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March 10, 2020

Gallstones Part #1

by Dr. Miles Nichols and Nicola Schuler, CNTP, MNT

This week we write about gallstones and why they develop. In next week’s part 2 on gallstones, we will discuss solutions and ways to prevent gallstones. Please stay tuned for part 2 next week.


Gallstone disease is quite common, affecting up to 15% of adults (Di Ciaula, 2018).

Gallstones are small, hard deposits that form inside the gallbladder. The gallbladder is under the liver in the upper right region of the abdomen.

Gallstones can vary in size from a grain of sand to the size of a golf ball. Some people develop just one gallstone, while others may develop many gallstones at the same time. Most gallstones are cholesterol gallstones, found in more than 80% of patients with gallstones (Di Ciaula, 2018).

Function of the Gallbladder & Bile:

The main purpose of the gallbladder is to store bile, which is needed for the digestion of fats in food. Bile from the gallbladder also helps to absorb fat-soluble vitamins and nutrients. Bile is produced by the liver. It travels from the liver’s hepatic ducts into the gallbladder, where it is stored. Eating a meal that contains even a small amount of fat signals the gallbladder to release bile, which flows through two small tubes or ducts into the upper part of the small intestine, where it will help to digest fats.

Gallstones Symptoms:

Symptoms may not be obvious until gallstones reach a certain size or if the gallstone obstructs the bile ducts. If a gallstone gets stuck in a duct and causes a blockage, the resulting signs and symptoms may include:

  • Severe and sudden pain in the upper right abdomen and possibly extending to the upper back between the shoulder blades
  • Back pain
  • Pain in the right shoulder
  • Fever and shivering
  • Severe nausea and vomiting
  • Jaundice (yellowing of the skin or eyes)
  • Clay colored stools or dark urine
  • Burping
  • Diarrhea and indigestion

It is best to prevent gallstones from forming, rather than having to address already formed stones. If people begin to struggle with fat digestion, that can be an early sign that there may be some need to address the gallbladder. A stool test can show steatocrit, a marker for fat in feces. This is a reliable marker and if elevated, might indicate an issue with the gallbladder. Sometimes this can elevate before someone experiences symptoms.

Another helpful way to look at gallbladder issues is by assessing for risk factors. If someone is overweight and has blood sugar imbalance or metabolic syndrome, as many Americans do in their 40’s or older, it can be helpful to consider gallbladder support, a steatocrit test or an ultrasound to see whether stones are in a period of early formation.

Risk factors for gallstones are (Di Ciaula, 2018):

  • Being overweight
  • Cigarette smoking
  • Physical inactivity
  • Diabetes
  • Hypertension
  • Hypercholesterolemia or high cholesterol
  • Cirrhosis
  • Certain medications for lowering cholesterol or those that have a high estrogen content

CAUSE OF GALLSTONES: The direct cause of gallstones is an excess of cholesterol, bilirubin or bile salts.

However, in Functional Medicine we are interested in getting to the root cause(s) of gallstones:

Major pathogenetic factors for cholesterol gallstones include (Di Ciaula, 2018):

  • Obesity
  • Type 2 diabetes
  • Non-alcoholic fatty liver disease
  • Metabolic syndrome itself: As defined by the presence of at least 3 of the following: abdominal obesity, high blood pressure, high fasting glucose, increased triglyceride levels and reduced HDL levels (Stinton LM, 2012). Metabolic syndrome has been associated with gallstone complications (Stinton LM, 2012).
  • Altered gut microbiota
  • Insulin resistance
  • Genetic background
  • Sluggish gallbladder
  • Inflammatory changes in the gallbladder
  • Slow intestinal motility
  • Increased intestinal absorption of cholesterol

It’s not your genes!

A genetic predisposition is not sufficient to promote cholesterol gallstones. This is supported by studies on twins, where genetic factors play a role in no more than 25 to 30% of subjects with gallstones (Di Ciaula, 2018). Genes can provide an increased risk of forming gallstones, but several environmental or epigenetic factors such as diet, physical activity levels and exposure to chemicals such as heavy metals or pesticides play a crucial role in determining if someone will develop gallstones (Di Ciaula, 2018).

“All disease begins in the gut.” Hippocrates

Gut bacteria collected from patients with gallstones show imbalances in the gut (Di Ciaula, 2018).

Leaky gut or intestinal permeability can also be a factor in gallstones (Kosters A, 2010). Please see our recent article on leaky gut and autoimmunity. As we have written, if the gut lining is permeable, then toxins, microbes and other undesirable substances will escape from the gut into circulation in the body. This will prompt an immune response to fight off the foreign invaders and inflammation will ensue. This inflammation will affect the functioning of the biliary system; the gallbladder, liver and bile ducts; which are involved in gallstone formation (Kosters A, 2010). Thus, leaky gut creates inflammation which will lead to issues with gallbladder function and an impaired gallbladder can contribute to gallstones.

