How To Heal Your Aging Gut Microbiome

How To Heal Your Aging Gut Microbiome

You can heal your aging gut microbiome through diet, pure and simple. Learn why beneficial gut bacteria are essential for healthy aging, and how to feed them the right nutrition.

How To Heal Your Aging Gut Microbiome

Schematic representation of physiological, nutritional and immune targets of intervention generally identified for elderly people. MUFA: mono-unsaturated fatty acids; NK: natural killer cells. From

Updated 7/19/2022

As you might expect, your aging gut microbiome is like everything else in your body that changes as you age. This is worrisome, because gut microbes influence your overall health in many important ways.

What we want to do as we get older is to ensure that our gut microbiome is healthy, and that means we need to take steps to cultivate the good bugs and discourage the bad bugs from becoming dominant.

To back up a bit, the gut microbiota is the assembly of microorganisms living in our intestine. Their genomes are known as the microbiome. The correct composition and functionality of this microbiome is essential for achieving and maintaining health.

Aging is related to changes in the gut microbiota which are frequently associated with physiological modifications of the gastrointestinal tract, as well as, to changes in dietary patterns, together with a decline in cognitive and immune function — all together contributing to frailty.

What we need to do is to adopt nutritional strategies directed at restoring the microbiota through the use of probiotics, prebiotics or specific nutrients in order to counterbalance the microbial alterations that will occur in many of us as we get older.

So, let’s dig in and find out why a healthy gut microbiome is essential for our health, and what to do to ensure that we’ve got the right bugs in our system.


Your Aging Gut Microbiome

Last month (February, 2021) the journal Nature Metabolism published new research about the important effects the gut microbiome has on human health in a paper called Gut microbiome pattern reflects healthy ageing and predicts survival in humans. And although the researchers who produce such studies will say that it remains unclear precisely how gut microbes impact human aging, some things are very clear, worth knowing about, and doing something about.

For instance, as reviewed by New York Times reporter Anahad O’Connor, the Nature Metabolism study of 9,000 people between the ages of 18 and 101 years old established the following three significant findings.

(1) A gut microbiome that continually transforms as you get older is a sign of healthy aging

The gut microbes of people who age healthily change over time — the kinds of microbes that dominate the gut in early adulthood gradually constitute a smaller proportion of the gut microbiome as they get older (distinctly beginning by age 40), while the less dominant species begin to proliferate. Inversely, the composition of the microbiomes of unhealthy people remain unchanged, and they tend to die earlier.

(2) It’s unknown if changes in the gut microbiome helped to drive healthy aging or vice versa

The causality vs correlation issue is often at the center of scientific research on aging, and other biological research. For instance, it’s accepted that our bodies become more inflamed as we age (which spawned the term “inflammaging”), but whether it’s the biochemistry of aging that instigates chronic inflammation or visa versa remains to be determined.

In the case of the gut microbiome, it has yet to be determined if a shift in the kinds of gut microbes is sparked by the aging process of healthy individuals, or if the remix of the microbes in the gut microbiome leads to healthy aging.

In the study, people with the most changes in their microbial compositions had better health and longer life spans, as well as higher vitamin D levels and lower levels of LDL cholesterol and triglycerides (a type of fat in the blood). Moreover, these better-agers required less medications, and displayed better physical health as measured by faster walking speeds and greater mobility.

(3) Those that aged better due to a changing diversification of gut microbes had health-promoting metabolites.

In biochemistry, a metabolite is an intermediate or end product of metabolism that has a variety of various functions, such as stimulatory and inhibitory effects on enzymes, signaling, and interactions with other organisms.

Those who aged well in the study had higher levels of several metabolites in their blood that are produced by gut microbes, including indoles, which have been shown to reduce inflammation and maintain the integrity of the barrier that lines and protects the gut.

Indoles are part of plant-based compounds called phytonutrients found in onions, garlic, cabbage, broccoli and other cruciferous vegetables (cauliflower, kale, garden cress, bok choy, Brussels sprouts, and similar green leaf vegetables). In some studies, scientists found that giving indoles to mice and other animals helps them stay youthful; they’re more physically active, mobile and resistant to sickness, injuries and other stresses commonly expressed in old age.

