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Do you want to start feeling better?

Yes, Where Do I Start?

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

Tend Your Inner Garden to Transform Your 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 patients. 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 is a panacea for every human health condition (or 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]. So, let’s start with what the gut microbiome is, and then we will dive into what you can do to keep it in balance. 

What is the Gut Microbiome? 

It may be strange to think about, but we have trillions of microbes all around and inside of us. Our gut specifically is home to more than 1,000 types of microorganisms, including many types of bacteria, viruses, archaea, and other single-celled organisms—this collection as a group is referred to as the gut microbiome. While microbes can be found all throughout the gastrointestinal (GI) tract from mouth to anus, the vast majority of the gut microbiome lives in your colon (large intestine) [1, 2]. You’re probably wondering where these microbes come from and how they end up in our intestines. Indulge me as I share a general timeline of human gut microbiota development and how we each end up with a unique gut ecosystem.

Gut Microbiome Development

The human gut microbiome may start taking shape in the womb, and it continues to develop in early life until the community becomes stable, usually by the age of three [2, 3]. This isn’t to say that the gut microbiome never changes once we hit this age, but in general your unique microbial footprint has been created by that time. 

Our gut microbiome is as unique as our fingerprint—meaning, there are no two alike [4]. We end up with our signature gut microbiome based on our specific influences and circumstances. Here are the major factors that help to shape the gut microbiome you’ll carry into adulthood [2, 3]:

What is the gut microbiome

As you can see, there are many variables when it comes to gut microbiome development. As I discuss in Healthy Gut, Healthy You, diet plays an important role in regulating gut microbial balance and diversity as we age, but medications, toxin exposure, and stress are all important variables as well.

Research suggests establishing a robust gut microbiome in childhood and maintaining gut microbial balance as we age is important for our future health. But I mentioned earlier that there are no two gut microbiomes alike, so how do we know what a healthy gut microbiome is? Let’s unpack that by getting into the concepts of eubiosis and dysbiosis.

Key Takeaway: Your gut microbiome begins to develop in the womb. It’s unique to you based on a variety of different factors and is mostly established by the time you hit age three. 

Eubiosis Versus Dysbiosis

Normally, the inhabitants of your gut live harmoniously with each other and with you. You provide their fuel (resistant starches, fermented foods, and dietary fiber), and they create substances (like vitamins and short-chain fatty acids) that your body needs to maintain homeostasis. This mutually beneficial relationship is referred to as eubiosis or balance in the gut microbial community [1].

When your gut microbiome is in balance, you can reap many benefits inside and outside the gut, like a healthy gut barrier, more thorough digestion, adequate production of short-chain fatty acids (SCFAs), vitamins, and antioxidants, and better insulin sensitivity. And it doesn’t stop there—a balanced gut microbiome means your immune system functions better, you have less inflammation, lower risk of pathogens taking hold in your GI tract, 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 symbiotic to unfriendly. 

When the balance in your gut starts to shift toward dysbiosis (an imbalance of gut microbes), you can begin to experience a myriad of negative effects. Of course, dysbiosis can trigger the usual suspects like gas, bloating, diarrhea, constipation, indigestion, reflux, food reactivity, and heartburn. But you can also experience symptoms that you may not necessarily tie to poor gut health, like [5]:

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

There are many conditions that have been associated with dysbiosis in various research trials. Here’s a table detailing some of the findings on the connection between dysbiosis and symptoms outside the gut:

