Nutrition Tips to Restore a Healthy Gut Microbiome

Published on: 09/12/2023

In this article, we will explore nutrition and lifestyle tips that have been proven to enhance the microbial diversity of your gut microbiome.

The gut microbiome is an ensemble of microorganisms, including bacteria, fungi, parasites, and viruses, that call your digestive tract home. Diversity and balance are vital for intestinal and overall health, as this symbiotic relationship between your body and the gut microbiome impacts various factors, including:

  • Detoxification
  • Mood
  • Mental function
  • Hormone production
  • Immunity
  • Intestinal permeability
  • Digestive function

Over the course of your life your gut microbiota is evolving constantly and is influenced by your environment, diet, genetics, and inflammation. Gut dysbiosis occurs when the microbial diversity in your gut is low, resulting in an imbalance between good and bad bacteria. This can lead to excessive growth of “bad” bacteria and increase the risk of opportunistic infections. When the variety of bacteria in your gut decreases, your chances of developing chronic illnesses can rise.

How to Increase Microbial Diversity

# 1. Probiotics

Probiotics are defined as “live microorganisms that, when administered in adequate amounts, confer a health benefit on the host”. Probiotics impact the colonization of the gut microbiome and strive to restore balance, alleviate symptoms, or even prevent/treat specific conditions. Probiotics come in supplement form or as specially crafted yogurt products. 

Probiotics are identified by their genus, species, strain-specific alphanumeric designations, and a product name that is a registered trademark ®. For example, UltraFlora® Women’s:

Product name: UltraFlora® Women’s

Genus: Lactobacillus

Species: reuteri and rhamnosus

Strain designation: RC-14 and GR-1

International strain depository designation: NCIMB 30242 and 30121

Examining Probiotic Effectiveness

Probiotics can be likened to medicines: when used appropriately, they can help resolve health problems. However, just as taking the wrong medication won’t yield the desired results, a probiotic that has been proven to alleviate symptoms of one condition shouldn’t be expected to assist on a different condition. For example, the above mentioned product, UltraFlora® Women’s, has been proven to help restore and maintain a healthy vaginal flora by reducing the number of urogenital pathogenic bacteria and yeast on vaginal surfaces. This product would not be helpful if you are experiencing another condition, irritable bowel syndrome for example.

Unlike medicines, probiotics aren’t subject to the same regulatory standards. This lack of regulation allows companies to make claims about their products that lack credible research support. Consequently, determining which probiotic to select and which ones have demonstrated effectiveness can be confusing.

What is recommended is that you visit the website for The Alliance for Education on Probiotics (AEProbio), which is an organization that offers a compilation of scientific evidence regarding the safety and efficacy of specific probiotic products. Their information is presented in a guide called “The Clinical Guide to Probiotic Products.” In this guide, you can search for your particular health issue and find what type of probiotic has been proven to he helpful.

United States:


How to Choose a Probiotic

  • Genus: To truly reap the benefits, you need to choose the right genus to address your particular issue or concern. Look at “The Clinical Guide to Probiotic Products” in the links provided above and search for your particular issue and what genus might be helpful.
  • Live Bacterial Cultures: Choose a product that contains live and active bacterial cultures, and it should indicate this on its packaging. 
  • Colony Forming Units (CFUs): this tells you the number of bacterial cells you’ll get in each dose. The general recommendation is to choose probiotic products with at least 1 billion CFUs. 

# 2. Fermented Foods 

Fermented foods have been a part of human culture for centuries. They are made by undergoing a natural process of microbial transformation with bacteria, yeast or fungi. Fermented foods may impact human health through various mechanisms, including :

  • Nutritional alterations of the raw ingredients – changing the nutritional composition or removing anti-nutritive factors (e.g. phytic acids).
  • Synthesis of bioactive compounds.
  • Modification of the gut microbiota with beneficial microorganisms.

Are fermented foods the same as a probiotic? 

Well, not exactly. Probiotics are products that require a particular type of bacteria with a well-defined health benefit. In contrast, fermented foods may not consistently contain the same quantity or variety of bacteria, which is why they don’t fit the precise probiotic definition. Although further research is required to fully establish the specific health advantages of fermented foods, this shouldn’t deter you from incorporating them into your diet, as they are highly likely to contribute positively to your overall health.

