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How to Create a Gut Healthy Nutrition Meal Plan

Medically reviewed by 
How to Create a Gut Healthy Nutrition Meal Plan

Did you know that a healthy meal plan isn't solely dependent on the food itself but also on its impact on the health of trillions of microorganisms living inside the digestive tract? This vast collection of bacteria, yeast, fungi, and other microorganisms in the gastrointestinal tract is known as the gut microbiome; this collection of microscopic residents not only influences gut health but also plays a significant role in overall well-being.

With functional gastrointestinal disorders (FGIDs) negatively impacting more than 40% of people worldwide, causing a myriad of symptoms that significantly affect the quality of life, it's an area well worth some attention (and intention) when it comes to improving and maintaining overall health.

The microbiome plays a key role in health and disease, influencing the risk for many chronic diseases and modulating the function of many body systems to contribute to how well the body functions as a whole. The microbiome has many functions supporting overall health, including regulating the integrity of the gut lining, producing nutrients, protecting against pathogens, and supporting proper immune function.

The good news is that evidence shows the gut microbiome rapidly responds to changes in our diet. Considering that many aspects of improving our health take time and patience, it's reassuring to know that changes in our diet produce quick changes in our microbiome.


Why is Gut Health So Important?

Gut health contributes to much more than just the gastrointestinal system. The gut microbiome is considered a critical factor in the regulation of overall human health. It influences the risk of many chronic diseases, including cardiovascular disease, Type 2 Diabetes, obesity, inflammatory bowel disease, and even cancer. Chronic diseases are the leading cause of death and disability in the United States, making the gut microbiome a promising area of focus, given its significant role in modulating these conditions.

The microbiome not only modulates the risk for disease but also influences how many body systems function, including modulating metabolic pathways, inflammatory markers, nervous system activity, gastrointestinal function, hormone regulation, and neurotransmitter production. With 70-80% of the body's immune cells residing in the gut, it's easy to see how gut health and the microbiome can influence the immune system.

This information clearly illustrates how far-reaching the gut microbiome influences our overall health. Focusing on gut health and a healthy microbiome can positively impact many body systems and factors contributing to overall health and disease prevention.

Symptoms of an Unbalanced Gut Microbiome

Dysbiosis occurs when there is a disruption between the beneficial and pathogenic (harmful) microorganisms in the gut. More specifically, features of dysbiosis include a decrease in beneficial microbes, an overgrowth of harmful microbes, and a decrease in the microbiome's diversity. Low microbiome diversity occurs when few types or species of beneficial microbes exist. Another feature of dysbiosis includes an increase in the permeability of the gut lining. This increase in permeability of the gut lining, often referred to as "leaky gut," allows bacteria to enter circulation, producing an inflammatory response.

Dysbiosis, or alteration in the gut microbiome, can lead to many signs and symptoms that range from mild to severe.

Gastrointestinal symptoms may include gas, cramping, bloating, diarrhea, constipation, belching, bad breath, nausea, acid reflux, vomiting, abdominal pain, food allergies or sensitivities, IBS/IBD, Crohn's, Ulcerative Colitis, or mucus in the stool.

Dysbiosis can also produce symptoms outside of the gastrointestinal tract. Some people experience symptoms like joint pain and inflammation, chronic fatigue, brain fog, ADHD or difficulty concentrating, anxiety, depression, acne, eczema, or psoriasis.

What Causes an Unbalanced Gut Microbiome

Knowing what causes an imbalance in the gut microbiome can help determine where to begin making lifestyle changes to support better gut health. Below we'll highlight several key factors that can cause imbalances in the gut microbiome.

Western Diet

A Western Diet high in refined sugars, poor-quality fats, processed foods, and low in fiber promotes shifts in the microbiome that leads to dysbiosis. Western Diets lead to low numbers of total bacteria and low numbers of specific beneficial strains of bacteria.

In addition to dysbiosis, diets low in fiber are also associated with other factors impacting gut health, including the degradation of the mucus barrier that lines the gut. This mucus barrier is an essential line of defense, protecting against pathogens.

Lifestyle Factors

In addition to diet, lifestyle factors that contribute to an imbalance in the microbiome include high stress levels, poor sleep habits, alcohol consumption, smoking, and hygiene. This high-stress lifestyle promotes inflammation and microbiome alterations, leading to dysbiosis, low diversity, and increased gut permeability.


Pathogenic microorganisms can cause infection in the gut, altering the microbiome and resulting in dysbiosis, as well as low diversity and increased gut permeability. These infections are accompanied by increased gut inflammation and can take a serious toll on overall health.


Xenobiotics are chemicals that are foreign to animal life. Xenobiotics shown to disrupt the microbiome include antibiotics, food additives, and medications. The negative impact of antibiotic use on the gut microbiome is widely known and accepted. However, the effect of other medications on the microbiome is rarely discussed. This systematic review reveals common prescription medications, such as PPIs, Metformin, NSAIDs, opioids, and antipsychotics, can also cause shifts in the microbiome resulting in dysbiosis.

Functional Medicine Labs to Test The Gut Microbiome

Your health practitioner may utilize several functional lab tests to evaluate your gut microbiome and overall gut health.

Comprehensive Stool Analysis

Comprehensive Stool Analysis testing is a great way to evaluate the microbiome and overall gut health. These tests offer a comprehensive overview of the gastrointestinal system's structure and function by providing information about inflammation, digestive function, microbiome diversity, and whether there is an overgrowth of pathogenic strains of bacteria, yeast, or parasites.