Sluggish Gallbladder Motility & Insulin Resistance:

Gallbladder motility issues is a major risk factor for cholesterol gallstone formation (Di Ciaula, 2018).

Insulin Resistance:

Hyperinsulinemia, or excessively high insulin levels, may play an important role in the cause of gallstones, even in individuals without diabetes and with normal serum glucose levels (Misciagna G, 2000).


Women have an increased prevalence of gallstones compared with men because of the influence of estrogen on cholesterol metabolism (Di Ciaula, 2018). Therefore, for prevention, it is important to avoid endocrine disruptors and exogenous estrogenic compounds. In addition, the hormone insulin is involved in gallstone development. Insulin resistance, diabetes and high levels of insulin are often seen with gallstones (Di Ciaula A, 2018).

——- To Be Continued ——

The causes of gallstones are varied but primarily relate to metabolic syndrome which is preventable, gut issues which can be treated and hormonal imbalances which can also be treated.

Please read on next week in Gallstones Part #2 where will discuss what to do if you have gallstones and how to prevent them from developing in the first place.

If you would like help with gallstones now, then please get in touch with us. Book a free 15-min discovery call to see how we can help you with your symptoms. We can answer your questions and help you book an initial consult with one of the functional medicine doctors in our clinic.


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March 4, 2020

PCOS: Polycystic Ovarian Syndrome, Part #2: The Solutions

by Nicola Schuler, CNTP, MNT and Dr. Miles Nichols

Last week, we wrote about Polycystic Ovarian Syndrome and what causes it (here). This week, we talk about the solutions to PCOS.


There are many things we can do in Functional Medicine to address root causes of PCOS and we will discuss them below.

—– But the most effective treatments for PCOS are: —–


Lifestyle corrections to address metabolic syndrome, improve gut health, prevent excessive immune activation and minimize exposure to toxins and inflammatory agents, appears to be the most sustainable therapy for PCOS (Patel, 2018).


Dietary changes are considered the first line of treatment for those with PCOS (Zhang F, 2019).

Hyperinsulinemia and increased androgens are part of PCOS. Carbohydrates are among the main stimulators of insulin release. Research shows that dairy products and carbohydrates elicit greater postprandial insulin secretion than non-starchy vegetables and fruits (Phy JL, 2015). One study demonstrated that an 8-week low-carb/low-dairy diet resulted in weight loss, improved insulin sensitivity and reduced testosterone in women with PCOS (Phy JL, 2015).

We recommend a diet that is:

  • Organic
  • Anti-inflammatory
  • Whole foods diet
  • Low in sugar
  • Paleo (grain & dairy free) or gluten-free Mediterranean diet
  • High in protein vs. carbohydrates
  • Moderate to low carb although this does depend somewhat on the specific case and any degree of adrenal or thyroid issues
  • Rich in omega-3 fats (fatty fish like wild salmon, sardines, herring, anchovy, walnuts, flaxseeds, chia seeds) and fiber-rich foods such as vegetables and fruits

Specific Foods:

  • Brightly colored vegetables and fruit are the best source of antioxidants to combat oxidative stress. Some characteristics of PCOS (obesity, abdominal adiposity, androgen excess and insulin resistance) contribute to oxidative stress and inflammation (Amini L, 2015). The best food source of antioxidants is a wide variety of fruits and vegetables, especially all types of berries (blueberries, goji berries, raspberries, strawberries, etc.), kale, red cabbage, beets, artichokes, spinach, broccoli, carrots, potatoes, asparagus, avocados, radish, lettuce, sweet potatoes, squash, pumpkin and collard greens.
  • Protein and glucose were compared as part of a PCOS diet (Kasim-Karakas SE, 2007). In patients with PCOS, glucose caused significantly more hyperinsulinemia than did protein (Kasim-Karakas SE, 2007). We therefore recommend increasing protein intake and restricting simple sugar intake in a PCOS diet (Kasim-Karakas SE, 2007).
  • Cinnamon increases antioxidant status, which helps to fight AGEs (Borzoei A, 2018). It also improves serum level of total cholesterol, LDL cholesterol and HDL cholesterol (Borzoei A, 2018).
  • Flaxseed oil supplementation for 12 weeks in women with PCOS significantly decreased insulin levels thereby improving insulin resistance, decreased triglycerides and cholesterol levels and improved the inflammation marker hs-CRP (Mirmasoumi G, 2018).
  • Walnuts and almonds consumption had beneficial effects on plasma lipids, LDL cholesterol and reduced androgens in PCOS (Kalgaonkar S, 2011).
  • Curcumin reduced insulin resistance, as well as inflammation markers (IL-6 and CRP) levels in PCOS rats that were treated with various concentrations of curcumin for 14 days (Mohammadi S, 2017).

Avoid Advanced Glycation End-Products or AGEs:

It is best to avoid AGEs as they contribute to PCOS (Rutkowska AZ, 2016). Food and smoking are the main sources of exogenous AGEs in daily life. The biochemical composition of a meal, cooking method and time and temperature of food preparation all affect the forming of AGEs (Rutkowska AZ, 2016).

