What Is the Gut Biome and How Does It Affect Our Health?

So far in this series on digestive health, we’ve looked at irritable bowel syndrome (IBS), small intestinal bacterial overgrowth (SIBO), and the benefits of the low-FODMAP diet in treating IBS.

1. The Basics of Irritable Bowel Syndrome (IBS)
2. Small Intestinal Bacterial Overgrowth (SIBO)
3. The Low-FODMAP Diet and Its Role In Treating IBS

Today, I want to talk about the gut biome – what it is, and how an imbalance in our biome can lead to a wide range of health problems. I’ll also talk about how to get tested, and natural approaches to restoring the delicate balance of this microscopic bacterial universe within our bodies.

What Do We Mean by “Gut Biome”?

The term “gut biome” (sometimes called the “microbiome”) refers to the collection of microorganisms that live in our digestive tract. This micro-ecology includes bacteria, archaea, protists, fungi, and viruses. Doctors believe trillions of these organisms live in the intestines of a single human being, each of which has a different kind of relationship with your body:

• Mutualism – where both your body and the microscopic organisms in your gut mutually benefit (we typically call these organisms “healthy bacteria”)
• Commensalism – where one organism (either the bacteria or your body) benefits and the other is unaffected
• Parasitism – where one benefits and the other is harmed

At least 1,000 different species of bacteria inhabit our intestines. Generally, the greater the diversity of mutually beneficial bacteria in the gut, the healthier the environment. When our digestive tract doesn’t have enough of these healthy bacteria, or the population of one species of bacteria increases or decreases to abnormal levels, it is called “intestinal dysbiosis”. This dysbiosis can cause a range of health issues (which we’ll explore in a minute).

How Do We Develop Our Gut Biome?

Everyone’s gut biome is unique – just like fingerprints. You started developing your biome the moment you were born.

When you were in your mother’s womb, your digestive system was fairly sterile. You got your first dose of bacteria just by being born and traveling through your mother’s vaginal canal. If you were born by Caesarian section, you didn’t receive this initial dose of bacteria, but you eventually became exposed through nursing and/or contact with your mother. This initial exposure to bacteria kick-started the lifelong symbiotic relationship you have with your gut microbiome.

What Causes an Imbalance in the Gut Biome?

Many external environmental and medical factors can alter the gut biome. Some of the most common triggers include:

• Food allergies and sensitivities
• Use of antibiotics
• Use of steroids
• Exposure to toxins, such as heavy metals
• Exposure to environmental molds
• Being born by Caesarian section
• Not being breast-fed as a baby

How Your Gut Biome Affects Your Health

The gut biome influences many systems in the body, including your:

• Digestive system
• Immune system
• Endocrine system (hormones)
• Neurotransmitter system
• Metabolic system

When the gut biome becomes imbalanced in one or more of these systems, it can increase your risk of developing a number of health issues, including:

• IBS symptoms
• Inflammatory bowel disease (IBD)
• SIBO (small intestinal bacterial overgrowth)
• Autoimmune disease
• Food allergies or sensitivities
• Cancer (such as breast, uterine, endometrial, stomach, colorectal, and lymphoma)
• Mood swings, anxiety, or depression
• Weight problems
• Decreased nutrient absorption, and subsequent vitamin or mineral deficiency

Let’s look at each of these systems in turn, and how the delicate balance of bacteria in the gut biome is so important to their proper functioning.

The Gut Biome and Your Digestive System

A diverse gut ecology with lots of beneficial bacteria keeps your intestinal tissue healthy. The biome becomes unhealthy when non-beneficial bacteria and pathogenic organisms make their home in our gut. That’s when digestive conditions like irritable bowel syndrome (IBS), small intestinal bacteria overgrowth (SIB0), and inflammatory bowel disease (IBD) are likely to develop.

As discussed in a previous article, IBS is an umbrella term that refers to symptoms of intestinal pain and bloating, together with diarrhea, constipation, or both. An imbalance of intestinal bacteria, or an overgrowth of parasites or fungi, is responsible for the gas, pain, bloating, and irregular bowel function associated with IBS. Thus, addressing the gut biome is fundamental in the treatment of irritable bowel syndrome.