Condition Dysbiosis Connection
Brain Fog
  • Non-celiac gluten sensitivity (NCGS) contributes to gut dysbiosis [6]. 38% of patients with suspected NCGS reported brain fog [7].
  • Headaches, brain fog, and fatigue are common symptoms of NCGS [8].
  • Brain fog is associated with many gut health conditions that involve imbalances in the gut ecosystem, including irritable bowel syndrome (IBS) and SIBO (overgrowth of bacteria in the small intestine) [9, 10], Crohn’s disease (a type of inflammatory bowel disease ) [11], celiac disease [12], and NCGS [7, 13]. 
Depression and Anxiety
  • Gut disturbances may play a key role in anxiety for people with IBS [14].
  • 39% of patients with NCGS report anxiety [7].Regulating intestinal microbiota improves anxiety symptoms [15].
  • IBS patients were three times as likely as healthy individuals to have either anxiety or depression [16].
  • Participants with IBS plus high anxiety and depression had lower microbial diversity than controls and subjects with only IBS [17].
  • Fatigue may occur in a large number of IBS patients [18, 19]
  • Treating leaky gut can reduce fatigue and other symptoms in patients with chronic fatigue syndrome [20].
  • Treating the gut with a low FODMAP diet can improve fatigue in those with IBS and fibromyalgia [21, 22].
  • One-third of people with functional GI complaints had a triad of IBS, fatigue, and musculoskeletal pain [23]. 
  • Migraine patients may be more likely to have IBS [24]. 
  • 54% of gluten-sensitive individuals identified headaches as a symptom [7].
  • Dietary changes significantly reduced the impact of migraine on patients with NCGS [25].
  • 54% of patients with suspected NCGS reported having headaches [7]. 
Joint Pain
  • A two-week elemental diet (a gut therapy often used for SIBO patients) improved joint stiffness and pain in patients with rheumatoid arthritis [26].
  • A diet low in starch and sugar reduced muscle and joint pain and tiredness in IBS patients (one-third of the patients no longer qualified for an IBS diagnosis after treatment) [27].
  • Research shows a connection between rheumatoid arthritis, a painful autoimmune disease, and gut imbalances [28, 29, 30].
  • Gut dysbiosis may also contribute to the development of osteoarthritis [31].
Skin Conditions
  • Skin issues related to gut health include acne [32], eczema [33, 34, 35] psoriasis [36, 37], and other autoimmune skin conditions.
  • There’s a much higher prevalence of rosacea in SIBO patients when compared to healthy controls [38].
  • 93% of rosacea patients with SIBO saw complete elimination or significant improvement in rosacea lesions after they treated their SIBO [38].
Sleep Disorders
  • Sleep disorders are more common in IBS patients than healthy controls [39].
Hormonal Imbalances
  • Gut inflammation can disturb the balance of female hormones [40]. 
  • Conditions associated with imbalanced hormones, such as PMS, PCOS, obesity, endometriosis, and breast cancer, are associated with imbalances in the digestive tract [41].
  • Gut inflammation can cause male hormone imbalances, resulting in fatigue, low libido, erectile dysfunction, muscle loss, and poor memory [42].
  • Stressors can alter the microbial balance and production of gut flora metabolites, which can cause physiological changes in the brain via the gut-brain axis [43].
  • Stress can disrupt the balance of the microbes in your gut microbiome, causing inflammation, immune system dysfunction, and an increase in digestive symptoms like bloating [44, 45].
  • Gut inflammation can damage your body’s ability to use thyroid hormone, leading to hypothyroid symptoms [46].
  • Hashimoto’s disease and Grave’s disease are autoimmune conditions that are closely linked to gut imbalances [47].
  • Treating certain gut infections has been shown to improve thyroid autoimmunity [48, 49, 50, 51, 52].
  • Patients with systemic lupus erythematosus (SLE) have lower gut microbiome diversity compared to healthy controls [53]. 

The moral of the story here is that your gut has a massively far-reaching impact on your health. As a clinician, I frequently meet with patients who have overlooked a problem in their gut as the true cause of their health ailments because the symptoms resemble something else. The good news is that diet, lifestyle, and other natural strategies can be harnessed to heal your gut. When you restore robust gut health, many of your nagging symptoms can be improved or completely reversed. So, let’s discuss how you can tend your inner garden to improve your health and quality of life.

Key Takeaway: 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 Your Gut Ecosystem

We’ve established that imbalances in the gut microbial community 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 you abuse the “outside” (your body) with unmanaged stress, lack of sleep and exercise, and an inflammatory diet, life on the inside (your gut microbiome) suffers.

Let me illustrate this further with an analogy. Your gut and gut microbiome are a life system as complex as a rainforest. This ecosystem lives in the environment that’s your body, just like some rainforests live in the environment of South America. It’s the health of the environment that dictates the health of the ecosystem. If the rainforest has an environment with plenty of rain, it will thrive; if there’s a drought, the rainforest can die. When it comes to your gut (the ecosystem) and body (the environment), a healthy body equals healthy microbes. Providing your gut microbes with the healthiest environment possible means you can reap all the benefits I shared earlier.

But we’re all different and require different things—what’s good for one person may be disastrous for another. It’s also important that you understand the gut microbiome can’t be micromanaged—it’s far too complex. While we have research data to suggest certain types of microbes are beneficial, it doesn’t mean we can just pop a pill and everything will balance itself out. 

