Blog Diets Microbiome Diet Shopping List For A Healthy Gut

Microbiome Diet Shopping List For A Healthy Gut

Your microbiome is the collection of all the microbes (bacteria, fungi, viruses) that live on and inside your body. The combination of these microbes is unique to each individual, and it’s influenced by many factors, including your diet. There are two types of bacteria that dominate your microbiome: firmicutes and bacteroidetes. The ratio of these two types of bacteria is thought to be linked to obesity (12). That’s not all; an imbalance of gut bacteria has been linked to a whole host of health problems, including diabetes, inflammatory bowel disease, and even depression (12). So what can you do to keep your microbiome healthy? Here’s a guide to the best (and worst) foods for your gut bacteria.


What Are The Best Foods For Microbiome?

To maintain a healthy gut microbiome, it’s important to eat a variety of fermented foods, high-fiber foods, and probiotic-rich foods. Here’s why each of these foods should make it to your gut health grocery list:

Fermented Foods

Fermented foods are rich in probiotics, which are live microorganisms that might have health benefits when consumed (4).

Probiotics are believed to help restore the balance of microbes in your gut, which can be disrupted by things like antibiotic use, a high-sugar diet, and stress (4).

Some fermented foods to include in your shopping list are:

  • Yogurt 
  • Kimchi 
  • Sauerkraut 
  • Pickles 
  • Tempeh
  • Miso paste 

High-Fiber Foods

High-fiber foods are an important part of a healthy gut microbiome. Fiber provides food for the beneficial bacteria in your gut and helps keep things moving through your digestive system (13).

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5000 Calorie Diet: What Is Clean Bulking And How Do You Get Started?

Some high-fiber foods to include in your shopping list are:

  • Beans and legumes 
  • Whole grains 
  • Vegetables 
  • Fruit


Probiotic-Rich Foods

Probiotic-rich foods are foods that contain live microorganisms, which can help promote a healthy gut microbiome (7).

Some probiotic-rich foods to include in your shopping list are:

  • Kefir 
  • Kombucha 
  • Coconut yogurt 
  • Sourdough bread

When shopping for these gut-healthy foods, look for products that are: 


Organic foods are free of pesticides. Some believe that these chemicals can disrupt the delicate balance of microbes in your gut.

Read More: Foods That Ferment In The Colon And Why Avoiding Them May Improve Digestive Health


The more processing a food undergoes, the fewer nutrients it contains, especially fiber. Choose whole, minimally processed foods as much as possible.

microbiome diet shopping list

Free Of Artificial Additives, Sweeteners, And Flavors

Some artificial additives, sweeteners, and flavors are believed to disrupt the balance of microbes in your gut (2).

What Are The Worst Foods For Your Microbiome?

The delicate balance of microbes in your gut can be easily disrupted by certain foods and substances. To maintain a healthy gut microbiome, it’s best to avoid or limit these items:


A diet high in added sugars may disrupt the balance of microbes in your gut and may promote inflammation (6). Read labels to identify hidden sources of sugar in your food.

Look out for names such as:

  • Dextrose 
  • Maltose 
  • Fructose 
  • Corn syrup 

Ultra Processed Foods

Ultra processed foods are often high in sugar, unhealthy fats, and artificial additives, all of which may disrupt the balance of microbes in your gut. Avoid the following processed foods:

  • White bread 
  • Pastries 
  • Cookies 
  • Crackers 
  • Chips
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microbiome diet shopping list


Excessive alcohol consumption can damage the beneficial bacteria in your gut and lead to inflammation (14). 


Caffeine might be harmful to gut bacteria and may also increase inflammation (1). It’s found in coffee, tea, energy drinks, and some sodas.

Artificial Sweeteners

Artificial sweeteners are thought to alter the composition of bacteria in the gut. These include aspartame, sucralose, and saccharin (2).

Processed Meats

Processed meats are high in saturated fat and sodium, and have been linked with a higher risk of colorectal cancer. These include meats like bacon, sausage, and lunch meats.


Too much sodium can alter the composition of gut bacteria and lead to inflammation. Avoid salty foods such as processed meats, chips, and fast food.

Greasy, Fried, And Fatty Foods

Greasy, fried, and fatty foods can lead to inflammation (6). They can also damage the lining of your gut.

This is because they contain high levels of unhealthy fats and possibly other chemicals that might be harmful to your gut microbiome.


Antibiotics kill both harmful and beneficial bacteria in your gut. This can disrupt the balance of microbes in your gut and lead to inflammation (12). Always take antibiotics as prescribed by your doctor, and ask them about taking a probiotic during or after your course of antibiotics to help restore your gut microbiome.

See also
Dairy-Free Diet Plan For Beginners: A Week's Worth Of Nutritious Meal Ideas

Read More: What Is The Best Diet For Indigestion? How To Manage Your Symptoms With Food

microbiome diet shopping list

What Can I Eat For Breakfast On The Microbiome Diet?

A healthy breakfast should contain foods that will nourish your gut bacteria. Here are some healthy and delicious breakfast meal ideas:

  • Omelet with vegetables and whole wheat toast
  • Scrambled eggs with avocado and whole wheat toast
  • Yogurt with fruit and nuts 
  • Smoothie made with yogurt, fruit, and green veggies 
  • Oatmeal with almond milk and berries 
  • Quinoa bowl with vegetables and an egg 

What Can I Eat For Lunch On The Microbiome Diet?