Examples of fermented foods with live microorganisms present include:

  • Yogurt: a dairy product made by fermenting milk with beneficial bacteria, primarily Lactobacillus bulgaricus and Streptococcus thermophilus. The fermentation process thickens the milk and gives yogurt its characteristic tangy flavor and creamy texture.
  • Kefir: Kefir is a fermented dairy or non-dairy beverage made from kefir grains. Kefir grains are small, gelatinous clusters of bacteria and yeast that are used as a starter culture. They look like small curd-like grains.
  • Miso: Fermented soybeans with salt and koji fungus. It is a thick paste with a strong umami flavor, varying based on color (white, yellow, red). Used as a seasoning, soup base, marinade, and condiment in Japanese cuisine.
  • Tempeh: Fermented whole soybeans bound together by a fungal culture. It has a firm texture, nutty flavor, often described as having a mild earthy taste. Cooked as a protein source, sliced in sandwiches, stir-fries, salads, or as a meat substitute.
  • Natto: Fermented soybeans with Bacillus subtilis bacteria. It has a sticky, slimy texture with a strong, pungent aroma and unique flavor. Often eaten with rice as a breakfast food, known for potential health benefits and acquired taste.
  • Fermented vegetables (not heated)
  • Kimchi: Typically made from Napa cabbage, radishes, scallions, and a mixture of seasonings, including chili pepper flakes, garlic, ginger, and salt. Fermented with lactic acid bacteria, often at room temperature. It has a spicy, tangy, and pungent flavour. Served as a side dish or condiment in Korean cuisine. 
  • Sauerkraut: primarily made from finely chopped cabbage and salt. Fermented through lacto-fermentation, typically at room temperature. It has a tangy and sour flavor with a crunchy texture and is commonly used as a condiment or side dish in various dishes. Often associated with German cuisine, but also found in other cultures.
  • Kombucha: fermented tea beverage that is made by fermenting sweetened black or green tea with a symbiotic culture of bacteria and yeast (SCOBY). It typically has a tangy, slightly effervescent taste and can be flavored with additional fruits, herbs, or spices.

# 3. Prebiotics

Prebiotics are nourishment for gut bacteria. They are not digested by human enzymes or absorbed in the small intestine, but instead, they reach the large intestine where they serve as fuel for the growth and activity of beneficial bacteria. They support health by: 

  • Fostering beneficial bacteria growth.
  • Reducing pathogenic bacteria.
  • Serving as fuel for short-chain fatty acids (SCFAs), such as acetate, propionate, and butyrate. SCFAs play important roles in energy production, gut health, and various physiological processes in the body.

Prebiotics are primarily found in high concentrations in various roots. Industrial extraction of prebiotics is often carried out using the Chicory root. Additionally, prebiotics can be found naturally in the following foods:

Allium Family

  • Onions
  • Leeks
  • Garlic
  • Chives
  • Shallots

Other Fruits & Vegetables

  • Asparagus
  • Sugar beet
  • Jerusalem artichoke
  • Fennel bulb
  • Tomatoes
  • Peas
  • Banana

Whole Grains

  • Oats
  • Barley
  • Rye
  • Quinoa
  • Buckwheat
  • Brown rice


  • Beans
  • Lentils
  • Soy beans


  • Human milk (great source of prebiotics for breastfed babies)
  • Cow milk


  • Honey
  • Seaweed
  • Microalgae


# 4. Glutamine

Glutamine, an amino acid found in all proteins, is abundant in various meats, animal products, and dairy items. It stands as the most prevalent amino acid circulating throughout your body. Furthermore, glutamine serves as the primary energy source for enterocytes, the cells that line your intestines, as well as for lymphocytes, essential components of the immune system.

Supplementing with glutamine might enhance gut health by fortifying the intestinal barrier. This is achieved through reducing intestinal permeability, aiding in the maintenance of tight junctions, and encouraging the growth of enterocytes.

For safety, it’s suggested that the maximum amount of glutamine supplementation, beyond regular dietary intake, should not exceed 14 grams per day.

# 5. Essential Fatty Acids

Numerous publications have explored the effects of carbohydrates (prebiotic fibers) on the microbiome, yet the impact of dietary fats remains less well-defined. Although research on fatty acids for gut health is relatively new, the available studies show promising results.

