Gut Microbiome Restoration

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What Is The Human Gut Microbiome?

The gut microbiome refers to the vast community of microorganisms—bacteria, viruses, fungi, and other microbes—that collectively live in our small and large intestines. Trillions of these microbes occupy our bodies, predominantly in the large intestine, and collectively make up the gut microbiome.

Although different types of microbes live in and on our bodies, bacteria are the most widely studied, with bacterial cells in the body outnumbering human cells by a ratio of roughly 40 trillion to 30 trillion. (Sender et al., 2016).

Our Gut Microbiome Is An Organ

Essentially, humans are more microbial than human, as the gut microbiome functions almost like an additional organ. Incredibly, these microbes can weigh between 2–5 pounds, which is about the same as our human brain.

A close, symbiotic relationship exists between gut bacteria and us, their human host, with this delicate balance playing a critical role in our overall health on a daily basis.

Disruptions to the natural composition of our gut microbiota—whether from diet, illness, stress, or external factors can lead to a wide range of health issues, including gastrointestinal disorders, metabolic imbalances, immune dysregulation, and more.

Maintaining microbial balance in our gut is therefore critical, as a balanced microbiome supports digestive health, immune function, and mental/neurological well-being (Madhogaria et al., 2022).

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Gut Microbiome – The Organ We Some How Forgot

The gut microbiome is critical to our health, influencing functions ranging from metabolism and immune response to mood and brain health. Certain bacteria within our gut have roles in maintaining health by producing substances called short-chain fatty acids (SCFAs), they do this through the fermentation of dietary fibre which reduce inflammation, and is a simple and cost-effective for the control of gut-related pathogens (Zhan et al., 2022).

However, some gut microbes, including certain bacteria and fungi can contribute to disease, particularly if there’s an imbalance in the gut microbial community.

For example, higher ratios of inflammatory bacteria or infectious strains like E. coli have been linked to gastrointestinal and systemic diseases, including obesity, diabetes, irritable bowel syndrome, and even heart disease. (Madhogaria et al., 2022).

Everybody Carries Their Own Personal Gut Microbiome

Environmental factors like diet play an immediate role in shaping our gut microbiome. Dietary quality, fiber intake, and prebiotic-rich foods all support beneficial bacteria populations, while certain patterns like FODMAP diets may influence symptoms in sensitive individuals. A study found that a person’s unique microbiome starting profile can influence how they respond to probiotics or change in diet, underscoring the personalised nature of gut health strategies (Hills Jr. et al., 2019).

The study of our gut microbiome has progressed significantly with DNA sequencing techniques such as metagenomics, which allows scientists to analyse microbial genetic material from stool samples. This new technology is opening doors to a more profound understanding of our gut microbiome’s composition, diversity, and functional roles in both health and disease (Malla et al., 2019).

Key Functions Of Our Gut Microbiome

Illustration of a glowing human digestive system surrounded by various bacteria and microorganisms, representing gut microbiome.

Our gut microbiome plays several key and essential roles in various bodily processes, from aiding digestion to supporting immune function and mental well-being.It is now evident that the gut microbiota has a profound effect on our immune system and can affect autoimmune-related diseases both within and outside our gut (Wu et al., 2012).

This complex network of gut/body interactions underscores how integral our gut microbiome is across various dimensions of health, from digestion and immune function right through to emotional resilience.

Here’s an overview of some the main gut microbiome functions and their importance:

Metabolism and Digestion

Gut bacteria break down complex carbohydrates and fibre into short-chain fatty acids (SCFAs) like butyrate, acetate, and propionate, which play a crucial role in reducing inflammation, regulating lipid levels, and serving as energy sources for colon cells. SCFAs also contribute to overall metabolic health and help manage blood sugar and cholesterol levels (Portincasa et al., 2022).

Immune System Support

By interacting with immune cells, our gut microbiome influences immune responses and the production of antibodies. This symbiotic relationship helps the body identify harmful pathogens while minimising autoimmune responses that could cause inflammation (Wiertsema et al., 2021).

Nutrient and Vitamin Production

Beneficial gut bacteria produce essential vitamins, including vitamin K and some B vitamins (such as B12 and folic acid), which support blood clotting, cellular function, and DNA synthesis (Rowland et al., 2017).

Brain Health and Mood Regulation

Through the gut-brain axis, gut microbes impact mental health by producing neurotransmitters like serotonin and gamma-aminobutyric acid (GABA), which influence mood, sleep, and stress levels. The gut produces nearly 90-95% of the body’s serotonin, and some bacterial species can synthesize GABA, potentially affecting anxiety and depression (Chaudhry et al., 2023).

