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What Is the Gut Microbiome & Its Impact on Your Health?

Written by Dr. Michael Ruscio, DC on October 17, 2024

Written by Dr. Michael Ruscio, DC on October 17, 2024 — Reviewed by Hilary Watts

• What is the Gut Microbiome?|
• Eubiosis Versus Dysbiosis|
• Optimizing Your Gut Ecosystem|
• Gut Balance = Better Health|

I spend a lot of time researching and talking about the gut microbiome. Not just because it fascinates me but because it’s an amazing organ that arguably impacts every aspect of our being.

The microbes in your gut influence gut health, but they also modulate functions like nutrient absorption, inflammation, and immune system function—this means the gut microbiome has far-reaching effects all throughout the human body. 

As a clinician and researcher, I’m always looking for the most impactful, efficient ways to improve the quality of life and health outcomes for my clients. If there’s one lever we can pull to accomplish both of these, it’s targeting gut health. 

I’m not suggesting that healing the gut will cure every human health condition, or that it’s the only necessary treatment. But since the gut microbiome is intimately tied to the rest of the body, it makes sense to pay attention to it 1. 

What is the Gut Microbiome? 

It may be strange to think about, but we have trillions of microbes all over us and inside us. 

Our gut is home to more than 1,000 types of microorganisms, including many types of bacteria, viruses, archaea (bacteria-like organisms), fungi, parasites, and protists (organisms that aren’t animals, plants, bacteria, or fungi). This collection as a group is referred to as the gut microbiota. 

The gut microbiome is the term for the genetic signature (genome) of the collection of organisms. You can think of the microbiome as a house and the microbiota as its inhabitants.

While microbes can be found all throughout the gastrointestinal (GI) tract from mouth to anus, the vast majority of the gut microbiome is in your colon (large intestine) 1 2. You’re probably wondering where these microbes come from and how they end up in our intestines. 

Gut Microbiome Development

The human gut microbiome starts taking shape in the womb, and it continues to develop in early life until it becomes stable, usually by the age of three 2. This isn’t to say that the gut microbiome never changes once we hit this age, but in general our unique microbial footprint is formed by that time. 

Our gut microbiome is as unique as our fingerprint—there are no two alike 3. We end up with our signature gut microbiome based on our specific influences and circumstances. 

Major factors that help to shape the gut microbiome we carry into adulthood are 2:

• Our mother’s gut, vaginal, and oral microbiome while we were in the womb
• Whether we were born vaginally or by C-section
• When we were born: prematurely, on time, or late
• Any antibiotics we might have had up to the age of three
• Whether we had breast milk or formula, and what kinds of solid foods we started to eat
• Our genetics, where we grew up, and our immediate environment (whether we had pets, siblings, too much or too little cleanliness, or stress)

Many variables affect gut microbiome development. Beyond the age of about three, as I discuss in Healthy Gut, Healthy You, our diet plays an important role in regulating gut microbiota balance and diversity. Medications, toxin exposure, and stress are also important variables.

Research suggests that establishing a robust gut microbiome in childhood and maintaining gut microbial balance as we age are important for future health. But I mentioned earlier that no two gut microbiomes are alike, so how do we know what a healthy gut microbiome is? 

Let’s unpack that with the concepts of eubiosis and dysbiosis.

Eubiosis Versus Dysbiosis

Many of the inhabitants of your gut live harmoniously with you. You provide their fuel (resistant starches, fermented foods, and dietary fiber) and a place to live, while they keep harmful microorganisms at bay and create substances (like vitamins and short-chain fatty acids) your body needs to function well. This mutually beneficial relationship is referred to as eubiosis or balance 1.

When your gut microbiome is balanced this way, it brings many health benefits. For example, it can promote:

• A healthy gut barrier
• More thorough digestion
• Increased energy from short-chain fatty acids (SCFAs)
• Better nutrient levels and absorption
• Better blood sugar control and insulin sensitivity 

It doesn’t stop there—a balanced gut microbiome also means your immune cells function better, you have less inflammation and a lower risk of gut pathogens, and you may be better able to maintain a healthy weight 1. 

But now we need to talk about what happens when this relationship goes from being mutually supportive to unfriendly. 

When the balance in your gut starts to shift toward dysbiosis (an imbalance of gut microbes), you can begin to experience many negative effects. 

Dysbiosis can trigger the usual suspects like gas, bloating, diarrhea, constipation, indigestion, reflux, food reactivity, and heartburn. But it can also produce symptoms you may not necessarily tie to poor gut health, like 4:

• Fatigue
• Depression or anxiety
• Brain fog
• Insomnia
• Acne or other skin conditions
• Hormonal imbalances
• Hypothyroid symptoms
• Joint pain
• Autoimmunity
• Dry or thinning hair
• Cravings
• Nutrient deficiencies
• Weight gain
• Headaches

If you have one or more of these symptoms routinely, it could indicate an imbalance in your gut microbial community. 

Many conditions have been associated with dysbiosis in various research trials. Here’s a table of findings on the connection between dysbiosis and symptoms outside the gut:

Many conditions like autoimmunity, skin issues, joint pain, and brain fog are rooted in poor gut health. Improving the balance of microbes in your gut can have a profound impact on your health. 

