Friendly Bacteria and Fungus Gut Relationship

author avatar Dr. Eric Berg 04/08/2024

The relationship between good bacteria and gut health is one of the most important in your body, but not many people understand it.

Learn about how your gut microbiome relies on friendly bacteria and what you can do to support your digestive health while improving your overall well-being.

Understanding the Gut Microbiome

Your gut is like a bustling city, home to trillions of inhabitants - bacteria and fungus. These tiny citizens play critical roles in your health, forming an ecosystem called the gut microbiome. Just think of it as New York City at a microscopic level.

In this metropolis within you, friendly bacteria and fungus coexist. But here's a surprising fact: while we've studied bacterial residents extensively, our knowledge about fungal denizens lags because they're tricky to culture.

The Bacterial-Fungal Alliance

Fungi also has an important role in the gut microbiome.

Friendly bacteria and fungus work together to keep your digestive tract healthy and efficient.

The Understudied Fungi

We often overlook fungal entities due to difficulties studying them. However, recent studies are starting to peel back layers of these mysterious microbes, revealing their importance for maintaining balance in our guts' delicate ecosystem.

Gut bacteria, gut flora, microbiome. Bacteria inside the small intestine

The Role of Environmental Changes in the Gut

Sudden shifts in the gut microbiome can have significant health consequences that it is important to understand.

Environmental Factors That Trigger The Switch

When the gut becomes unbalanced, once friendly bacteria can end up harming your digestive system.

Different factors can trigger this unbalance. These include high sugar intake, overuse of antibiotics, stress levels, and even lack of sleep.

Your gut is an ecological wonderland that thrives on equilibrium and a disruption could lead your microbes to cause you harm.

Defining Mutualism, Commensalism, and Parasitism

Our gut is a complex system and each bacteria or fungus plays a specific role in this environment. To better understand their roles, let's explore the three main types of relationships: mutualism, commensalism, and parasitism.

Exploring Mutualism in the Gut

Mutualistic relationships are beneficial for the gut and for the bacteria involved.

An example would be certain bacteria producing essential vitamins, which we cannot produce ourselves but need to survive. In return for these vital nutrients, we give the bacteria space to live and thrive within us.

Commensalism - A One-Sided Benefit

Commensals are bacteria who benefit without causing any harm or advantage to the host organism, essentially freeloading off your gut's resources.

For instance, many fungi living inside our guts extract nutrition from what we eat but don’t necessarily offer anything beneficial back.

Parasitism - The Unfriendly Relationship

Parasitic interactions are when one party gains at the expense of another.

Some gut microbes can become parasites when they outnumber the good bacteria, causing health issues like gastrointestinal disorders. Not all microbe-related connections are the same.

The Balancing Act Between Bacteria and Fungus

Though bacteria are commonly discussed concerning gut health, fungi also play a vital role.

Like bacteria, our guts are home to various friendly fungi essential in maintaining balance within our microbiome.

Fungi may not be as well-examined due to the challenges in culturing them, yet they certainly don't come up short regarding their jobs. Fungi can help keep bacteria in check by preventing them from turning pathogenic or harmful.

The Unseen Work Behind Gut Balance

To fully appreciate how fungi maintain harmony among billions of microbes living inside us requires understanding mutualism – one relationship between different species where both parties benefit.

This mutualistic partnership allows these microscopic organisms (both fungal and bacterial) to work harmoniously to achieve optimal health for their host.

Mutualism aside, though, commensal relationships exist where one organism benefits without harming or helping its partner.

Fungal Friends vs Bacterial Bullies

Dysbiosis is an imbalance resulting from drastic shifts within our gut ecosystem, such as taking antibiotics or antifungal treatments.

When the bacterial population gets out of hand due to an absence of friendly fungi (thanks to that round of antibiotics), pathogenic bacteria can take over and cause problems.

The Impact of Antibiotics and Antifungal Treatments on Gut Health

The effects of antibiotics and antifungal drugs must not be disregarded when discussing intestinal well-being.

The Consequences of Antibiotic Use

Antibiotics are effective weapons against bacterial infections but indiscriminately attack beneficial and harmful bacteria.

They kill both harmful bacteria causing your illness and the friendly ones that keep your gut healthy. This disruption to your microbiome often leaves room for fungus to flourish.

One surprising outcome is an increase in fungal infections post-antibiotic use. When antibiotics wipe out bacteria indiscriminately, it creates a vacuum that fungus happily fills. The result? A disrupted balance within our guts.

Antifungal Treatments and Their Effects

Just as antibiotics can lead to fungal overgrowth, so can antifungals cause bacteria issues. Research shows how some patients develop bacterial infections after aggressive antifungal treatments – an unfortunate irony.

While these drugs do well at tackling pathogenic fungi head-on, they may inadvertently give harmful bacteria free rein by disrupting the delicate microbial ecosystem inside us.

Natural Remedies for Pathogenic Fungus and Bacteria

Our bodies are a complex and varied habitat of beneficial bacteria and fungi; however, certain species may become pathogenic when the equilibrium is disturbed.

But when this balance gets disrupted, some species can become pathogenic - harmful to our health. Fortunately, there are natural remedies available that may help keep these unwanted guests under control.

Bottle of oregano essential oil

The Power of Oregano Oil

Oregano oil is no ordinary kitchen herb. Packed full of compounds like carvacrol and thymol, it has potent antimicrobial properties.

These active components disrupt the cell membranes of pathogens, making oregano oil an effective deterrent against bacterial and fungal invaders.

So, how do you use oregano oil? Dilute it with a carrier oil (like coconut or olive) before applying topically on skin infections. Orally ingesting capsules can also aid gut health, but consult your healthcare provider first.

Gymnema sylvestre

Gymnema sylvestre, known as the 'sugar destroyer,' isn't just helpful in controlling blood sugar levels, it also has anti-fungal properties.

Studies suggest gymnema can inhibit yeast growth, including Candida albicans, one common cause behind thrush and other unpleasant infections.

Gymnema is typically consumed as a tea or taken in capsule form after meals. But always remember to check dosage instructions carefully.

Friendly Bacteria and Butter

Many people following a keto diet wonder, "Is butter keto-friendly?" The answer is generally yes, as butter contains minimal carbohydrates, making it suitable for low-carb diets.

Beyond its keto compatibility, butter can also have a role in supporting gut health. It contains butyric acid, a short-chain fatty acid that acts as a food source for friendly bacteria in the gut.

These beneficial microbes are crucial to digestion, immunity, and overall well-being. So, while enjoying butter on a keto diet, you may also indirectly support your gut microbiome, which can have long-term health benefits.


The symbiotic relationship between beneficial bacteria, fungi, and gut health is essential yet often overlooked.

Environmental factors, such as antibiotic use and high sugar intake, can disrupt this delicate balance, leading to gut dysbiosis and potential health issues.

Understanding microbial relationships and exploring natural remedies like oregano oil and Gymnema sylvestre can help support gut health.

Even dietary choices, like consuming butter, can indirectly influence gut microbiome balance. By fostering a healthy gut ecosystem through lifestyle choices and natural interventions, we can promote digestive health and overall well-being.

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