Intestinal Barrier Function and Protection

The gut microbiota strengthens the intestinal barrier by preventing harmful bacteria and Candida levels from penetrating the gut lining. This barrier reduces inflammation and maintains immune tolerance to prevent disease. Disruption of this balance, often referred to as “leaky gut,” can lead to systemic inflammation linked to conditions such as diabetes and cardiovascular disease (Takiishi et al., 2017).

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Exercise and Lifestyle Habits for a Balanced Microbiome

Physical activity, regular hydration, and proper rest are vital for a healthy microbiome. Exercise improves digestion and encourages a diverse microbiota, while drinking water supports digestive processes (Wegierska et al., 2022).

Reducing alcohol and using antibiotics only when essential can also help avoid disrupting gut flora. Balancing these habits with mindful relaxation can have significant, positive effects on your microbiome over time.

A healthy microbiome offers far-reaching benefits, including enhanced immunity, reduced risk of chronic diseases, and better mental health. Maintaining this balance involves consistent attention to diet, stress, and lifestyle factors.

Prioritising a diet rich in natural foods and avoiding disruptors like excessive antibiotics and daily alcohol can help you sustain microbiome health well into the future, making it a valuable investment in your overall wellness. Let’s look at one of the most important factors when it comes a healthy gut microbiome, our diet.

Restoring a balanced microbiome is essential for addressing digestive conditions like Candida yeast infections, SIBO, IBS, and IBD. Tailoring your diet to include foods that support gut health is a powerful approach. Choosing foods that either contain beneficial bacteria or promote the growth of these microbes helps the gut re-establish its healthy bacterial balance.

A tabletop filled with a variety of fresh vegetables, seeds, beans, and nuts. A wooden bowl contains carrots, asparagus, tomatoes, and more. A white plate has chickpeas, avocado, cabbage, and cucumbers.

The Role of Diet in Gut Microbiome Health

Restoring balance within the gut microbiome is central to improving various health issues like Candida infections, SIBO, IBS, and IBD. Achieving a healthy bacterial equilibrium can be accomplished through careful dietary choices, specifically by incorporating foods rich in probiotics or those that encourage beneficial bacteria growth.

Our microbiome declines when we consume too much processed food, drink too much alcohol, and don’t exercise enough. (Conlon et al., 2015). Many studies involving animals have revealed that diet-induced epigenetic changes are not limited to only one generation, these changes ripple down to descendants. (Hunter 2008)

Monitoring how different foods affect your digestion and overall wellness can provide valuable insights into what best supports your gut health.Being mindful of our food choices and noticing how they affect your digestion can go a long way in managing gut health. A balanced diet rich in natural, whole foods forms the foundation of a thriving gut microbiome. Whole, unprocessed foods, including fruits, vegetables, whole grains, and legumes, are abundant in the fibre essential for feeding beneficial gut bacteria.

Probiotic-rich foods like yogurt, kefir, and fermented vegetables help diversify gut bacteria, while certain antimicrobial foods regulate yeast levels and dysbiotic bacteria, fostering microbial harmony.

Impact of Modern Diets on Microbiome Balance

A wooden platter with breaded fish, chicken wings, mozzarella sticks, French fries, and three small bowls of mustard, mayonnaise, and ketchup sauces showcases the indulgence of fats and oils in our diet on a dark textured surface.

Diet plays a pivotal role in shaping the gut microbiome. Studies show that certain dietary patterns can alter microbial composition, leading to increased levels of potentially harmful bacteria (Shock et al., 2021).

Modern Western diets, high in processed foods and sugars and low in fibre, are strongly linked to imbalances in the gut flora and can even contribute to chronic conditions like obesity, heart disease, diabetes, and cancer. (Clemente-Suárez et al., 2023).

In contrast, diets filled with fresh fruits, vegetables, whole grains, and lean proteins help prevent these diseases and support a balanced gut microbiome (Aziz et al., 2024).

Fibre and SCFAs:
Dietary fibre is essential for the production of short-chain fatty acids (SCFAs), which help maintain gut lining integrity, regulate inflammation, and support immune health. High-fibre diets have shown protective effects against allergic and autoimmune disease, while low-fibre diets are associated with reduced SCFA production and a higher tendency toward inflammatory conditions (Gill et al., 2022).

A balanced diet doesn’t only nourish the body; it nourishes the gut microbiome, leading to benefits like enhanced immunity, resistance to infections, and better digestion. Let’s now look at the key drivers of optimal gut health – beneficial bacteria and what feeds them.