Inflammatory bowel disease (IBD) includes conditions like Crohn’s and ulcerative colitis. The hallmark symptoms of IBD are pain and inflammation, which can occur with diarrhea, blood in the stool, and general symptoms of fatigue. The disease is caused by a combination of genetics, the immune system, and environmental triggers. While we can’t control our genes, we can support our immune system by keeping our gut flora healthy, and address environmental triggers such as parasites and viruses. All of this can help restore balance within the gut biome, and minimize the risk of requiring bowel removal (an unfortunate consequence in many IBD cases).

SIBO (which I discussed in detail last time on this blog) is a bacterial overgrowth in the small intestine that results in an increase in methane and hydrogen gases. These, in turn, cause abdominal pain and bloating.  Addressing the overgrowth restores balance to the gut biome and can reduce (or eliminate) your symptoms.

The Gut Biome and Your Immune System

One of the many roles of the gut biome is to maintain and regulate the immune system. In fact, the largest portion of our immune system is actually housed in the digestive tract, in a part of the intestinal tissue known as “GALT” (Gut Associated Lymphoid Tissue). Lymphoid tissue is where lymphocytes (a kind of white blood cell) are produced, such as natural killer cells, T-cells and B-cells. B-cells produce antibodies – one of the pillars of our immune system – which the body uses to respond to foreign invaders. These invaders enter our bodies via the food we eat, the water we drink, and the things we touch (if we then put our fingers in our mouths, without first washing our hands).

The immunologic benefit of our gut biome begins immediately after birth. As soon as our gut starts to seed its own bacteria, these microorganisms initiate a “conversation” with our immune system by exchanging chemical signals. These signals help the immune system recognize the difference between helpful and harmful bacteria, thus beginning the body’s long-term programing for immune defense and antibody production.

When our gut biome is unhealthy, it becomes harder for our immune systems to function properly. If it becomes chronically unhealthy, it can even confuse our immune system and cause autoimmune diseases such as rheumatoid arthritis, Celiac disease, Hashimoto’s thyroiditis, lupus, and many others. Autoimmunity is when our immune system starts attacking our own bodies, instead of foreign invaders. Many modern doctors believe chronic internal inflammation and gut dysbiosis can trigger autoimmunity.

Food allergies and food sensitivities are also linked to our immune system. And because our intestines are loaded with antibody-producing B-cells, our gut is primed to be the origin of such food reactions. The connection between the gut biome and food allergies/sensitivities – especially in children – has been confirmed by many studies. For example, research¹ has shown that infants with low bacterial diversity have an increased risk of developing food sensitivities(especially to egg, milk, and peanuts), and toddlers with low bacterial diversity have an increased risk of developing full-blown food allergies.

Some doctors believe the gut bacterium called “Helicobacter Pylori” (most commonly associated with heartburn) slightly increases one’s risk of developing stomach cancer and duodenal ulcers², as it deactivates a part of the immune system that regulates inflammation. Research has shown that the changes in the gut biome of the intestines can promote the growth and spread of tumors. One theory is that a protein secreted by bacteria suppresses the DNA repair protein inside the cells of the intestinal lining, making the cell vulnerable to becoming cancerous.

The Gut Biome and Your Endocrine System (Hormones)

Gut bacteria also help in the production and regulation of our hormones. For example, male sex hormones (androgens) are synthesized by bacteria in the digestive system. Healthy gut bacteria are also vital in enabling our bodies to break down and metabolize estrogens, and excrete potentially dangerous estrogens associated with an increased risk of breast, endometrial, and uterine cancers.

The Gut Biome and Your Neurotransmitter System

Neurotransmitters are chemical messengers that carry signals from nerve cells to other cells in the body.  One of the most important neurotransmitters related to the gut is serotonin. While some serotonin is produced in the brain, over 75% of our serotonin is produced in our intestines. When bacteria in the gut become imbalanced, serotonin production can decrease. A long-term reduction in serotonin can lead to mental health problems, including mood swings, anxiety, and depression, as well as intestinal motility problems (diarrhea or constipation).

