Digestion, Immunity

Candida, SIBO, and Leaky Gut: How our gut health intersects with our physical & mental health

Our intestinal microbiome, which is a living collection of bacteria and fungi, is intricately connected with all the other systems in our body. Gut flora is especially critical in the functioning of our digestion, immune system, and mental health. Even before we are born our microbiome starts forming, and research continues to demonstrate how our microbiome at birth impacts us well into adulthood. However, we have the power to influence our microbiome at any point in our lives.

Wholism and the Microbiome

Wholism is the idea that everything is interconnected, and to find a cure we need to look at the issue from a holistic perspective. Naturopathic Medicine explores the ways in which our health is impacted by internal and external environments. We consider how our microflora is affecting the functioning of the rest of our body. To stay healthy we need to be in  harmony with nature on a daily basis, including the trillions of bacteria and yeast circulating in our gut. It’s not hard to imagine how “approximately 100 trillion microbes from over 1000 species and more than 7000 strains” residing in the gut have an important role to play in our health.

Those microbes directly affect every aspect of our health and wellbeing. As we will discuss below, if we don’t have enough beneficial bacteria to support us, our immune system, digestion, and mental state become compromised. An imbalanced gut can lead to allergies, autoimmune disorders, and mental disorders like anxiety and depression.

All disease begins in the gut


How does our Gut affect our health?

Impacts our Immunity

The gut and the immune system work together to protect us from foreign invaders like harmful bacteria and viruses. They work hand in hand as healthy microbes promote a functioning immune response and the immune system promotes the growth of healthy bacteria. The bacteria in our gut plays a critical role in balancing immunity.

According to this study, 70-80% of our immune system is in the gut. Healthy microbes promote antibody and T-cell production, critical in activating our immune response. A change in our microbiome can lead to a weakened immune response and inflammation. 

The microbiome also promotes the functioning of our T-helper cells, which are anti-inflammatory and help regulate our immune system, according to this study.

Gut-brain connection

The saying “go with your gut feeling” doesn’t come from nowhere. The gut is often called the “second brain” because of the strong connection between the gut and our mental state. This “second brain” is composed of the ENS (enteric nervous system), which is composed of 100 million nerve cells lining the gastrointestinal tract. The ENS controls digestion and releases signals between our gut and brain. 

Research has also shown the intertwined relationship between the gut and our emotions. Studies reveal that 80-95% serotonin (the “happy chemical”) is produced in the gut. Norepinephrine, which aids in producing GABA (the “calm” neurotransmitter) is produced in the gut as well. Normal production of these chemicals depends on short chain fatty acid production by healthy microbiota.

Perhaps even more impactful on mental health is neuroinflammation, much of which is triggered imbalances in our gut flora. The blood-brain barrier is compromised by dysbiosis, or  dysfunctional flora, as well. In turn, this excess permeability in the BBB allows the inflammatory messengers access to neurons and glial cells. Probiotic supplementation reverses this microglial activation and can have a positive effect on most neurodegenerative and mood disorders.

How do you know if you have an imbalance in your gut?

Since the gut is so intertwined with both our immune system and our brain, there are many signs our gut is out of balance. 

Here are some common symptoms of a microbial imbalance:

  • Digestive issues
  • Tiredness/ fatigue
  • Headaches
  • Sugar cravings
  • Recurring UTIs in women
  • Brain fog
  • Anxiety & Depression
  • Sleep disturbances
  • Allergies

Three common problems that occur in the gut are candida overgrowth, SIBO, and leaky gut.

  1. Candida, or yeast overgrowth, often occurs after antibiotic treatment, during chemotherapy, in pregnancy, or in individuals who have diabetes or are immunocompromised. From a naturopathic perspective, the first step to treating candida overgrowth is to identify and address the underlying cause of the imbalance. Killing off the excess yeast can be done through a combination of diet changes, nutritional supplements,  herbs, and homeopathics which target candida. After that, probiotics and prebiotics are important to replete your gut with good bacteria and yeasts.
  2. SIBO (Small Intestinal Bacterial Overgrowth) occurs when bacteria populate  the Small Intestine before reaching the large intestine and colon. Hypochlorhydria, or low stomach acid, is often at the root of SIBO, but slowed intestinal motility and a weakened immune system can also contribute. Common symptoms of SIBO include bloating, gas, abdominal pain, diarrhea, constipation, and skin rashes. SIBO is quite common, and 80% of patients with IBS actually have SIBO. When the bacteria builds up in the small intestine, it interferes with digestion and vitamin absorption, can create toxic by-products, and cause leaky gut. This article will dive more into what to look for in a probiotic if you suspect you have SIBO.
  3. Leaky Gut or intestinal hyperpermeability is a condition where the intestinal lining becomes compromised and food particles, microbes, and toxins can enter the bloodstream. This creates inflammation as the body tries to attack those particles, which can lead to autoimmune disorders as the immune system is constantly activated. Stress, imbalances of the gut flora, gluten and gliadin, glyphosate, and overconsumption of alcohol have all been implicated in the creation of this condition.