Close-up illustration of multiple blue rod-shaped bacteria against a blurry blue background.

Essential To Any Gut-Healthy Diet: Prebiotics and Probiotics

A healthy gut microbiome creates an environment where beneficial bacteria thrive and pathogenic or opportunistic microbes, such as Candida, are kept in check. This microbial balance is central to preventing dysbiosis, which can lead to symptoms like bloating, inflammation, and even systemic issues.

Probiotics and prebiotics work together as complementary elements to maintain and restore a healthy gut microbiome. Incorporating both into the diet creates a synergistic effect, fostering a balanced microbiome.

Fermented foods deliver live bacteria (probiotics), while fibre-rich fruits and vegetables provide the necessary fuel (prebiotics) to sustain them.

This combination helps restore gut health and contributes to better digestion, immune resilience, and overall well-being. But what are prebiotics and what are probiotics, can I get these through my diet? Yes, you can!

Page of Interest: Prebiotic and Probiotic Foods

Probiotics

Probiotics are live microorganisms, they are beneficial bacteria found in certain foods or supplements. They actively replenish the microbiome by introducing new bacterial strains that can help restore balance, especially after disruptions like antibiotic use, illness, or stress.

Probiotic-rich foods such as yogurt, kefir, sauerkraut, kimchi, and miso introduce beneficial bacteria into the gut, boosting microbiome diversity. Spending time outdoors and engaging in regular physical activity also support microbial health. These bacteria play a role in digestion, immunity, and even mental health by influencing the gut-brain axis.

Prebiotics

Prebiotics are non-digestible fibre that serve as nourishment for beneficial bacteria, fueling their growth and activity in the gut. Naturally present in high-fibre foods like bananas, onions, garlic, oats, and asparagus, prebiotics act as food sources for probiotics, allowing them to thrive, flourish, and multiply. By nourishing the beneficial bacteria already present in the gut—and those introduced through probiotics—prebiotics play an essential role in maintaining long-term microbiome health.

In addition to supporting gut flora, high-fibre, prebiotic-rich foods provide other health benefits. They help stabilize blood sugar levels, keep you feeling fuller for longer, and support regular digestion. Foods like fruits, vegetables, legumes, nuts, and whole grains are excellent sources of prebiotics, and including them regularly in your diet can be a powerful way to bolster gut health.

A healthy gut microbiome can be naturally antimicrobial to excessive levels of Candida albicans as well as dysbiotic (imbalanced) bacteria. A balanced microbiome supports the growth of beneficial bacteria, which helps keep potentially harmful organisms like Candida and certain opportunistic bacteria like E.coli under control through several mechanisms:

Competitive Inhibition: Beneficial bacteria in the gut occupy available resources and space, making it difficult for harmful bacteria and fungi like Candida to establish dominance. This competition limits the growth of pathogenic microorganisms, creating a stable microbial environment that favors health (Ricci et al., 2022).
Production of Antimicrobial Substances: Some beneficial bacteria, such as Lactobacillus and Bifidobacterium species, produce lactic acid, hydrogen peroxide, and bacteriocins. These compounds can lower the gut’s pH or directly inhibit pathogens, making the environment less hospitable for yeast overgrowth and dysbiotic bacteria (Tegegne et al., 2022).
Immune System Support: A balanced microbiome plays a critical role in modulating the immune system. It helps the body recognise and respond to pathogens like Candida effectively without overreacting. This balance reduces inflammation and can prevent conditions where the immune system might otherwise react to harmless organisms, contributing to overall gut health (Belkaid et al., 2014).
Short-Chain Fatty Acids (SCFAs): Beneficial bacteria, especially those that ferment dietary fiber, produce SCFAs like butyrate, which nourish the gut lining and support its integrity. A strong gut lining acts as a barrier, preventing pathogens from crossing into the bloodstream and controlling the environment within the gut to limit the growth of pathogenic microbes.

Incorporating Phytonutrients and Reducing Sugar Intake

Phytonutrients, found in vibrant fruits and vegetables like tomatoes, carrots, leafy greens, and citrus fruits, are linked to numerous health benefits, including reduced inflammation and enhanced gut health. Meanwhile, cutting back on added sugars is crucial; sugar is known to lower beneficial bacteria levels and raise Candida levels, leading to increased inflammation.

Making these dietary changes may seem overwhelming at first, but approaching them as a gradual, long-term lifestyle shift can improve your success. For those seeking structured guidance, the Candida Cleanse Program may be an effective option, offering a comprehensive approach based on years of clinical practice.

By focusing on a diet that supports microbial health, you’ll not only nurture your microbiome but also improve digestion, immune function, and overall well-being.

