rarer species of bacteria may prove to be a boon if they bring new benefits, and they could take over many of the roles and functions that were previously held by the young, core microbiome.

Thus, when we’re trying to gauge someone’s health based on their microbiome — or if we’re trying to improve their microbiome to keep them healthier as they age — we likely want to focus on capability, not on diversity alone. It’s okay for our microbiome to pick up more rare species as we age, as long as those species can still meet our needs.

And what should we do, to get the “right” microbiome as we get older?

First, we should acknowledge that some of this is out of our control, and will be determined by our genetics.

Despite this, we can still work on improving our gut microbiomes through lifestyle choices — high fiber diets, consuming more unprocessed foods and fermented foods, and avoiding highly processed foods that can cause less desirable species to grow.

And as we get older, typical probiotics may be even less effective, given our greater bacterial diversity. A stronger focus on prebiotics and overall healthy diet is a safer bet than trying to find the perfect probiotic to add.

In summary: our guts change, but we should embrace it

It’s widely accepted among scientists that our microbiome changes as we get older. It’s probably a good thing; our microbiome is always shifting to meet our body’s precise conditions, and those change as our bodies get older.

When it comes to aging, it seems that the gut microbiome is more reactive to our body, rather than driving our body to get old. We shouldn’t be looking to our microbiome to be a Fountain of Youth, but should work to make sure it meets the needs of our aging body, providing the inputs we need to keep ourselves healthy at any age.

Results from our monkey relatives suggest that shifts in the gut microbiome are inevitable. Our best bet is to focus on embracing the rise in diverse, rarer species, providing the right lifestyle and inputs to ensure that the newcomers still fulfill the tasks (immune modulation, SCFA synthesis, etc.) that we want to see.

Here’s to all the newcomers, the exotics, the unusual bacteria that will arrive in our guts as we age — welcome, one and all!

Except for C. difficile. Stay out, and don’t show your face around here!

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A microbiome scientist working at a tech startup in Silicon Valley, Sam Westreich provides insights into science and technology, exploring the strangest areas of biology, science, and biotechnology.

Mountain View, CA
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