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Bacteria, fungi, yeast, protozoa, parasites, and viruses lurking in your gut might sound like a scene straight out of a horror movie. But believe it or not, these microorganisms hold the key to your overall health and well-being. They make up a vast community of trillions (with a “T”) of organisms known as the microbiome, which resides in and on all of our bodies. What’s fascinating is that each person has a unique microbiome, as individual as a fingerprint.
The human microbiome can be found in various parts of the body, including the skin, mouth, gastrointestinal tract, and respiratory tract. However, the most extensively studied and largest microbial community exists in our gut—referred to as “the gut microbiome.”
In my journey to health, I couldn’t help but stumble across the mountain of information on the subject of the microbiome. Through webinars, courses, reading the research and my own personal experience, I’ve learned a lot about the body’s microbiome. Contrary to what you might think, the organisms residing in our large intestine are not invaders but rather welcome and beneficial colonizers. It’s astonishing to know that they weren’t even acknowledged until the late 1990s. And nowadays, the microbiome is one of the hottest topics in the health sector due to its profound influence on our well-being.
Some say that our first encounter with the microbiome occurs not in the womb, but during the journey through the birth canal into this world. However recent research suggests that there may be some colonization in the womb prior to birth. That said, the birth canal is loaded with bacteria, and this is actually a good thing. Interestingly, infants delivered via C-section have a significantly different microbiota compared to those born vaginally. The bacterial organisms found in C-section infants resemble those found on their mother’s skin surface and in hospitals, rather than the ones present in the birth canal.
As such, development of the gut microbiome starts early in life and continues throughout our entire life cycle. Many factors can shape our microbiome, such as lifestyle, stress levels, exercise habits, sleep patterns, and medications. However, it is our diet that has a tremendous impact on this microbial community within us.
One thing I know for sure is that providing our microbiome with the nutrients it needs to thrive and maintain our well-being is of utmost importance.
While the field of microbiome research is rapidly evolving, with new insights emerging about the composition and function of microbial communities and their impact on human health, we know that the microbiome interacts with the human body in various ways and that the bacteria in the gut microbiome have a profound influence on our overall health.
These colonizers affect our metabolism, assist in weight management, aid in digestion and nutrient absorption, regulate and train our immune system, protect against harmful bacteria and pathogens by producing antimicrobial compounds, synthesize essential vitamins, and even influence our mood, mental health, and response to medications.
Studies have shown that disruptions or imbalances in the microbiome, known as dysbiosis, can be associated with a wide range of health conditions, including gastrointestinal disorders, metabolic disorders, autoimmune diseases, allergies, and even mental health disorders.
Understanding the microbiome and its influence on health has paved the way for new approaches in medicine, such as personalized medicine and microbiome-based therapies.
Assessing the health of your microbiome is a complex task and there is still much to learn about the intricacies of microbial communities and their impact on human health. But because of the advances in understanding and study about the microbiome there are simple tests available these days to determine the health of your microbiome (more on that in a moment). However, there are a few indicators that can provide some clues into the overall health of your microbiome:
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- Diversity: A healthy microbiome is characterized by a diverse group of microbial species. Higher microbial diversity is generally associated with better health outcomes. Microbiome testing can analyze the composition of your microbial community and provide insights into its diversity. I get my “gut intelligence” test done through a company in San Jose, CA called Viome www.viome.com (no, they are not paying me for this referral/endorsement).
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- Symptoms and Conditions: Paying attention to any digestive issues such as bloating, gas, constipation, or diarrhea, can indicate an imbalance in your gut microbiome. Additionally, certain health conditions like inflammatory bowel disease, irritable bowel syndrome, allergies, or skin conditions may be linked to microbiome dysbiosis.
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- Diet: Your diet plays a significant role in shaping your microbiome. A healthy microbiome thrives on a diverse range of plant-based fibers, fruits, vegetables, whole grains and fermented foods. Consuming a diet high in processed foods, added sugars, sugar substitutes, and unhealthy fats generally negatively impact the microbiome.
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- Antibiotic use: Frequent or prolonged use of antibiotics can disrupt the balance of your microbiome by killing beneficial bacterial along with the harmful ones. While antibiotics are absolutely necessary in certain situations, it’s important to be mindful of their potential effects on the microbiome.
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- Stress Levels: Chronic stress can influence the composition and function of the microbiome. High-stress levels may lead to an imbalance in the microbial community. Incorporating stress-reducing techniques such as meditation, exercise, and adequate sleep may support a healthier microbiome.
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- Recurring Infections: Frequent or recurring infections such a urinary tract infections, yeast infections or respiratory infections may be linked to an imbalanced microbiome.
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- Skin Conditions: Skin conditions like acne, eczema or psoriasis may be associated with an unhealthy microbiome.
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- Fatigue and Mood Disorders: Emerging research suggests a connection between the gut and brain. Chronic fatigue, low energy levels, mood disorders like anxiety or depression and cognitive issues could potentially be linked to an imbalanced microbiome.
What is microbial diversity? Microbial diversity is considered a key characteristic of a healthy microbiome. A diverse microbiome is generally associated with better overall health and functionality because different bacterial species perform different functions in the body.
A diverse microbiome ensures that there are multiple species capable of carrying out specific essential tasks, such as breaking down complex carbs, synthesizing vitamins and aiding in immune system development and regulation. Each bacterial species has its own unique metabolic capabilities. A diverse microbiome increases the likelihood of efficient processing and utilization of various nutrients. A diverse microbiome helps in training and educating the immune system. Exposure to a variety of microbial antigens helps the immune system develop tolerance to harmless substances and launches war against harmful pathogens. And finally, a diverse microbiome acts as a barrier to potential pathogens by using beneficial bacteria to limit the growth and colonization of harmful microorganisms thus reducing the risk of infections.
