6 Signs of an Unhealthy Gut, 7 Likely Causes & the Best Foods for Gut Health

When the ancient Greek father of medicine, Hippocrates, said “All disease begins in the gut,” he was probably right. Poor gut health has been linked to a broad range of diseases and health conditions, from depression to diabetes, cancer to obesity, and autism to autoimmune disease. Search the medical literature and you’ll probably find links between the gut and any illness you can imagine.

So—all the world’s health issues solved, right? Not exactly.

Gut health is one of those topics that gets more complicated the deeper you go. The more you read about gut bacteria, the less you realize you know and the less you realize anyone knows, even the researchers. It’s infinite onions, all the way down. The layers never stop, and exposing them eventually makes you want to cry. (Speaking of which, onions are actually a very good food for gut health).

All that said, the scientific community is honing in on the signs and symptoms of an unhealthy gut. We know how to heal an unhealthy gut, or at least improve gut health. An incredible amount of research has determined the best foods for gut health, and we know the worst foods for gut health. We understand that gut health comes down to supporting healthy gut bacteria and avoiding leaky gut. Top-down micromanagement might not work yet, but big-picture, bottom-up intervention does.

Gut Inflammation: Signs of an Unhealthy Gut

Some of the signs are obvious. Others are more pernicious. Not all of these will apply to someone with unhealthy gut bacteria or leaky gut, but some will.

Chronic Constipation, Bloating, and/or Diarrhea

Everyone gets a little constipated now and then. We’ve all had the runs, and we’ve all felt bloated after a particularly large meal. As long as these conditions are acute—as long as they’re brief and transient—they don’t indicate any serious gut inflammation. It’s when constipation or diarrhea or bloating endure and become chronic conditions that you should pay close attention. Chronic constipation, bloating, and diarrhea are signs of an unhealthy gut biome.

Obesity or Overweight

Although the connection hasn’t been established as causal, there is a consistent and significant association between obesity/overweight and poor gut health. If you are obese, you very likely have room to improve the health and function of your gut.

Food Intolerances and Allergies

If the integrity of your gut is compromised due to excessive gut inflammation or missing gut bacteria, undigested components of the foods we eat can slip past the intestinal barrier and into our bodies where they trigger an allergic reaction. This appears to be a necessary step in the development of a food allergy, and a 2011 review concluded that an overly leaky gut facilitates this transportation and leads to the inducement of allergy.

Depression and Anxiety

Researchers have long puzzled over observations that mental health conditions like depression and anxiety often present with common gastrointestinal complaints like constipation and diarrhea. It’s not just circumstantial: gut bacteria produce large amounts of neurotransmitters like serotonin, interact with neural pathways involved in anxiety and depression, and help form the gut-brain axis.

Animal studies show that replacing the gut bacteria of anxious mice with gut bacteria from fearless mice makes the anxious mice more brave, while giving bold mice bacteria from anxious mice makes them more anxious. In human subjects, a probiotic supplement (containing L. helveticus R0052 and Bifidobacterium longum R0175) reduces measures of anxiety and depression, and by some accounts, 35% of depressed patients have leaky gut.

Skin Problems (Eczema, Psoriasis)

In the last section, I told you about the gut-brain axis. There’s also a gut-skin axis: a constant interplay between the health of your gut and the health of your skin. People who have eczema are also likely to have leaky gut, while psoriasis patients show clear signs of unbalanced gut bacteria.

Autoimmune Disease

One of the world’s premier autoimmune disease researchers, Dr. Alessio Fasano, considers poor gut health a necessary pre-condition for all autoimmune diseases. It’s a similar situation to the allergy/intolerance issue: a leaky, inflamed gut allows outside proteins and other food components into the body, the immune system mounts an immune response to deal with the invaders, and this response gets out of hand and redirected toward the body’s own tissues.

Okay, so how does it all happen? Apart from food, which I’ll get to later on…

What Causes an Unhealthy Gut?

There are many potential causes of poor gut health.

Stress

Stress can directly induce leaky gut (PDF) and stress can take many forms, as we all know. Bad finances, marital strife, unemployment, too much exercise, lack of sleep, extended combat training, and chronic under-eating all qualify as significant stressors with the potential to cause leaky gut, especially chronically and in concert with one another.

Poor Sleep

Sleep is restorative, and restorative sleep means you’re lowering stress and improving gut health. If your circadian rhythm starts to shift, starts getting a little dysfunctional, your gut health soon follows.

Inadequate Dirt Exposure

Too sterile an environment causes too sterile a gut. We are made to spend time in nature, feet and hands getting dirty, exposed directly to the natural soil teeming with trillions of bacteria. We’re meant to eat produce directly from the ground, and nature didn’t intend for us to always wash it. (That said, if you didn’t grow it yourself, it’s best to wash your produce.) Exposure to healthy soil may even bestow upon us anti-anxiety gut bacteria—gut microbes that actually make us less anxious.

Not Enough Exercise (or Too Much)

Exercise has been shown to directly improve gut function, increasing the production of beneficial short cain fatty acids by gut bacteria. When you stop training, the gut benefits cease.

Just don’t do too much. An acute bout of intense training causes a transient rise in leaky gut that subsides and even improves several hours after the session. This is fine. This is normal. This is adaptive. But if you start stringing together intense training sessions without adequate rest, the exercise becomes a chronic stressor and the transient rise in leaky gut starts looking more permanent.