To avoid AGEs:

  • Quit smoking
  • Avoid fried and fast foods
  • Fill your plate with fruits and vegetables
  • Don’t cook at very high temperatures
  • Cook low (temperature) and slowly (instead of short cooking times at very high heat)
  • Keep it moist – cook with liquids instead of just dry cooking
  • Cook more at home


Exercise is one of the key approaches to PCOS because it can help lose weight and reduce insulin resistance / increase insulin sensitivity, a critical part of addressing PCOS. Again, we caution here that status of HPA axis health is an important consideration in exercise recommendations. Assuming there are no contraindications to exercise, then we recommend pursuing whatever exercise or activity that you love and starting slowly if you are new to exercise.


  • Intermittent Fasting (IF) can be very effective in increasing insulin sensitivity. However, this depends on the case as we would not pursue IF if someone is suffering from moderate to severe HPA axis dysregulation, is pregnant or breastfeeding or has a history of eating disorders.
  • Maintain a healthy weight. If overweight or obese, lose weight.
  • Balance blood sugar and resolve insulin resistance.
  • Address metabolic syndrome – including high cholesterol, high blood pressure, insulin resistance and/ or high blood sugar, abdominal adiposity. These can all be improved with diet and lifestyle changes.
  • Rebalance hormones. Work with us to use blood and DUTCH testing to eliminate any hormonal imbalances, especially involving insulin and androgens. As part of the rebalancing of hormones, check thyroid hormone levels.
  • Address any potential gut issues and support gut health generally. Correct any imbalances or dysbiosis in the gut bacteria. Fix leaky gut as intestinal permeability has been linked to PCOS (Zhang F, 2019). One study has found that modification of gut microbiota with probiotic, prebiotic and synbiotics shows these can help to treat PCOS (Yurtdaş G, 2019). Synbiotics are a combination of prebiotics and probiotics that have a synergistic effect by inhibiting the growth of pathogenic bacteria and enhancing the growth of beneficial organisms (Yurtdaş G, 2019).
  • Avoid exposure to environmental toxins, endocrine disruptors, BPA, chemicals, pesticides and other toxins. Eat an organic diet, clean up your personal care and household cleaning products. Use the EWG database to check the safety level of various personal care products

SUPPLEMENTS that can be helpful:

  • Magnesium and zinc have beneficial anti-inflammatory and antioxidant effects (Ebrahimi FA, 2018).
  • Myo-inositol is a common form of inositol, a vitamin-like substance. Myo-inositol improves insulin sensitivity and supports normal follicle development (Unfer V, 2017). It addresses both the sex hormone imbalance and improves the insulin sensitivity, which are two of the primary drivers in PCOS (Unfer V, 2017).
  • Quercetin is a flavonoid found in some plants that has antioxidant, anti-inflammatory and antiallergic properties and is used for the treatment of metabolic and inflammatory disorders (Pourteymour Fard Tabrizi F, 2020). Quercetin is anti-oxidative due to its ability to reduce the generation of free radicals (Pourteymour Fard Tabrizi F, 2020). Fruits and vegetables, particularly onions, apples, berries, citrus, red grapes, nuts, seeds and tea, are a good source of quercetin.
  • Vitamin D supplementation in women with PCOS significantly decreased the inflammation marker, hs-CRP, and significantly increased total antioxidant capacity (TAC) levels (Akbari M, 2018). We recommend testing your vitamin D levels before supplementing. We like to see vitamin D levels around 40-60 ng/mL.
  • Vitamin D and probiotic co-administration has positive effects on mental health, hormonal, inflammatory and oxidative stress parameters in women with PCOS (Ostadmohammadi V, 2019). Taken together, vitamin D and probiotics significantly improved general health scores (Ostadmohammadi V, 2019).
  • Berberine can help reduce elevated blood sugar, improve insulin sensitivity, and reduce inflammation and obesity (Wang H, 2018). This is especially effective in cases where fasting insulin and/or glucose are elevated.

As always, please get in touch with us. If you or someone you know is suffering from PCOS, get in touch with our clinic today. Book a free 15-min discovery call to see how we can help you with your symptoms. We can answer your questions and help you book an initial consult with one of the functional medicine doctors in our clinic.



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February 28, 2020

PCOS: Polycystic Ovarian Syndrome, Part #1: The Causes

by Nicola Schuler, CNTP, MNT and Dr. Miles Nichols

This week, we discuss Polycystic Ovarian Syndrome and what causes it. Next week, please read on for our article on the solutions to PCOS.


Polycystic ovary syndrome (PCOS) is a hormonal imbalance that affects women. It involves reproductive and hormonal disturbances, primarily anovulation (when a woman does not ovulate) and high levels of androgen or male hormones in women (Diamanti-Kandarakis E, 2012). Hormonal issues are typically accompanied by metabolic disturbances such as increased blood pressure, high blood sugar, insulin resistance, excess body fat around the waist and abnormal cholesterol or triglyceride levels (Diamanti-Kandarakis E, 2012).