Candida Overgrowth, SIBO, and Leaky Gut may sound foreign but they are incredibly common. Naturopathic medicine examines how these imbalances in the gut can lead to other serious conditions so taking care of your gut health is extremely important.

What can lead to an imbalanced gut flora?


Continuous or prolonged use of antibiotics can cause microbial dysbiosis, the disruption of gut microbes in the gut. This is because antibiotics don’t just kill the bad bacteria, but they also can wipe out the good bacteria. According to this study, taking antibiotics even for one week can change the makeup of your gut for up to one year.

Prolonged use of antibiotics also poses the risk of antibiotic resistance, that is the antibiotic could no longer be efficient at killing the bacteria.

Of course there are situations in which antibiotics are needed. If you do have to go on antibiotics it is a good idea to take probiotics as well to help restore your gut. You should take a probiotic with multiple strains (more specific details on how to find a good probiotic below) a few hours apart from the antibiotic so they don’t contradict each other. This has been shown to help patients restore their microbiome following disturbances to their gut. 

Birth Control Pill

Your gut and your hormones are extremely reliant on each other. Dr. Jolene Brighten, author of Beyond the Pill, explains that the pill is linked to an increased risk in Autoimmune disease, heart attack, thyroid and adrenal disorders, infertility, and even breast and cervical cancer”.

These risks are due to the way that the birth control pill impacts gut flora. Studies are revealing the complications of the birth control pill on gut flora. 

Estrogen is also shown to enhance the inflammatory process of the immune system, so by taking that hormone every day, you are much more prone to autoimmune disorders. This study of over 750,000 women indicated that the use of birth control pills increased risk by up to 30% for developing inflammatory diseases like Crohn’s Disease and Ulcerative Colitis.

The birth control pill is so widespread but the risks are not well known. This isn’t to say that you shouldn’t ever use the birth control pill, but you should be aware of the risks so that you can make informed decisions and implement extra measures to help protect your gut if needed.


Your microbiome is directly impacted by the food you eat. By fueling your diet with diverse whole foods, you feed the good bacteria in your gut. However, gluten and grains, dairy, soy, sugar, caffeine, alcohol, processed food, and inflammatory fats can all contribute to inflammation and imbalance the bacteria in your gut. 

While it’s important to be informed about how our microbiome impacts our bodies, we should always note that there are so many ways we can take care of our gut health, which you can read more about here.

Other Sources:

Adaes, Sara. “How The Gut Microbiota Influences Our Immune System.” Neurohacker Collective, 2019, neurohacker.com/how-the-gut-microbiota-influences-our-immune-system.

Baker, Louise. “Why Your Birth Control Could Be Damaging Your Gut Health.” Peaceful Dumpling, 30 Jan. 2020, www.peacefuldumpling.com/birth-control-damaging-gut-health.

Bishehsari, Faraz, et al. “Alcohol and Gut-Derived Inflammation.” PMC, 2017.

Kelly, John R., et al. “Breaking down the Barriers: the Gut Microbiome, Intestinal Permeability and Stress-Related Psychiatric Disorders.” Frontiers in Cellular Neuroscience, vol. 9, 2015, doi:10.3389/fncel.2015.00392.

“Listen to Your Gut!” Institute for Natural Medicine, 28 May 2019, naturemed.org/listen-to-your-gut/.

Robertson, Ruairi. “What to Eat Before and After Antibiotics.” Healthline. Https://Www.healthline.com/Nutrition/What-to-Eat-Antibiotics#section3, 2017, www.healthline.com/nutrition/what-to-eat-antibiotics#section3.

Vasiluk, Luba, et al. “Oral Bioavailability Of Glyphosate: Studies Using Two Intestinal Cell Lines.” Environmental Toxicology and Chemistry, vol. 24, no. 1, 2005, p. 153., doi:10.1897/04-088r.1.

Writer, Psychiatry Advisor Contributing. “Gut Microbiota Can Drive Neuroinflammation in Major Depressive Disorder.” Psychiatry Advisor, 14 Dec. 2019, www.psychiatryadvisor.com/home/depression-advisor/gut-microbiota-can-drive-neuroinflammation-in-major-depressive-disorder/#:~:text=Gut%20Microbiota%20Can%20Drive%20Neuroinflammation%20in%20Major%20Depressive%20Disorder,-Psychiatry%20Advisor%20Contributing&text=The%20onset%20of%20depressive%20symptoms,influences%20treatments%2C%20according%20to%20researchers.

Zhang, Sheng, and De-Chang Chen. “Facing a New Challenge.” Chinese Medical Journal, vol. 132, no. 10, 2019, pp. 1135–1138., doi:10.1097/cm9.0000000000000245.

Zong, Ye, et al. “Chronic Stress and Intestinal Permeability: Lubiprostone Regulates Glucocorticoid Receptor‐Mediated Changes in Colon Epithelial Tight Junction Proteins, Barrier Function, and Visceral Pain in the Rodent and Human.” Neurogastroenterology & Motility, vol. 31, no. 2, 2018, doi:10.1111/nmo.13477.