Too Many Antibiotics

Antibiotics are great at killing pathogenic bacteria attacking you, but they also tend to be indiscriminate. They do not distinguish between friendly bactieria and harmful bacteria in your gut biome. The broad spectrum antibiotics we commonly take also wipe out the bacteria living in our guts, leading to gut bacteria imbalances and poor gut function.

After addressing the major causes of poor gut health, is there anything you should avoid eating? Are there foods you should focus on eating to improve your gut health?

What Are the Worst Foods for Gut Health?

The worst foods for gut health are no surprise to regular readers of this site, but that doesn’t make them any less important to avoid.

Refined Carbohydrates

When we eat refined carbs like grains or sugar, glucose is immediately released into the digestive tract, increasing the concentration of carbohydrate available to your gut biome. This concentrated influx of dense carbohydrate into the gut produces an inflammatory microbial population that increases production of bacterial endotoxin and increases leaky gut. Meanwhile, the lack of prebiotic fiber means your beneficial gut bacteria have no food to consume.

Gluten

Gluten, a protein found in wheat, barley, and rye, causes your body to release zonulin—a chemical messenger that tells your intestinal junctions to open up. Many people can handle this increase in zonulin, but if you’re already suffering from poor gut health or are sensitive to gluten, the zonulin response may be strong enough to trigger leaky gut.

What Are the Best Foods for Gut Health?

• Fermentable fiber
• Chocolate
• Berries
• Red wine
• Skin, bones, and broth
• Fermented foods
• Resistant starch
• Meat
• Pistachios
• Onions, garlic, and leeks

Fermentable fiber

Without food, your gut bacteria suffers. And the best food for your gut bacteria is fermentable fiber, found in many different plants. Asparagus, carrots, Jerusalem artichokes, and alliums like garlic and onions are your best bet.

Chocolate

Besides being delicious, high-cacao dark chocolate is an excellent source of prebiotic fiber (fiber your gut bacteria can consume) and prebiotic polyphenols (plant compounds that also feed your gut bacteria).

Berries

Name a berry and it’s been shown to improve gut health. Strawberries feed the gut biome and improve the gut function of diabetic mice. Blackberries restore gut health and trigger neuroprotective effects. Eating blueberries leads to compositional changes to the gut bacteria linked to improved metabolic health. And black raspberries have been shown to cause “anti-inflammatory” bacterial profiles in the gut.

Red wine

Although too much alcohol can have a detrimental effect on gut health, moderate amounts of red wine polyphenols may have prebiotic effects on the gut bacteria.

Skin, bones, and broth

Skin, bones, and broth offer gut health benefits in a number of ways. First, they provide “animal fiber,” collagenous and gristly substrate that our gut bacteria can digest and prosper on. Next, they offer ample amounts of gelatin, which can help repair damaged gut lining. In a pinch, collagen can fill the gap.

Fermented foods

This is an obvious one, but it’s incredibly important and more complex than you probably think. First of all, fermented foods like yogurt, sauerkraut, pickles, kefir, and dozens of other varieties seed our guts directly with beneficial probiotic bacteria. That has real benefits—though they don’t “form colonies” and you do have to continually eat fermented foods for the full benefit. Some fermented foods also have the ability to “train” your resident bacteria to digest new compounds. One example is fermented milk: in one study it didn’t colonize the gut but led to increased microbial expression of carbohydrate metabolizing enzymes in the existing bacteria.

Resistant starch

Resistant starch isn’t like other starches. Our stomach acid and digestive enzymes cannot break it down, but our gut bacteria can digest it. Multiple studies indicate that resistant starch consumption generally leads to an increase in “beneficial” colonic bacteria and a reduction in “pathogenic” colonic bacteria, including a boost to bifidobacteria and a decrease in firmicutes and a huge boost to butyrate production. The best sources of resistant starch are green (unripe) bananas and raw potato starch.

Meat

Meat usually doesn’t pop up on these lists, but that’s a huge mistake. Red meat especially provides ample B-vitamins required for energy generation and general physiological maintenance, including gut function. It’s a nutrient-dense “safe” food for even damaged guts who need to be careful about the plant foods they eat. And if you’re eating a significant amount of meat, you’ll have less room to eat the refined carbs and refined sugar that really cause gut issues.

Pistachios

Pistachios are the most potent nut for improving gut health. Other nuts like almonds are good too, but pistachios produce  a biome richer in butyrate-secreting bacteria which is extremely beneficial to several body systems.

Onions, garlic, and leeks

Onions, garlic, leeks, and other members of the allium family offer concentrated doses of fructo-oligosaccharides, some of the best-studied and most beneficial fermentable prebiotic fibers in the plant kingdom. Plus, they’re delicious, and humans have been eating them for thousands of years (if not longer).

Some people will react poorly to some of the foods listed in the “Best” section. If your gut health is compromised and your gut bacteria dysfunctional, you may very well have trouble consuming fermentable fiber, resistant starch, berries, and other fibrous foods without bloating, gas, stomach pain, constipation, and diarrhea. Please read my article on FODMAPs to understand how to work around this issue and maintain your gut health.

Thanks for reading, everyone. If you have any questions about gut health or the info contained in this post, let me know down below!

References

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