Then how do we improve our microbiome? We feed it the fuel it needs to thrive.
What do our friendly gut microbes love to eat? The short answer is that the microbiome is fueled by fiber! Plant based foods like vegetables, fruits, nuts, seeds, legumes, whole grains and fermented foods rich in probiotics (such as, pickles [the ones that are naturally fermented without vinegar], kefir, kimchi, yogurt, miso, sauerkraut, tempeh and kombucha). Of course we all know that these foods contain a lot of nutrients such as, vitamins, minerals and essential fatty acids, probiotics and other health promoting compounds, but one of the most positive effects of plant-based and fermented foods center around how our gut microbes metabolize them. These foods make our gut microbes happy and more metabolically active, which is a good thing.
More about probiotics and the effects on the microbiome: There is a lot of hype around the health benefits of probiotics and how it affects the microbiome. First of all, let’s talk about what a probiotic is. Probiotics are the good or helpful bacteria that reside in the gut that help to maintain our health. They play an important role in a healthy microbiome. But what probiotics should you eat? A good list of probiotic foods is noted above (kefir, kimchi, yogurt, miso, etc.).
If you are looking for probiotic supplementation, which probiotic to buy can be complicated question as different strains of probiotics have different effects and benefits. If you are unsure the most suitable probiotic to take for your specific situation, consult with a health care professional to determine the right probiotic for you. Or, if you choose to use Viome to test your microbiome, they’ll recommend which probiotic supplementation is best for you (if you need one). That said, here’s several ways that a good probiotic can help your microbiome:
1. Probiotics can help restore the balance of beneficial bacteria in the microbiome. Probiotics introduce beneficial microorganisms, which can help restore the diversity and stability of the microbiome where things like antibiotics, poor diet, stress or illness can create a microbial imbalance.
2. Probiotics support the integrity of the gut barrier, which is crucial for preventing harmful substances from crossing into the bloodstream. They help strengthen the tight junctions between cells in the intestinal lining, reducing the permeability of the gut and promoting a healthy gut barrier.
3. Probiotics interact with the immune system in the gut, influencing its response. They can help regulate immune function, promoting a balanced immune response and reducing inflammation.
This modulation can be beneficial in conditions where allergies, inflammatory bowel disease, and certain autoimmune disorders exist.
4. Probiotic microorganisms can produce various beneficial compounds, including short-chain fatty acids, and antimicrobial substances that provide energy to colon cells and have anti-inflammatory properties. Antimicrobial substances also help inhibit the growth of harmful pathogens in the gut.
5. Probiotics assist in the digestion and absorption of nutrients. They can help break down complex carbohydrates, produce enzymes that aid in digestion, and promote the bioavailability of certain nutrients. This can improve overall digestive health and nutrient utilization.
6. Probiotics have shown promise in managing or preventing certain conditions, such as diarrhea, irritable bowel syndrome, and certain types of colitis. They are also being investigated for their potential role in mental health, skin health, and other areas.
What is a pre-biotic (vs. a probiotic) and how does that help the microbiome? Pre-biotics can be found in foods like bananas, onions, leeks, jicama, garlic, and asparagus, all of which contain pre-biotic (but non-digestible) fibers that help to increase the growth of specific organisms in the gut. Essentially they are fuel for the good bacteria in the gut. Here’s how pre-biotics help the microbiome:
1. As I mentioned, pre-biotics serve as a source of nutrition for beneficial bacteria in the gut, such as Bifidobacteria and Lactobacilli. These bacteria ferment pre-biotic fibers and use them as fuel to thrive and multiply. By providing this nourishment, pre-biotics promote the growth and activity of beneficial bacteria in the microbiome.
2. Pre-biotics contribute to the overall diversity of the gut microbiome. By providing specific fibers that selectively promote the growth of beneficial bacteria, pre-biotics help maintain or enhance microbial diversity. And create a balanced microbial ecosystem which can inhibit the growth of potentially harmful pathogens and promote a healthier gut environment.
3. When pre-biotics are fermented by beneficial bacteria, they produce short-chain fatty acids that can provide energy for colon cells, help regulate the gut barrier function, reduce inflammation, and support overall gut health.
4. Pre-biotics can enhance the absorption of certain minerals, such as calcium and magnesium. They can also influence the bioavailability of other nutrients, including vitamins and antioxidants. By improving nutrient absorption, pre-biotics contribute to overall nutrient utilization and support optimal health.
There is so much to unpack about the human gut microbiome and its impact to your health and wellbeing. This post is just scratching the surface with a brief introduction/overview. Studies are continually being done on the human microbiome. It would be an understatement to say that this field is constantly evolving and we learn more and more every day.
For now, just know that when you make decisions about what to you put in your mouth, you are not only fueling your body, you are fueling the organisms living within your body…the bacteria, fungi, yeast, protozoa, parasites, and viruses in your gut.
You can choose to either fuel those colonies within you with foods that boost your health and energy or foods that zap it. By nurturing a healthy microbiome, you will be supporting your overall health and well-being, building a strong immune system, as well as potentially preventing or managing certain health conditions.
If you have specific concerns about your microbiome or it’s impact on your health, it’s best to consult with a healthcare professional or specialist in gut health such as a gastroenterologist or functional medicine practitioner. They can provide personalized guidance and recommendations based on your body and your specific circumstances.
The journey to a healthier, happier you is so worth it. I know because I lived it.
I stopped chasing weight loss and started focusing on my health—and that single shift changed everything. I lost 140 pounds, but more importantly, I found clarity, energy, and a life that finally feels like mine. I tell the whole story in my book. Click HERE to learn more.