It is estimated to affect 2–20% of reproductive-aged women (Pourteymour Fard Tabrizi F, 2020). This, of course, is a massive range, largely because PCOS goes undiagnosed in so many cases. Many clinicians report at least half of infertility cases in women involve PCOS.

PCOS can lead to an increased risk of developing several medical complications including:

  • Insulin resistance
  • Type 2 diabetes
  • High cholesterol
  • High blood pressure
  • Heart disease
  • Stroke
  • Sleep apnea
  • Possibly an increased risk of endometrial cancer (Roos N, 2011)

SYMPTOMS of PCOS include:

  • Irregular periods or no periods at all
  • Heavy periods
  • Pelvic pain
  • Cysts on the ovaries
  • Difficulty getting pregnant (because of irregular ovulation or failure to ovulate)
  • Insulin resistance
  • High testosterone which can cause excessive hair growth (hirsutism) – usually on the face, chest, back or buttocks
  • Weight gain
  • Thinning hair and hair loss from the head
  • Oily skin or acne
  • Patches of thick, darker, velvety skin on the neck, arms, breasts or thighs
  • Anxiety or depression
  • Sleep apnea


  • Obesity is a risk factor for PCOS (Kakoly NS, 2019). One study found that 60% of women with PCOS are obese (Roos N, 2011).
  • Gut dysbiosis and leaky gut: We will cover this issue in greater detail below
  • Metabolic syndrome: a set of conditions that include increased blood pressure, high blood sugar / insulin resistance, excess body fat around the waist and abnormal cholesterol or triglyceride levels. These often occur together and increase risk of heart disease, stroke and type 2 diabetes.


The specific cause of PCOS is unknown.

It is a multifactorial disorder mainly brought on by genetic and environmental factors (Zhang F, 2019). It is thought that high levels of male hormones or androgens prevent the ovaries from producing hormones and making eggs normally (Pourteymour Fard Tabrizi F, 2020). Genes, insulin resistance and inflammation have all been linked to excess androgen production.

The best current understanding of the biochemistry involves the 17,20-lyase enzyme (Keleştimur F, 1999). This enzyme is secreted by the adrenal glands. 17,20-lyase helps with the conversion of cholesterol to the androgen hormones testosterone and DHEA (Keleştimur F, 1999). Then aromatase enzyme converts some of that testosterone into estrogen (Keleştimur F, 1999).

Because 17,20-lyase is upregulated with PCOS and is involved with producing testosterone and DHEA, it makes sense that in lab reports for individuals with PCOS, we often see elevated testosterone and/or DHEA-S in the blood (Keleştimur F, 1999). There can also be estrogen dominance because some of the excessive testosterone is getting converted into estrogen with the aromatase enzyme. When estrogen, in relationship to progesterone, becomes proportionately elevated, we can see symptoms associated with estrogen dominance.

Insulin resistance (and/or hyperinsulinemia) -> 17,20-lyase enzyme upregulation -> increased testosterone and DHEA -> potential for increased estrogen from aromatase enzyme converting more testosterone into estrogen

Interactions between genetic, behavioral and environmental factors are involved in the development of PCOS so epigenetic (environment and lifestyle) factors are of prime importance (Pourteymour Fard Tabrizi F, 2020). Some researchers think that it manifests largely due to poor lifestyle habits (Patel, 2018).


  1. Diet:

Diet is the major environmental factor in developing PCOS (Diamanti-Kandarakis E, 2012). Excess calories leading to obesity is widely recognized to have an aggravating impact. Obese women with PCOS treated with a 1,000 kcal diet for 6–7 months showed body weight loss of 5–10% and improvements in their health including renewed ovulation, increasing pregnancy rate and lower levels of insulin and androgens (Zhang F, 2019).

It is well-established that excessive sugar and refined carbohydrates in the diet contribute to many of the problems linked with PCOS such as obesity, insulin resistance, dyslipidemia, diabetes and dysbiosis.

Even someone with normal weight may still have metabolic syndrome. Although waist circumference is one risk factor, there can be others like high blood pressure, high triglyceride, and high fasting glucose. Even just high fasting insulin with normal blood sugar could be a risk factor.

Another damaging dietary factor may be the high content of advanced glycated end products (AGEs) in food (Diamanti-Kandarakis E, 2012). AGEs are harmful compounds that are formed when protein or fat combine with sugar in the bloodstream. This process is called glycation. Diet is the biggest contributor of AGEs.

  1. The Gut:

The gut has recently been discovered to be linked to PCOS and its development. Research has found a clear association between changes in the gut microbiome and PCOS (Yurtdaş G, 2019).

Essentially, dysbiosis or unbalanced gut bacteria, due, for example, to a poor diet with a high-sugar intake, leads to leaky gut. We wrote about leaky gut here. Leaky gut causes an excessive immune system reaction that can interfere with insulin and drive up insulin levels. This leads to increasing testosterone produced by the ovaries, which interferes with normal follicle development and causes PCOS (Tremellen K, 2012).

