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When most people think of gut health, they think of intestinal problems. I remember the day that I realized that “gut health” is synonymous with total body health. This was many years ago, before terms like “leaky gut,” “microbiome,” and “probiotics” were commonplace. I was taking a science class for my nutrition program. One of the assignments was to research all of the ways that the microbiome influences health. Within minutes, I realized we were talking about way more than just digestion or elimination considering how far-reaching the effects are of a microbiome that is compromised.

The nutrition buzzwords like “leaky gut,” “microbiome,” and “probiotics” aren’t always heard or understood fully even by people who are well-versed in nutrition. Gut health is a complex issue starting with the food you put in your mouth, how well it digests, how well nutrients can absorb, and the numerous other health factors you have going on that impact your microbiome. There are multiple ways to address gut health that go well beyond popping a daily probiotic pill (although you should do that, too). And if you’re experiencing problems that you think may be related to your gut, it can be difficult to identify root causes of those problems.

There are three distinct phases, and in order to have good gut health, we need all of them to be working as they should. Let’s break them down, one by one, and cover the essentials, as well as how to troubleshoot problems.

Of course, problems can occur at any or all stages, and sorting through them can be complex. The good news is that supporting gut health becomes a simple task when you support each phase by understanding what each one needs.


Digestion starts the second you take a bite of food and begin to chew. Saliva helps to break down nutrients, and as the food travels down the esophagus into the stomach, it is mixed with stomach acid and various enzymes to continue the digestive process.

But it doesn’t end there. In fact, a majority of the digestive process takes place in the small intestine, which people are less familiar with. Sadly, “intestines” get lumped in with one thing and one thing only: bowel movements. But there are two intestines: small and large, and they perform vital tasks for the the entire digestive process, not just getting rid of the waste.

The small intestine is actually quite long—about 20 feet in most adults. Here, the partially digested contents from the stomach continue to be broken down with added enzymes as well as chemical additions from the liver and pancreas.

Troubleshooting: Heartburn, acid reflux, ulcers, and eating in too much of a rush can all hinder the digestive process. Eating on the fly almost always results in inadequate chewing, placing a heavier burden of break down on the stomach. If you’re low in stomach acid (and most people who deal with heartburn or reflux are), you’ve just triggered unpleasant symptoms that can last for hours or even days.

Boosting digestion starts with more mindful chewing habits, followed by an understanding of the digestive process. If you deal with heartburn or reflux, or just tend to feel uncomfortable after meals, you probably need more enzymes to do the breakdown work in your stomach. It’s always best to check with your doctor before starting anything, but asking about a broad spectrum enzyme support is a good place to start.


Some nutrients are absorbed in the small intestine, too, like iron, vitamin B12, and water. Digestion can be as efficient as possible, but if absorption is hindered, your body doesn’t get the benefit of the foods it just spent energy to break down.

All absorption happens in the intestines, with certain nutrients only absorbable once they reach the large intestine, like water and electrolytes. Additionally, the large intestine makes critical nutrients for the body: vitamin K and biotin (a B vitamin), where they are also absorbed.

Believe it or not, this is where most of the problems occur. The small intestine can face a host of problematic factors when it comes to absorbing the food. One of the biggest problems is poorly digested contents from the stomach, which places a bigger burden of digestion on the small intestine and leaves less time for proper absorption. This is remedied by addressing the digestion tips above.

Another major absorption issue is SIBO, or small intestinal bacterial overgrowth. We know that bacteria are good for us in the form of probiotics. We have both good and bad strains in our bodies, but the good ones are needed to keep the bad in check. However, good or bad, when bacteria gets in places it doesn’t belong, discomfort and absorption problems occur.

Troubleshooting: When bacteria that belongs in the microbiome (the large intestine) migrates up into the small intestine resulting in SIBO, it can cause a host of problems, like bloating, cramping, problems absorbing nutrients, nausea, diarrhea, and more. Treatment of SIBO ranges from strain-specific antibiotics to kill off the bacteria from where it doesn’t belong, to dietary alterations to avoid feeding the bacteria that is living in the small intestine.

Absorption problems can happen in the large intestine, too, if there is too little or too much water (diarrhea or constipation), and if the microbiome lacks enough good bacteria to manufacture nutrients, like vitamin K.

Absorption issues are best fixed by addressing digestion as well as looking into conditions which might be causing absorption problems. This could be SIBO, but it could also be other conditions, like leaky gut or Celiac disease, both of which alter the way that the small intestine works and can leave it open for damage. You also do want to support the large intestine and microbiome with good bacteria, which need to be replenished regularly. So taking a daily probiotic is a great idea, but it can’t single-handedly fix all gut health issues. Working with your doctor and a nutritionist can help you identify exactly what foods are problematic for you, so you can foster better absorption.


After the nutrients are absorbed into the bloodstream, they still need to be transported and used. This process is the third and final step in ensuring that your overall gut health is protecting your total body health.

This process can be hindered if you’re low in certain nutrients, like electrolytes or the minerals iron and calcium, since these are necessary for healthy blood and the absorption of nutrients and fluids into and out of cells.

Troubleshooting: If you have digestive or absorption problems, or both, your body’s ability to use these nutrients it’s working so hard to get might be compromised. This can be fixed by addressing both of the previous stages, but also by ensuring the type of nutrients you’re eating are high quality and the easiest to absorb.

This means eating whole, unprocessed foods as much as possible, since nothing beats the purest form of nutrients found in nature. Supplements can help, but it’s important to choose the most bioactive forms of nutrients, since supplements that can’t be absorbed are just wasted money.

How do you know if your supplements are good quality? Odds are almost always that if they’re super cheap to purchase, the nutrients inside are also cheap and hard to absorb and use. All nutrients have more active or absorbable forms, and it takes a little research to uncover this. The best way to ensure you’re getting good quality nutrients is to stick to practitioner-trusted brands, like Pure Encapsulations, Thorne, and Seeking Health, which are my top three go-tos for nutrient support.

When it comes to supplementation, if you’re going to spend money to correct nutrient imbalances, you might as well ensure you’re actually getting benefits from them. You won’t get any benefits from something that your body can’t digest, absorb, and use.

The Bottom Line

Gut health is tied to nearly every element of health, from digestion to immunity to mental health to inflammation, chronic disorders, and even risk of future disease. But supporting it goes way beyond popping a daily pill. Like many other aspects of health, what you do with your diet and overall lifestyle routine has far-reaching effects, and your gut health is not immune.

Speaking from the experience of having had a host of gut health problems—everything from leaky gut, Celiac disease, and food allergies—fixing the problems is worth the effort. It can feel overwhelming to overhaul your diet, and increasing doses of probiotics can sound simpler. But consider looking at it this way: It’s not about following a rigid diet, rather, it’s about giving your body what it needs to function well. We each only have one body, so let’s be kind to it, and what we’ll see in return is an all around increase in the quality of our lives.