High-Fibre and Fermented Foods for Gut Diversity

Recent research from Stanford School of Medicine reveals that diets rich in fermented foods significantly increase gut microbial diversity and reduce inflammation. This study observed two groups: one following a high-fibre diet and another consuming a high-fermented-food diet (Weaver 2021).

Only those in the fermented food group showed an increase in microbial diversity, with even small amounts of fermented foods like yogurt, kefir, and kimchi making a measurable difference. The fibre-focused group, on the other hand, did not experience an increase in diversity despite higher fibre intake. These results suggest that fibre alone may not be sufficient to enhance microbiota diversity, underscoring the unique role of fermented foods.

The Benefits of Pairing Fermented Foods with Meat

Recent research has shown that a high meat intake can induce destruction of gut microbiota, which in turn impairs the colon barrier integrity. (Li 2021)

If you eat meat, adding a small amount of fermented food to your meal can be beneficial. Studies indicate that high meat consumption can disrupt gut microbiota and weaken the gut barrier, especially by decreasing beneficial lactobacillus populations, which are essential for maintaining a balanced microbiome. By adding fermented foods like sauerkraut or kimchi alongside meat, you can counter some of these effects and support a healthier microbial community in the gut. (Leeuwendaal et al., 2022).

For those with Candida, concerns about consuming “bad yeasts” in foods like sourdough bread are generally unfounded. Fermented foods support microbial diversity without introducing harmful yeasts, offering a safe way to support gut health during treatment for Candida and other gut issues.

Key Components of a Microbiome-Supportive Diet

Whole, Fibre-Rich Foods

Assorted fresh vegetables, including tomatoes, bell peppers, broccoli, and carrots, closely packed together, viewed from above.

Fresh fruits, vegetables, whole grains, and legumes are essential for nourishing the microbiome. The fibre in these foods serves as a prebiotic, directly feeding beneficial bacteria.

These bacteria, in turn, produce short-chain fatty acids (SCFAs) that help reduce inflammation, strengthen the gut lining, and regulate lipid levels.

Prebiotic fibre from sources like oats, bananas, and onions, especially forms like fructooligosaccharides (FOS) and galactooligosaccharides (GOS), are particularly beneficial for feeding Bifidobacteria and Lactobacilli.

TIP: While some individuals with Candida or SIBO may not tolerate high-fibre foods immediately, incorporating small servings of fermented foods can offer a gentler approach to improving gut health. Gradually increasing tolerance to fibre-rich foods like vegetables, fruits, and legumes can further support a healthy microbiome without causing digestive distress.

Probiotics and Fermented Foods

A wooden bowl filled with yogurt, topped with granola, blueberries, and raspberries, placed on a wooden board with a blue surface underneath.

Probiotic foods like yogurt, kefir, sauerkraut, and kimchi provide live beneficial bacteria that enhance microbial diversity in the gut. Introducing these foods regularly can fortify the gut’s beneficial bacteria, improving resilience to harmful microbes and enhancing immune response.

When consumed with protein-rich meals, fermented foods can mitigate the growth of certain bacteria that are less favourable, making them an ideal pairing with meals like meat.

Antimicrobial Foods

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Foods with natural antimicrobial properties, such as garlic, ginger, and coconut oil, play a unique role in supporting gut balance.

These foods help limit harmful microbes like Candida and prevent pathogenic bacteria from over-colonising the gut, promoting a healthier bacterial environment without disrupting beneficial species.

Health Benefits Well-Beyond Digestion

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A diet that promotes microbiome health also supports the immune system, enhances mental health, and fosters greater resistance to infections.

This holistic approach helps in managing inflammation, improving nutrient absorption, and even stabilising mood by impacting the gut-brain axis.

Together, fibre, probiotics, and antimicrobial foods work synergistically to maintain a resilient, balanced microbiome, creating a foundation for overall wellness and vitality.

In summary, achieving a balanced microbiome through diet involves nourishing good bacteria, controlling harmful microbes, and prioritising foods that support diverse microbial populations. This comprehensive approach has far-reaching health benefits that extend beyond the gut, impacting immunity, mental clarity, and overall health.

Read: 50 Healthiest Snack Ideas

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Gut Microbiome – Key Diet and Lifestyle Takeaways:

A diet high in fibre, especially from fruits, vegetables, and whole grains, nourishes gut bacteria.
Incorporating small portions of fermented foods daily supports microbiome diversity.
Regular exercise, hydration, and balanced lifestyle habits foster gut health.
Signs of improvement include better digestion, moods and mental clarity, and more energy.