  1. Hereditary Factors:

Exposure to high levels of androgens (or male hormones) in females during fetal development might result in long-term changes in gut microbiota in the daughters of PCOS patients (Zhang F, 2019). Prenatal androgen exposure can cause infant gut dysbiosis and altered abundance of bacteria, suggesting that androgen excess in immature fetuses could result in long-term alterations in gut microbiota and lead to increased risk of developing PCOS (Zhang F, 2019).

  1. Environmental exposure to industrial products:

Environmental toxins, especially, Bisphenol A (BPA), is thought to contribute to PCOS (Diamanti-Kandarakis E, 2012). Toxins, such as plasticizers, BPA and phthalates, act as endocrine disruptors in the development of PCOS (Diamanti-Kandarakis E, 2012).

Extensive exposure to environmental toxins and their role in contributing to PCOS are supported by extensive data (Rutkowska AZ, 2016). Acute or prolonged exposure to EDCs (endocrine disrupting chemicals) can disrupt hormones and reproductive function (Rutkowska AZ, 2016). They may also interfere with metabolic factors such as obesity, insulin resistance and hyperinsulinemia that can exacerbate the possibility of developing PCOS and contribute to PCOS in the form of type 2 diabetes and cardiovascular disease (Rutkowska AZ, 2016).

  1. Dysregulation of the sympathetic nervous system or HPA axis:

Dysregulation of the sympathetic nervous system may also act as an important component in PCOS (Shorakae S, 2015). Women with PCOS show increased rates of dysregulation of the hypothalamic-pituitary-adrenal (HPA) axis (Peecher DL, 2019). The key clinical features of PCOS are anovulation, hyperandrogenism and hyperinsulinemia, which are closely related with a dysregulated endocrine system (Wang F, 2017).

Cortisol (as part of the HPA axis) dysregulation can also affect insulin levels, playing a role in the endocrine dysfunction in PCOS patients (Wang F, 2017).

——– To Be Continued Next Week ——-

Please stay tuned and read our next article on PCOS Part #2 where we will discuss solutions on how to manage and address PCOS using Functional Medicine.

As always, please get in touch with us. If you or someone you know is suffering from PCOS, get in touch with our clinic today. Book a free 15-min discovery call to see how we can help you with your symptoms. We can answer your questions and help you book an initial consult with one of the functional medicine doctors in our clinic.




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February 10, 2020

Addressing Trauma & PTSD using Functional Medicine Part #2

by Nicola Schuler, CNTP, MNT and Dr. Miles Nichols

Last week, we wrote about trauma and the many ways in which it can physiologically affect the body (see here for the full article). This week, we focus on solutions to address trauma using Functional Medicine.


Is there a Functional Medicine approach?

What does Functional Medicine do in cases of trauma or PTSD?

In Functional Medicine, we will assess the general state of health in the person suffering from trauma or PTSD. This includes looking very deeply at gut health, the HPA axis, sources of potential inflammation, chronic hidden infections and many other aspects of health.

  • IMPROVE GUT HEALTH: As we have written about in our Gut Series, we work extensively on improving gut health. We seek to identify any GI infections or overgrowths, dysbiosis or other gut issues, resolve them and rebalance the gut to an optimal state. You can read up on our approach in the Gut Series starting here. Or for a quicker and more individual approach, call us for a free discovery call.
  • ADDRESS HPA AXIS DYSREGULATION: In our approach, we also look into the status of the HPA axis in our patients. We can do specific testing using the DUTCH test to identify hormonal imbalances and address them through diet, supplements and lifestyle changes. It is important, in the case of trauma, PTSD, anxiety and other stressful states, to help the central nervous system to move out of sympathetic mode (typically called ‘fight or flight’ mode) and into parasympathetic mode (typically called ‘rest and digest’ mode). It is also important to reset any disruptions to the circadian rhythm of the body as this will strongly impact the rhythm of cortisol and other stress hormones. We can help you to do this.
  • BALANCE BLOOD SUGAR: It seems a simple thing but imbalanced blood sugar can have quite a strong impact on mood and anxiety, as well as deeper implications for insulin resistance ad possible diabetes. We can help you to adopt a diet that balances out blood sugar issues.
  • REDUCE INFLAMMATION: Inflammation can be a consequence as trauma negatively impacts the microbiome, the HPA axis and the limbic system function. We can help to identify what may be causing inflammation and to reduce and calm the inflammation with our FM approach.

SUPPLEMENTS: There are a number of supplements that have proved in research to be helpful with cases of trauma:

  • Cannabidiol or CBD
  • Blueberries
  • Curcumin
  • Omega-3 fatty acids
  • Silymarin or Milk Thistle

OTHER THERAPEUTIC OPTIONS: In addition to the above suggestions, there is a wealth of therapy options and activities that have shown to help in coping with trauma. Research shows that each of these modalities can be very effective in addressing trauma and in reducing the symptoms of PTSD, anxiety or depression often associated with exposure to trauma. Different modalities work better or less well on different people, as we are all individual. It is worth trying a few different techniques to find the one or the combination that best helps a particular individual struggling with trauma or PTSD.