The Gut Biome and Your Metabolic System

“Metabolism” refers to how efficiently our body generates and utilizes energy and nutrients. The gut biome plays a significant role in our metabolism. For example, when beneficial bacteria are plentiful and doing their jobs properly, they help your body to produce ample supplies of B vitamins and vitamin K. The roots of vitamin deficiency can often be traced back to a lack of diversity in the gut bacteria.

Many doctors have also identified a correlation between intestinal flora and obesity; people who have a hard time with weight management also tend to have an altered gut biome. This is because some gut bacteria are less efficient than others, and create fat instead of energy and vital nutrients. Thus, weight loss is one of the many potential metabolic benefits of repopulating the gut with beneficial bacteria.

How and Why to Test Your Gut Biome

There are specialty labs that will perform a stool analysis to provide information about the bacteria culture in your digestive system. These tests can also help identify underlying parasites or other causes for the imbalance in your gut biome.

Getting tested can be especially helpful if you have chronic health problems and want to look more deeply at your gut ecology to see if it is at the root of your condition. Even if you currently have no negative symptoms, a gut biome test can give you a picture of your overall health, and help you make lifestyle changes to prevent disease from occurring in the future.

If your doctor is unable to arrange a gut biome test for you, please feel free to write to me via the contact form on this website and we can arrange a way for you to be tested. I can also meet with you to explain the results after you receive them, and advise you on what course of action you may wish to take.

How Do You Maintain a Healthy Gut Biome?

The gut biome is a diverse, living ecosystem that needs to be nourished. Creating a healthy gut biome is a lifelong process that includes:

• A healthy diet to feed the gut bacteria, which are alive and need to be fed. A diet with lots of fresh fruits, vegetables, beans, legumes, and (if you are not a vegan/vegetarian) clean, hormone-free meats and fish.
• Elimination of all foods to which you are allergic or sensitive. These foods can cause inflammation in the intestinal wall and contribute to bacterial imbalances.
• A regular source of probiotics (e.g. lactobacillus acidophilus and Bifidobacterium), either through fermented foods in the diet (such as yogurt, kefir, kombucha, miso, sauerkraut, olives, and pickles) or through probiotic supplements. There are also probiotics designed just for infants to help them develop a healthy gut ecology from the initial weeks following birth. Infant probiotics are found in powder form and applied around the nipple of a nursing mom, can be put on a finger, or a pinch may be added to a bottle.
• Addressing any underlying SIBO issues, candida overgrowth, or parasite infection.
• Herbal medicine (berberine species, garlic, oregano, neem, cinnamon) to kill off pathogenic bacteria and treat the “biofilm” – a slimy coating on bacteria, which protects them and helps them stick to each other as they multiply.
• Regular exercise has been shown to be beneficial to gut flora.

Closing Thoughts

The foundation of good health really does begin in the gut. I hope the information I have shared in this article has helped you gain a better understanding of the importance of the gut biome, and its connection to many vital systems of the body.

If you are suffering with health issues and you suspect they may be gut-related, I strongly urge you to get tested. By identifying which bacteria are present in your digestive tract and analyzing the ratios between them, you and your naturopathic doctor can work together to decrease pathogenic bacteria that may be causing your troublesome symptoms. From my experience, I assure you that a positive shift in gut flora can occur within just a few months of starting your healing regimen.

If you or someone you know suffers with health issues that you suspect may be related to the gut biome, I invite you to drop me a line on the “contact us” page on this site and request a free initial consultation to discuss your needs. I treat patients locally at my practice in Issaquah, Washington, and worldwide via phone or Skype.

Next time, we’ll look at the role of fiber in the diet, and the important part it plays in our digestive health. I hope you’ll subscribe to this blog so you can receive that article and all future articles on A Path to Natural Health.

Health is a journey we travel over our lifetime. Learn everything you can to make your journey a happier one.