Do you get the idea that diet plays a key role in keeping the right gut bugs thriving as you age?

If yes, you’re spot on!


Nutrition and The Gut Microbiome

On March 23, 2021, the Harvard Gazette published an article called In the gut microbiome, at least, it’s nurture, not nature. It begins with a statement that is gradually being proved to be incontrovertibly true:

“We are what we eat, and so are our microbiomes”

As I did above with the New York Times article, I’ll cut to the chase in summarizing this one. In her review of human evolutionary biologist Rachel Carmody’s recent study about the role of genetics vs environment on the gut microbiota, Harvard Correspondent Clea Simon makes two points.

(1) Genetics plays a small role on the microbiome as compared to environmental influences, such as diet

Dr. Carmody’s research on several different mammals, including humans, reveals that diet not only changes the gut biome, but does so fast. She said:

Within 24 hours of seeing a new diet, the gut microbiome looks and behaves very different[ly].

(2) The gut microbiome substantially impacts human health

The “internal environment” of the gut microbiome has been linked to a range of human diseases, including metabolic diseases like atherosclerosis and Type 2 diabetes, cancer, neurodegenerative diseases, and autoimmune disorders.  Dr. Carmody:

“In some ways, it’s great news that the gut microbiome is so sensitive to environmental conditions, as this means we can manipulate it more easily to improve human health,” Carmody said. “But it’s a double-edged sword, as all the changes our recent lifestyles have had on the microbiome may create opportunities for mismatch with human biology, which changes on much slower timescales.”

Dr. Carmody’s research findings are underscored by an earlier study published in 2017 called Nutrition and the gut microbiome in the elderly. What follows are two key findings of this study.

(1) Nutrition is a key component of aging healthily, but unfortunately, many older people eat too little (especially protein) and eat non-nutritious foods

As a consequence, of overall poor nutrition, the health of the gut microbiome of the elderly is often compromised.

Approximately 30% of people over 50 do not meet the Recommended Dietary Allowances (RDA) for protein, one of the main factors limiting muscle synthesis in the elderly. Another nutrient for which intake falls short of the recommended intake is dietary fiber, important for maintaining intestinal health and protecting against cardiovascular disease. Also, in almost every dietary survey conducted over the past few decades, older adults have inadequate intakes of iron, vitamin B6, vitamin B12, folic acid and vitamin D.

Protein-calorie malnutrition is one of the main causes of immune deficiency in elderly. An inadequate protein intake may lead to a decrease in the amino acids, compromising the immune system functioning. In addition, monounsaturated fatty acids, β-carotene and vitamins A, B6, C, and D, and bioactive compounds have been linked to a better immune response.

(2) Two common traits across individuals’ aging gut microbiomes are indigestible fiber and probiotics

Although there is wide variability among the microbiomes of individuals across various age groups and environments, two consistently common traits are that:

  • The levels of short chain fatty acids (SCFA, a type of fermented fiber, mostly), the main bacterial metabolites in the colon, are too low in the elderly to help maintain a healthy gut microbiome; and
  • Consuming foods and supplements rich in prebiotics and probiotics can be helpful.
Prebiotics Feed The Bugs

Prebiotics are a source of food for your gut’s healthy bacteria. They’re carbs your body can’t digest, and so they get right to your lower digestive tract, where they act like food to nourish healthy bacteria.

SCFAs are examples of a type of prebiotic. In her article What Are Short-Chain Fatty Acids And Why Should You Care?, science writer Leanne Edermaniger explains why you need to focus on consuming SCFAs for the benefit of your gut microbes — which means for your benefit as well.

“Short-chain fatty acids are produced by beneficial bacteria in your microbiome and they’re essential for your gut, body, and even brain health”, she says. SCFA can be made from all carbohydrates, but mainly from prebiotic dietary fibers that feed beneficial bacteria.

Five good prebiotic foods you can eat are:

  1. Chicory Root
  2. Dandelion Greens
  3. Jerusalem Artichoke.
  4. Garlic
  5. Onions

Here are 14 more.