In our clinic, we can help you with meditation, brain photobiomodulation, acupuncture and self-care techniques. Please ask us if you want more info on any of these:

  • Meditation & mindfulness: We practice and teach Sheng Zhen Meditation –
  • Neurofeedback
  • Vielight or brain photobiomodulation
  • Yoga
  • Tai Chi
  • Acupuncture
  • Aerobic exercise
  • Eye Movement Desensitization and Reprocessing or EMDR
  • Emotional Freedom Technique or EFT
  • Self-care across the board, including anything calming to the individual
  • Cognitive behavioral therapy
  • Hypnotherapy
  • Group therapy

As always, please get in touch with us. If you or someone you know is suffering from trauma, get in touch with our clinic today. Book a free 15-min discovery call to see how we can help you with your symptoms. We can answer your questions and help you book an initial consult with one of the functional medicine doctors in our clinic.

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February 3, 2020

Addressing Trauma & PTSD using Functional Medicine Part #1

by Nicola Schuler, CNTP, MNT and Dr. Miles Nichols

This week we are writing on trauma:

Trauma is not uncommon. One study in the US found that 74.2% of women and 81.3% of men reported experiencing at least one traumatic event in their lifetime (Mock SE, 2010).

How does trauma affect the body and how we can resolve it using Functional Medicine?

  • TRAUMA: a psychological, emotional response to a deeply distressing or disturbing event or experience. Examples are being in a serious accident, having an illness or injury, losing a loved one or going through a divorce. It includes more extreme experiences that are severely damaging, such as abuse, rape or torture.

The trauma or the incident is typically said to be ‘outside the realm of normal human experience’ and that it would be a highly distressing experience for anyone (Levine, 1997).

Three categories of TRAUMA have been established:

  • Complex trauma
  • Post-Traumatic Stress Disorder (PTSD
  • Developmental trauma disorder

SYMPTOMS of trauma are numerous and may appear at different points in time (Levine, 1997):

  • Hypervigilance or being ‘on guard’ at all times
  • Feeling helpless
  • Flashbacks
  • Extreme sensitivity to light or sound
  • Exaggerated emotional or startle responses
  • Nightmares and night terrors
  • Abrupt mood reactions including rage, fear, temper tantrums or frequent crying
  • Shame, guilt, self-blame
  • Reduced ability to cope with stress
  • Difficulty sleeping
  • Panic attacks and anxiety
  • Avoidance behaviors, avoiding certain situations

THE BIOLOGY OF TRAUMA: What are trauma’s effects on the body?

There are a number of physiological ways in which trauma appears in the body and can lead to a cascade of biological changes and stress responses (Center for Substance Abuse Treatment, 2014):

  • Changes in Brain Function
  • Changes in HPA Axis (or Stress Response) Function
  • Higher Propensity for Chronic Illness
  • Higher Propensity for Mental Health Issues
  • Effects of Adverse Childhood Experiences (ACE’s) or Childhood Trauma
  • Epigenetic Effects
  • Changes in the Gut Microbiome

The mechanisms for many of the changes are complex. Rather than go into details on each, we will just focus on the epigenetic effects in this article because they are fascinating and relevant to how stress can become prevalent and pass from generation to generation.

Epigenetic Effects: Epigenetics is how trauma can affect our long-term health as well as that of future generations. Chronic illness is a result of genetic and epigenetic factors (Klengel T, 2015). A person may have a genetic predisposition towards a disease. The disease won’t necessarily materialize, unless epigenetic factors i.e. environmental influences ‘turn on’ the gene. Environmental factors, particularly severe stress or trauma, can lead to lifelong changes in the form of epigenetic modifications that can impact health or disease (Klengel T, 2015). Trauma is one of the epigenetic factors that can turn on ‘negative’ genes. It can be a trigger, or most likely one of many triggers, for chronic disease.

Trauma can even have biological and behavioral consequences on the offspring of exposed individuals (Youssef NA, 2018). There is strong evidence of an enduring effect of trauma exposure passed to offspring trans-generationally via the epigenetic inheritance mechanism of DNA methylation alterations which can change the expression of genes (Youssef NA, 2018).

For example, a mother experiencing stress, with high cortisol levels during pregnancy, may lead to the child having a larger amygdala (fear center in the brain). This could contribute to the child being more hypervigilant towards stressors that would not be an issue for other people. This would then contribute to a myriad of other physiological changes in the nervous system, metabolism and cardiovascular system. This may contribute to increased risk for chronic disease.

Perception of Stress: There is a big difference between a stress itself and the perception of that stress. For example, primates have been studied to look at how their cortisol levels respond to different situations. One alpha male leader of a group of primates may have very little stress hormone output when another alpha male from a different tribe is close by because that first male does not feel threatened. However, the other male may have a high output of corticosteroid (stress hormone) because that male interprets the situation as potentially threatening. The interpretation of the situation is more impactful than the situation itself for the release of stress hormones.