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How to Tell if Your Gut Microbiome Is Improving

When your microbiome is on the mend, you’re likely to notice several positive changes. You can tell your microbiome is improving when you start noticing fewer digestive issues like bloating, gas, or irregular bowel movements; instead, your digestion feels calm, with steady, well-formed daily bowel motions.

As inflammation decreases, you might feel relief from pain in areas like your gut, back, or joints. Mental clarity and mood often improve, with sharper focus, less anxiety, and an increased desire to connect socially.

Better sleep becomes noticeable, with fewer wake-ups and a more refreshed feeling in the morning. You might also find yourself less reliant on medications for common issues like indigestion or headaches, and naturally more inclined toward fibre-rich, gut-friendly foods that further support long-term health.

Here’s a check-list on how to tell if your gut microbiome is on the mend:

Improved Digestive Comfort:
You may experience less bloating, reduced gas, and overall fewer gut issues. Your digestive system feels calmer, with a noticeable reduction in noises or discomfort. Bowel habits are steadier, with reduced constipation or diarrhoea.
Healthy Bowel Movements:
You’re likely to have one or two well-formed bowel movements a day, without repeated or urgent trips to the bathroom. Elimination becomes easier, with no feelings of incomplete evacuation.
Reduced Pain and Inflammation:
Chronic pain or inflammation in various areas—such as the gut, neck, lower back, or joints—begins to subside as your microbiome stabilises.
Sharper Mental Clarity:
A well-balanced microbiome can help sharpen your focus and memory, making it easier to concentrate and recall information.
Improved Mental Health:
With a healthier gut, you might notice a more positive outlook, greater social engagement, and a stronger desire to spend time with family and friends.
Lowered Stress and Anxiety:
Your overall stress and anxiety may decrease, accompanied by a reduction in tension around the head, neck, and face.
Better Sleep Patterns:
You may find it easier to fall asleep, stay asleep through the night, and wake up feeling more refreshed and energetic.
Reduced Dependence on Medication:
An improving microbiome often means fewer trips to the pharmacy for antacids, pain relievers, or other over-the-counter remedies.
Enhanced Dietary Awareness:
You become more mindful of dietary choices, naturally gravitating toward healthier, fiber-rich foods that support long-term microbiome health.

If you’ve had a comprehensive stool test, an increase in beneficial bacteria—especially when reaching a 4+ rating—typically aligns with these improvements.

Over time, as you build resilient colonies of good bacteria, you’re less likely to experience issues with Candida or other yeast, both in your gut and beyond.

We have have developed a complete Candida Cleanse treatment program that includes dietary adjustments, lifestyle changes, probiotics, enzymes, and natural antifungals, based on 35 years of experience. For more details, visit Yeastrix.

Eric Bakker N.D New Zealand naturopath in a suit stands in front of a wall displaying framed naturopathic certificates and a human body anatomy poster.

Eric’s Holistic Approach to Gut Microbiome Restoration

After years of clinical experience, I’ve seen that the key to overcoming gut microbiome dysfunction isn’t a quick fix—it’s a comprehensive, holistic approach that addresses the root causes, not just the symptoms.

Long-term relief from gut dysfunction and resulting chronic illness requires attention to multiple areas of health, from personal hygiene to gut health and immune resilience. It’s totally achievable.

In addition to understanding the role that diet, lifestyle, and stress plays when it comes to gut microbiome health, it’s vital to build a defence from within. Supporting the gut and immune system with high-quality supplements, probiotics, and nutrient-rich dietary choices is essential.

Eric’s Guidelines for Optimal Gut Microbiome Health

In my clinical experience, these habits support a balanced microbiome and great gut health:

Learn how to chew your food, relax, and avoid screens when you eat.
Increase daily intake of high-fibre foods, especially fresh fruits and vegetables.
Limit meat intake, prioritising fresh fish, tofu, eggs, beans, etc., as a protein source.
Add small portions of fermented foods to your daily diet, such as yogurt, kefir, or kimchi.
Include beans, lentils, and chickpeas regularly for fibre and variety.
Drink sufficient water daily.
Exercise regularly, walk daily, and practice relaxation to reduce stress.
Minimise alcohol intake.
Minimise antibiotic and drug intake.

Eric Bakker N.D.

Greetings! I am a naturopathic physician from New Zealand. Although I’ve retired from clinical practice since 2019 after 34 years of clinic. I remain passionate about helping people improve their lives. You’ll find I’m active online with a focus on natural health and wellbeing education through my Facebook page, Reddit page and YouTube channel, including this website.