Probiotics Are the Bugs

Probiotics are bacteria, the beneficial microbes that you want in your gut. Yogurt, kefir and sauerkraut are three common probiotics, among many. And, of course, there exists a wide variety of probiotic supplements that millions of us use.

That said, the efficacy of probiotic supplements is questionable, but probiotics are typically well tolerated by the human body, so they’re unlikely to cause any harm, except perhaps to your wallet. (The good ones are expensive.)

One of the biggest reasons why many probiotics aren’t very effective is that they only contain a small number of different strains of bacteria, whereas the healthy human gut contains thousands of different strains, and trillions of individual bacteria.

If you’d like to try probiotics, I suggest you try one or more of the following three that are often touted by biohackers focused on optimizing gut health.

P3-OM Probiotic by BiOptimizers

P3-OM probiotic is a patented blend that contains a strain of bacteria called L. plantarum that’s particularly effective at eliminating gut pathogens.

Primal Defense Ultra (soil-based probiotic)

Garden of Life Whole Food Probiotic Supplement, Primal Defense Ultra Ultimate (whew) is a soil-based probiotic.

Soil is where humans typically come into contact with many of the bacteria that form our biome and protect us from various ills. For instance, children who grow up on farms are exposed to a wide variety of bacteria through their environment, and research has shown that they display greater resistance than other children to conditions such as asthma.

Biogaia Gastrus L. reuteri 

Lactobasillus reuteri is a unique bacterial strain found in our gut biome in that it lives in the upper intestine (most of the strains in our gut biome occupy our lower intestine), is one of the few bacteria native to our gut, and can be found in the digestive systems of many vertebrate animals.

L reuteri offers many health benefits. It boosts the immune system by lowering inflammatory cytokines and improving T-cell function. It heals “leaky gut” by repairing the holes in the gut lining that cause this condition, and it kills pathogenic “bad” bacteria by creating antimicrobial compounds.

L reuteri also confers a particularly unique benefit — It boosts the neuropeptide oxytocin. Oxytocin is referred to as the “love hormone,” because our bodies release it when we engage in pleasurable activities.

Biogaia Gastrus L. reuteri tablets contain two of the most well-researched strains of L. reuteri, but they’re on a patent, which means that if you want these strains, you’ll have to buy it, as opposed to trying to ingest them in food.


Test Your Microbiome

The viome microbiome test reveals the precise food and supplements you need to restore your microbiome health.

There are several at-home tests you can take provided by various companies.

You buy the test, they send you their kit, you take a swab of, um, the “material”, place it in a vial and send it off to be analyzed.

Viome appears to be among the best companies that offer microbiome tests. Three tests are offered by Viome:

Full Body Intelligence™ — Food + supplement recommendations determined by over 50 health scores and based on an analysis of your gut microbiome, human cells, and oral microbiome.

Health Intelligence™ — Food + supplement recommendations determined by over 30 health scores and based on an analysis of your gut microbiome & human cells.

Gut Intelligence™ – Food + supplement recommendations determined by over 20 health scores and based on an analysis of your gut microbiome.

Note: I have no personal experience with Viome.


Your Takeaway

When you’re feeding yourself, think about your microbes too, because, in effect, they are you —  from a cellular perspective there are more than them in you than human cells.

Remember this:

  • The quality of your aging gut microbiome closely tracks the overall health you experience as you age.
  • You can improve the well your aging gut microbiome supports your healthspan — those years over which you’re healthy — by feeding it the right nutrients.
  • No matter how old you are, feed your gut microbiome foods and supplements rich in fiber — such as prebiotics — as well as probiotics.
  • To ensure your gut microbiome is supporting your health, as opposed to encumbering it, get it tested by Viome..

There’s much more to know about the importance of your microbiome and how it can either support or diminish your health. If interested, check out my posts on this topic.


Last Updated on February 7, 2024 by Joe Garma

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Joe Garma

I help people live with more vitality and strength. I'm a big believer in sustainability, and am a bit nutty about optimizing my diet, supplements, hormones and exercise. To get exclusive Updates, tips and be on your way to a stronger, more youthful body, join my weekly Newsletter. You can also find me on LinkedIn, Twitter and Instagram.

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