Akkermansia muciniphila is a perfect example of this. I go into great detail in this video about the misleading truth about this commensal gut bacteria. This microbe is taking social media and functional medicine clinics by storm lately due to its proposed health benefits [54]. While mechanistically, it seems fantastic, when you dive into the research, the claims that are being made about Akkermansia may not live up to scrutiny. Let me explain.

In my clinical experience, adding in one strain of bacteria without first focusing on the environment sets you up for less-than-stellar results. This is why I advocate for an individualized, root-cause approach to gut health that focuses on your specific ecosystem. We need to first dedicate ourselves to the foundations that create a healthy gut environment (i.e., diet, sleep, stress management, time in nature, exercise, and social relationships) before we try to manipulate the system with one strain or type of microbe. So, what does that look like in practice? Let’s go into the specifics of how to build a foundation that supports great gut health.

Key Takeaway: The gut ecosystem is complex and can’t be micromanaged. Rather than tactics that aim to control specific bacteria, like strain-specific probiotics, it’s best to focus on personalized interventions that nourish and support gut microbial balance. 

Diet and Lifestyle for Gut Microbiome Balance

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

  • Reducing allergens and intolerances
  • Providing an appropriate amount of microbial fuel (prebiotics and FODMAPs)
  • Managing carbohydrate intake to promote great blood sugar control
  • Focusing on wholesome, unprocessed foods

Fortunately, we have a spectrum of choices when it comes to diet therapy. If you’re generally healthy and want to maintain your vibrant body, a Mediterranean-type diet is a great option. If you’re struggling with negative gut or other symptoms, you may 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 your specific needs and lifestyle. It may be best to work with a 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 patients who have the most balance in their lives tend to improve the most. 

Here are some lifestyle changes that may help you enhance your gut health:

What is the gut microbiome

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

Probiotics for Gut Microbiome Balance

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

  • Increase the bacterial diversity, or health, of your bacterial community [55, 56, 57]
  • Fight pathogens (harmful bugs) and their toxins [55, 56, 58, 59, 60]
  • Promote a more rapid recovery from imbalanced gut organisms [55, 56]
  • Promote a healthy immune response in your gut [55, 56, 61, 62, 63]
  • Reduce gut inflammation [55, 56, 57]
  • Encourage the growth of healthier microbes in your gut [55, 56, 61]
  • Reduce leaky gut (damage to your gut lining) [55, 56, 64, 65, 66]

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 these three categories [67]:

What is the gut microbiome

In the clinic, we favor a triple therapy probiotic approach—this means we use all three probiotic categories in combination. Not only have we found this method to provide the most benefit, research supports the use of a variety of different species of probiotics [68, 69, 70]. 

Here’s a list of the conditions probiotics have been shown to improve:

As you can see, probiotics may be beneficial for almost any condition you can think of. But I want to add an asterisk here—creating a healthy foundation for your gut ecosystem (with diet and lifestyle) is crucial for your long-term success. If you start with probiotics and neglect food, sleep, stress, exercise, nature, and the like, you’re putting the cart before the horse and probably won’t see maximum benefit. 

If you’re open to trying probiotics, here’s the protocol we’re using in the clinic:

What is the gut microbiome

If you’ve tried probiotics before without much success, you may not have given it enough time or used a therapeutic dose, so I encourage you to try again using this protocol. 

Key Takeaways: A gut-healing diet and lifestyle modifications create the foundation for a balanced gut microbiome. If you need additional support, layering in probiotics can help get you across the finish line. 

Gut Microbiome Balance = Better Health 

Your gut microbiome is the unique ecosystem of bacteria, fungi, and archaea that live in your GI tract. The health of your gut microbiome is impacted by a variety of factors, like where you live, your health as a child, your diet and lifestyle, and the medications you use. A gut microbiome in balance is associated with robust health. On the flip side, when your gut microbiome is out of balance, you can suffer from not only gut symptoms but issues that seemingly don’t have anything to do with your gut, like brain fog, skin issues, depression, autoimmunity, headaches, and joint pain. 

More often than not, gut microbiome imbalances are a symptom of larger issues like poor diet, unmanaged stress, insufficient or restless sleep, and lack of exercise. The great news is that there’s a lot we can do to help reestablish a symbiotic relationship with your gut microbes. Diet and lifestyle are the foundation, and then we can layer in probiotic supplements to help maintain a healthier community of microbes in your gut. 

If you work through these simple strategies but still find you’re 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 patients 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.

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