These gut-friendly lunch ideas are both nutritious and delicious:

  • Vegetable soup with whole wheat avocado toast
  • Salad with grilled chicken or fish 
  • Burrito bowl with brown rice, beans, vegetables, and guacamole 
  • Sushi roll made with brown rice 
  • Vegetable wrap with hummus 
  • Turkey and avocado sandwich on whole grain bread 

What Can I Eat For Dinner On The Microbiome Diet?

Dinner should also feature gut-friendly ingredients. Here are some yummy and nutritious dinner ideas:

  • Roasted chicken or fish with vegetables and quinoa
  • Stir-fry made with lean protein and vegetables with brown rice
  • Vegetable and chickpea curry with brown rice 
  • Grilled steak with roasted vegetables and baked potato
  • Shrimp pasta made with whole grain noodles and veggies


What Can I Snack On The Microbiome Diet?

These gut-friendly snack ideas are both satisfying and healthy:

  • Hard-boiled egg 
  • Apple with almond butter 
  • Vegetables with hummus or guacamole 
  • Yogurt with fruit 
  • Trail mix made with nuts, seeds, and dried fruit 
  • Rice cake with nut butter and banana 
  • Celery sticks with peanut butter
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What Is The Fastest Way To Heal Gut Microbiome?

When your gut microbiome is  out of balance, you may experience digestive issues, low energy levels, and inflammation. To restore balance to your gut microbiome, you may need to remove the foods that are damaging it and eat more of the foods that support a healthy gut.

The best way to do this is to follow a gut-healthy diet. Aside from the diet plan we’ve provided, there are several lifestyle changes you can make to support a healthy gut. 

Managing Stress

Stress triggers the release of cortisol, a hormone that may interact with the gut microbiome (9). To protect your gut, manage stress with relaxation techniques such as yoga, meditation, and deep breathing.


Exercise is important for gut health because it reduces inflammation and supports a healthy immune system (l). Aim for 30 minutes of moderate to vigorous exercise most days of the week.

microbiome diet shopping list


Getting enough sleep is crucial for a healthy gut. When you don’t get enough sleep, it can lead to inflammation and disrupt the balance of microbes in your gut (5). Aim for 7-9 hours of sleep each night. 

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Quit Smoking

Smoking damages the lining of the gut and increases inflammation (14). If you smoke, quitting is one of the best things you can do for your gut health. 

Take Supplements

While following a gut-healthy diet is the best way to heal your microbiome, there are several supplements that can also support gut health. Always talk to your doctor before starting a supplement.


Probiotics are live bacteria that support gut health. They can be found in fermented foods such as yogurt, kimchi, and sauerkraut. You can also take probiotic supplements.

microbiome diet shopping list


Prebiotics are non-digestible fibers that feed the beneficial bacteria in your gut. They can be found in foods such as bananas, garlic, and onions. You can also take prebiotic supplements. 

Omega-3 Fatty Acids

Omega-3 fatty acids are anti-inflammatory and support gut health. They can be found in oily fish such as salmon, mackerel, and sardines, or in walnuts and flaxseeds. You can also take omega-3 supplements. 


L-glutamine is an amino acid that supports gut health. It can be found in meats, poultry, fish, and eggs. It works by reducing inflammation and supporting the growth of new cells in the gut. 

Vitamin D

Vitamin D is important for gut health because it supports the immune system. It can be found in fatty fish, mushrooms, and fortified foods. You can also get vitamin D from sun exposure. 

The Bottom Line

A healthy gut microbiome is important for overall health. Eating a variety of fermented foods, high-fiber foods, and probiotic-rich foods can help maintain a healthy gut microbiome.



This article is intended for general informational purposes only and does not address individual circumstances. It is not a substitute for professional advice or help and should not be relied on to make decisions of any kind. Any action you take upon the information presented in this article is strictly at your own risk and responsibility!


  1. Effect of coffee or coffee components on gut microbiome and short-chain fatty acids in a mouse model of metabolic syndrome (2018, 
  2. Effects of Sweeteners on the Gut Microbiota: A Review of Experimental Studies and Clinical Trials (2019, 
  3. Exercise Modifies the Gut Microbiota with Positive Health Effects (2017, 
  4. Fermented-food diet increases microbiome diversity, decreases inflammatory proteins, study finds (2021, 
  5. Gut microbiome diversity is associated with sleep physiology in humans (2019, 
  6. How Western Diet and Lifestyle Drive The Pandemic of Obesity And Civilization Diseases (2019, 
  7. Probiotics, prebiotics and synbiotics (2015, 
  8. Role of Dietary Nutrients in the Modulation of Gut Microbiota: A Narrative Review (2020, 
  9. Stress, depression, diet and the gut microbiota: human-bacteria interactions at the core of psychoneuroimmunology and nutrition (2020, 
  10. The Effect of Gluten-Free Diet on Health and the Gut Microbiota Cannot Be Extrapolated from One Population to Others (2018, 
  11. The effects of dairy and dairy derivatives on the gut microbiota: a systematic literature review (2020, 
  12. The Firmicutes/Bacteroidetes Ratio: A Relevant Marker of Gut Dysbiosis in Obese Patients? (2020, 
  13. The Health Benefits of Dietary Fibre (2020, 
  14. The interaction between smoking, alcohol, and the gut microbiome (2017,
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