The same is true of humans. Someone who feels continually threatened by family pressures, economic constraints and a toxic work environment may have chronically elevated cortisol levels and be much more susceptible to chronic diseases. Another individual in similar circumstances may downplay those issues and focus on their core friend network where they happen to be honored and respected and remain largely unthreatened. The identification and interpretation are both important for when a person feels threatened and releases stress hormones. The epigenetic variables before birth also play into how large and active the amygdala is and how sensitive to stress a person is.

As you can see, there is a complex mix of variables that is important to consider with relation to stress and trauma. The perception of and identification with traumatic experiences plays a role as well as genetics, upbringing, personal development work, practices like meditation and more.

Please stay tuned and read our next article on Trauma Part #2 where we will discuss solutions on how to manage and address trauma using Functional Medicine.

As always, please get in touch with us. If you or someone you know is suffering from trauma, get in touch with our clinic today. Book a free 15-min discovery call to see how we can help you with your symptoms. We can answer your questions and help you book an initial consult with one of the functional medicine doctors in our clinic.


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January 21, 2020

Autoimmunity & the Gut Part #4: Predicting Autoimmunity

by Nicola Schuler, CNTP, MNT and Dr. Miles Nichols

This week we continue to look at autoimmunity and gut health. This article focuses on possible ways of predicting autoimmunity by looking at specific gut bacteria.

Dr. Alessio Fasano, whom we wrote about last week, has said that the reason someone develops autoimmunity or AI later in life is due to gut bacteria and a change somehow in the composition of the gut bacteria (Fasano A., 2019).

Gut health has been found to affect the possibility of developing an AI disease (Felix KM, 2017). Dysbiosis (an imbalance between good gut bacteria and bad gut bacteria) is the key culprit as it can lead to leaky gut. Leaky gut is a significant contributing factor to Autoimmunity.

In our functional medicine clinic, we focus on testing for and resolving causes for dysbiosis. Examples of important tests we do include SIBO (Small Intestine Bacterial Overgrowth) Lactulose Breath Testing and a comprehensive stool analysis looking for parasites, helicobacter pylori, candida, viruses, worms, and more. To find out more about becoming a patient, click here.

Predicting Autoimmunity:

Most autoimmune diseases progress gradually over time, often without symptoms (Rose, 2016). During this time, serious tissue damage may occur (Rose, 2016). Ideally, it is important to diagnose autoimmune diseases as early as possible, to avoid irreversible tissue damage.

After genetic factors, autoantibodies are the best predictors of impending autoimmune disease, at this time (Rose, 2016). Autoantibodies are an antibody (a protein) produced by the immune system that is directed against one or more of the person’s own tissue or organs. These autoantibodies are the hallmark of autoimmune disease.

Multiple studies have found that these autoantibodies develop in a person’s body approximately 7 years before a diagnosis of AI is made (Rose, 2016) and (Arbuckle MR, 2003).

While autoantibodies are known to be a predictor of AI, research is also currently looking to specific gut bacteria to try to predict AI.

Because studies show blood markers can detect autoimmune tendencies before symptoms arise, testing for autoantibodies, even when free of symptoms, can be helpful. In our clinic, we do preventive and predictive comprehensive blood screening for autoimmune diseases. We measure what are called antibodies (molecules that tell us the immune system is attacking something) to different body tissues, like the thyroid as one example, to find out if there is a possible issue with autoimmunity. The common tests that we do for most patients to look for autoantibodies include Thyroid peroxidase (TPO) antibodies, Thyroglobulin antibodies (TGA), Antinuclear antibodies (ANA), Antiparietal cell antibodies (APCA), Rheumatoid Factor (RF), Anti-CCP3 (related to rheumatoid arthritis that can cause joint issues) and sometimes several ENA markers as well.

Have you been screened for antibodies? Do you have family history of autoimmune disease or unexplained symptoms but no one has thought to test for autoimmune issues? If so, get in touch with us to find out more about working with our clinic.

Different AI Conditions and Predictive Factors:

Many studies have found that people with various AI conditions (such as Type 1 Diabetes, Multiple Sclerosis, Rheumatoid Arthritis, Lupus or SLE, Celiac Disease, Autoimmune Arthritis, Asthma) have some degree of gut dysbiosis. Often, they will not have enough specific good gut bacteria and / or they will have too much specific bad gut bacteria. This is precisely what dysbiosis is. As we have mentioned, this state of dysbiosis will lead to leaky gut, which is one of three factors that contribute to autoimmunity, along with genetics and an environmental trigger. Please refer to our articles on AI, AI #1, AI #2 and AI #3, if you would like a deeper explanation.


It is clear that dysbiosis exists in the gut of AI patients. More information is needed in order to use these findings for future diagnoses and therapeutic approaches.