The Genova GI Effects test is an excellent choice for this type of test as it evaluates the gut microbiome and other aspects of gut health, including digestion, inflammation, and immune function. Zonulin is available as an add-on to this test, which is a marker used to assess for compromised intestinal permeability. The GI Effects also offers microbe sensitivity testing to determine which prescription medications and natural agents will be effective against any pathogens present. This is extremely helpful information in developing an effective individualized treatment strategy.

Intestinal Permeability Testing

Testing for an increase in a protein called zonulin indicates whether there is increased gut lining permeability or "leaky gut" present. This marker can be assessed by adding zonulin to a comprehensive stool test or evaluated with a separate blood test. The Advanced Intestinal Barrier Assessment, or Advanced IBA, is a blood test that looks at several markers, including zonulin, associated with intestinal permeability.

Breath Testing

If your practitioner suspects disruption in the microbiome of the small intestine, a breath test may be ordered to evaluate for Small Intestine Bacterial Overgrowth (SIBO). This test involves drinking a sugar solution and measuring methane and hydrogen levels on six breaths collected in tubes at specific times.

Organic Acid Testing

Organic Acid Testing (OAT) is a urine test that comprehensively analyzes overall health, including intestinal microbial overgrowth. This test also provides information about the nutritional status of various vitamins and minerals as well as detoxification function, which can be helpful information in crafting a comprehensive treatment plan to address both gut health and overall health.

How to Create a Gut Healthy Diet Meal Plan

The fact that diet significantly impacts the microbiome is great news for anyone who wants to improve, maintain, or restore gut health. At this point, you may be wondering what foods to focus on for a gut-healthy diet. There are several categories to consider in a gut-healthy meal plan. These foods support gut health by impacting the integrity of the gut lining, reducing inflammation in the gut, and supporting an increase in microbiome diversity.

The Mediterranean Diet

The Mediterranean Diet is well known as a balanced diet that promotes overall health, but it is also shown to promote beneficial changes in the microbiome associated with gut health. The Mediterranean Diet is high in fiber, healthy fats, polyphenols, and other antioxidants. It is also low in dairy products, processed foods, and sweets. The main foods comprised in this diet are olive oil, fruits and vegetables, nuts and seeds, whole grains, legumes, fish, poultry, and red wine.

Foods to Avoid

As discussed above, we know that alcohol and foods in the typical Western Diet, which includes poor-quality fats, refined sugars, and processed foods, contribute to dysbiosis. These foods should be avoided or limited for a gut-healthy diet and meal plan.


Fermented foods contain beneficial bacteria, probiotic strains, that positively benefit gut health. Yogurt and probiotic fermented milk are shown to support microbiome changes associated with gut health. Various other fermented foods that benefit gut health include vinegar, sauerkraut, kimchi, and other fermented vegetables, legumes, and fish.


Prebiotics are defined as substrates consumed by host microorganisms that produce a health benefit. In other words, they are foods that feed the beneficial bacteria in the gastrointestinal tract, creating a beneficial health effect.

Fiber, resistant starch, polyphenols, and omega-3 polyunsaturated fatty acids are all shown to function as prebiotics, supporting microbiome and gut health improvements.

Fiber and resistant starch are non-digestible carbohydrates that support a healthy microbiome and gut. They are fermented in the large intestine, producing short chain fatty acids, which are used as a source of energy for the microbiome. Specific foods high in prebiotic fiber include fruits and vegetables, such as tomatoes, artichokes, asparagus, garlic, onions, chicory, leafy green vegetables, and berries, as well as legumes, and whole grains, such as oats. Foods high in resistant starch include cooked and cooled rice and potatoes, raw oats, plantains, green bananas, cashews, quinoa, beans, and lentils. Adults should aim for 28 to 35 grams of fiber per day for a gut-healthy diet.

Polyphenol-rich foods include fruits, vegetables, seeds, cocoa, tea, and wine.

Sources of omega-3 polyunsaturated fatty acids include fish and seafood, chia seeds, flaxseeds, and walnuts.

Probiotic & Prebiotic Supplements

Probiotic and prebiotic supplements can be an excellent addition to a gut-healthy diet to support balance in the gut microbiome. Probiotics' effects on health largely depend on which strains are used, called strain specificity. So, it's important and helpful to discuss with your healthcare practitioner which specific probiotic supplement will best support your health.

Prebiotic supplements work synergistically when used in conjunction with probiotics. However, they also have wonderful benefits for the microbiome when used independently.


The gut microbiome is pivotal regarding overall health by playing a key role in chronic disease prevention and modulating the function of various body systems.

Whether regulating the integrity of the gut lining, producing nutrients, protecting against pathogens, or supporting proper immune function, the gut microbiome is an amazing asset to overall health when adequately supported. With this in mind, eating in a way that promotes balance in the microbiome is a fantastic way to support your overall health and take action toward preventing chronic disease.

On the most basic level, creating a gut-healthy diet can be achieved by including fermented foods, foods high in fiber, polyphenols, and omega-3 fatty acids, and avoiding foods known to disrupt the microbiome. A Mediterranean-style diet is a fantastic model when considering how to construct your own gut-healthy style of eating.

Supporting a balanced, healthy microbiome with a gut-healthy diet is an excellent healthy lifestyle practice that delivers rapid changes in the microbiome and supports your total well-being.

The information provided is not intended to be a substitute for professional medical advice. Always consult with your doctor or other qualified healthcare provider before taking any dietary supplement or making any changes to your diet or exercise routine.
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