Optimizing the Gut Ecosystem

We’ve established that imbalances in gut microbial species are associated with chronic illnesses and a variety of symptoms. But I want to make it clear that gut dysbiosis itself is rarely the root cause. 

Rather, dysbiosis develops secondary to other problems. Think of it this way: Life on the outside affects life on the inside. If we abuse the “outside” (the body) with unmanaged stress, a lack of sleep and exercise, and an inflammatory diet, life on the inside (the gut microbiome) suffers.

I advocate for an individualized, root-cause approach to gut health that focuses on each client’s unique gut microbiome . 

Optimizing gut health requires dedication to the foundations that create a healthy gut environment. These include:

• A nutrient-dense, anti-inflammatory diet
• High-quality sleep
• Effective stress management
• Gut-boosting exercise
• Supportive social relationships

Let’s examine these diet and lifestyle pillars via my work with clients.Diet and Lifestyle for Gut Microbiome Balance

In my experience in the clinic, diet is unquestionably the most impactful intervention for improving gut health. The overall goals of diet therapy for balancing the gut ecosystem include:

• Reducing allergens and intolerances
• Providing an appropriate amount of microbial fuel (prebiotics and certain food fibers called FODMAPs)
• Managing carbohydrate intake to promote great blood sugar control
• Focusing on whole, nutrient-dense foods
• Reducing highly processed foods with added sugar

Fortunately, there’s a spectrum of choices when it comes to diet therapy. For clients who are generally healthy and want to maintain their vibrance, a Mediterranean-type diet is a great option. 

Those who are struggling with symptoms in the gut or elsewhere often do well by starting with the Paleo diet and moving on to a more restrictive option, like a low-FODMAP diet, if needed. 

Since there’s no one perfect gut microbiome diet, the key is to find what works for each person’s specific needs and lifestyle. I recommend working with a gut-focused clinician, registered dietitian, or certified nutrition specialist who can tailor a meal plan for you. 

While food is really important for gut health and gut microbiome balance, we can’t forget about environmental factors and lifestyle. One of the things I’ve realized over the years is that my clients who have the most balance in their lives tend to improve the most. 

I encourage the following lifestyle changes to help my clients enhance their gut health:

• Reduce toxins
• Get enough sunshine
• Walk as often as possible
• Manage stress
• Spend time in nature
• Get enough exercise, but not too much
• Get restful sleep
• Cultivate healthy relationships and social connections

For many people, improving diet quality and getting lifestyle dialed in is enough to bring balance back into the gut ecosystem. But for those who’ve made good progress but still struggle with symptoms, probiotics are a great next step. 

Probiotics for Gut Microbiome Balance

Probiotic supplements can help improve the balance of organisms in the gut, reduce overzealous immune system activity, and reduce inflammation. They’re antibacterial, antifungal, and antiparasitic, which means probiotics can help clean out bad bugs and promote a healthier community of microbes in the gut. If you’re interested in the specifics, probiotics can 40 41:  

• Increase the health of the bacterial community Fight pathogens (harmful organisms) and their toxins 
• Promote a faster recovery from imbalanced gut organisms 
• Promote a healthy immune response in the gut 
• Reduce gut inflammation 
• Encourage the growth of healthier microbes in the gut 
• Reduce leaky gut (damage to the gut lining) 

But with all the probiotic options out there, how do you know which one to choose? Nearly every probiotic product can be classified into one of three categories 42:

• Lactobacillus and Bifidobacterium species
• Saccharomyces boulardii, a type of yeast

Soil-based probiotics, typically Bacillus species

In the clinic, we favor a triple therapy probiotic approach—this means we use all three probiotic categories in combination for at least 2–3 months. Not only have we found this method to provide the most benefit, but research supports the use of a variety of different species of probiotics 43 44 45.

Studies have shown that probiotics can improve a wide range of conditions, such as autoimmune diseases 46, gut disorders 47, seasonal allergies 48, and hormone imbalances 49:

Probiotics may be beneficial for a wide array of conditions, especially when they are part of a diet and lifestyle that support the gut ecosystem. 

However, starting with probiotics while neglecting to improve food, sleep, stress, and exercise is like putting the cart before the horse—it probably won’t yield much benefit. 

Gut Microbiome Balance = Better Health 

The health of the gut microbiome is impacted by a variety of factors, starting in your mother’s womb and continuing throughout life. 

A balanced gut microbiome is associated with robust health. On the flip side, an imbalanced gut microbiome can contribute to gut symptoms and issues that may not seem related to the gut. 

Gut microbiome imbalances may stem from larger issues like poor diet, unmanaged stress, inadequate sleep, and a lack of exercise. The great news is that healthy diet and lifestyle habits can reestablish a healthy microbiota. 

If you are struggling with nagging symptoms, my book, Healthy Gut, Healthy You, includes the entire step-by-step gut healing process I use in the clinic. If you’d like more personalized support, please contact us at the Ruscio Institute for Functional Health to schedule an appointment.

The Ruscio Institute has developed a range of high-quality formulations to help our clients and audience. If you’re interested in learning more about these products, please click here. Note that there are many other options available, and we encourage you to research which products may be right for you. The information on DrRuscio.com is for educational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.