Omega-3 Fatty Acids

Initial evidence indicates that the consumption of Omega-3s impacts the gut microbiome in three main ways:

  1. Modulating the type and abundance of gut microbes, thereby establishing an optimal balance between “good” and “bad” bacteria.
  2. Increasing the production of anti-inflammatory compounds by the gut microbiota, particularly short-chain fatty acids like butyrate.
  3. Reducing levels of proinflammatory endotoxins.

These effects collectively contribute to lower gut inflammation and permeability, thereby preserving the integrity of the intestinal wall.

Types of Omega-3s:

  1. Alpha-linolenic acid (ALA): found in plant-based foods such as flaxseed (ground), walnuts, chia seeds, soy, hemp seeds, pumpkin, seeds, and almonds. 
  2. Eicosapentaenoic acid (EPA) and Docosahexaenoic acid (DHA): found in fish such as anchovies, salmon, sardines, tuna, trout, and halibut.


Butyrate is a short-chain fatty acid produced by bacteria in your gut when they break down dietary fiber. It serves as the primary energy source for colon cells and may offer additional health benefits, such as immune system support, inflammation reduction, and disease prevention.

To increase butyrate levels, the most effective approach is to consume foods rich in fiber; your gut microbiome will handle the rest. Butyrate is also present in full-fat dairy products such as butter, cheese, ghee, and full-fat milk, as well as in butyrate supplements.

# 6. Culinary Herbs and Spices

Spices and herbs have been used for centuries, both for culinary and medicinal purposes. Not only do spices enhance the flavor, aroma, and color of food and beverages, but they can also offer protection against acute and chronic diseases. They serve as antimicrobials, preventing the overgrowth of harmful bacteria in our gut. Additionally, they possess potent antioxidant properties and can aid in reducing inflammation.

  • Ginger
  • Turmeric
  • Basil
  • Rosemary
  • Cumin
  • Cinnamon
  • Cardamom
  • Thyme

# 7. Non-Dietary Lifestyle Factors: smoking, exercise, stress, and sleep

Non-dietary lifestyle factors play a significant role in shaping the delicate balance of the gut microbiome. Smoking, exercise, stress, and sleep wield considerable influence over the composition and function of your gut microbial communities.

  • Smoking has been linked to unfavorable changes in gut microbiota composition, potentially contributing to digestive disorders.
  • Regular physical activity has shown the potential to enrich microbial diversity and promote the growth of beneficial bacteria, fostering a healthier gut environment.
  • Chronic stress can disrupt the equilibrium of the microbiome, leading to imbalances that may impact overall well-being.
  • Adequate sleep, a cornerstone of good health, also contributes to a thriving gut microbiome by supporting its diverse microbial populations.

Collectively, these non-dietary lifestyle factors underscore the intricate interplay between our habits and the microbial inhabitants that significantly influence our health and bodily functions.

Concluding Thoughts

In conclusion, the gut microbiome is a fascinating and dynamic ecosystem within our bodies, influencing numerous aspects of our health and well-being. Maintaining diversity and balance in this complex community is essential for optimal intestinal and overall health. As we’ve explored various factors that impact the gut microbiome, from probiotics to prebiotics, essential fatty acids, and even non-dietary lifestyle choices, it becomes clear that we have a powerful role to play in nurturing this symbiotic relationship. By making informed choices about what we consume and how we live, we can support the flourishing of beneficial bacteria and promote a thriving gut microbiome. Ultimately, a healthy gut contributes to a healthier life, and it’s a journey well worth embarking upon for the sake of our long-term well-being.

As a registered dietitian, I’m here to guide you on your path to a healthier gut and a healthier you. If you’re intrigued by the power of the microbiome and its potential impact on your health, I invite you to get in touch with me. Let’s work together to uncover your individual nutritional needs and develop a personalized plan that supports your gut health journey.


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Verena is a Registered Dietitian specializing in women’s hormonal health, fertility, and oncology.  The primary aim of this blog is to offer information that empowers individuals to align their lives with their body’s inherent rhythms. Within these pages, you’ll encounter a blend of evidence-based recommendations grounded in modern medicine, complemented by natural healing approaches and insights from traditional wisdom.

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