One huge challenge ahead is to differentiate cause from effect: is the gut bacteria the cause of AI disease or a result of the disease itself?? (Felix KM, 2017). Is the presence of certain bacteria a predictor of AI or a result? Future research will have to focus on this question as the answer is not entirely clear at this time (Felix KM, 2017).

What is clear is that the importance of diet and the composition of the gut microbiome play a critical role in health (Rose, 2016).  This is why we always look at gut health in our clinic and in functional medicine. You can review some of our approaches to gut health here and here or you can read the whole Gut Brain Axis Series of blogs, starting here, that we have been working on for the past several months.

Or better yet, get in touch with us today! Book a free 15-minute discovery call to see how we can help you with any active or potential AI conditions.


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December 11, 2019

What is the Connection between Autoimmunity & the Gut ? Part 3

The Microbiome-Autoimmune Connection, Part 3: Dr. Alessio Fasano’s work on Autoimmunity

by Nicola Schuler, CNTP, MNT and Dr. Miles Nichols


This week we will review the groundbreaking work of Dr. Fasano and autoimmunity. Autoimmunity is when the immune system becomes overactivated and attacks the body’s own tissue.

What causes this attack? Read on for more details.

These are three steps that can cause an autoimmune condition:

  • a genetic tendency
  • an environmental trigger
  • a leaky gut

To prevent and address an autoimmune condition, it is vital to work on improving your gut health. We can help you to do that.

Zonulin is a substance found in the gut that controls permeability or leakiness. There are tight junctions, which are like doors, on the gut lining. Zonulin opens these doors. Then food molecules, toxins and bacteria can get out of the gut tract and into circulation in the body. We call this condition, when the doors are open, leaky gut.

We want to avoid leaky gut because these food molecules and other things that escape from the gut into the body through these doors, cause an immune system reaction and inflammation. Over time, this immune system reaction becomes an overreaction and can lead to autoimmunity.

One thing that causes zonulin to increase and to open these doors is dysbiosis. Dysbiosis is when there is an imbalance in gut bugs in the microbiome. This happens when you have more bad gut bacteria crowding out the good gut bacteria. Gluten (anything containing wheat, rye, or barley or anything made from these contains gluten) also raises zonulin and opens these doors. Gluten is the main trigger for celiac disease, which is an autoimmune condition.

It is possible to improve dysbiosis, by reducing the bad gut bacteria and increasing the good gut bacteria. We can help you to do this. Then zonulin will not increase and your gut won’t be leaky, which reduces the chances of getting an autoimmune condition.

In scientific research, solutions to autoimmunity are being studied. One of these is a pill that would block zonulin from increasing. This would prevent the development of a leaky gut, one of the steps leading to autoimmunity. In other research, it was found that a certain probiotic can prevent leaky gut.

A healthy gut is so important for good health overall.

You might be wondering how you can improve your gut health. Is it as simple as taking a probiotic? Or what about prebiotics? Or how about stool testing or parasite treatments? What about Small Intestinal Bacterial Overgrowth? Or candida overgrowth?

In reality, any gut issues can cause leaky gut and contribute to autoimmunity. It is not as simple as taking a probiotic for most people. That is where functional medicine lab testing and targeted treatment for root causes of gut imbalance comes in. By following our functional medicine process, we have seen autoimmune markers in the blood like ANA (commonly positive with Lupus) become “negative” on multiple occasions after working for several months with people in our clinic. We have also seen dramatic reductions in thyroid antibodies (autoimmune conditions like Hashimotos and Graves) through our process at Medicine with Heart. If you would like to find out more about working with us (we work with people all over the world), please CLICK HERE to book a 15-minute discovery call.

Please stay with us for next week’s article when we will look at some ways of predicting autoimmunity. Read this article here for ways to address an autoimmune condition. Or better yet, call us and book a free discovery call to see how we can help you with an autoimmune condition and/ or to improve your gut health!


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November 12, 2019

Autoimmunity & the Gut Part 2: The Gut-Brain Axis Series, The Microbiome-Autoimmune Connection

by Nicola Schuler, CNTP, MNT and Dr. Miles Nichols

Last week in Autoimmunity & the Gut Part 1, we introduced what is autoimmunity (AI) and discussed some gut issues that can contribute to autoimmunity; such as leaky gut and dysbiosis. This week we look at specific microbiome issues in common AI diseases and we will give you ways to manage and address an autoimmune condition.

As we saw last week in Part 1, certain pathological bacterial strains are found in dysbiosis and with certain AI conditions.


  • RHEUMATOID ARTHRITIS (RA): As we saw last week, patients with new-onset RA have higher levels of a pathological bacterial strain called Prevotella copri (Bo Li, 2018). A study comparing RA patients and healthy controls confirmed a disturbed microbiome i.e. dysbiosis, which was partially resolved after RA treatment (Bo Li, 2018). Other studies have distinguished patients with RA from healthy controls as having dysbiosis (Thomas S, 2017). Current treatments for rheumatoid arthritis target symptoms. However, by focusing on the role played by gut bacteria, new treatment options looking at reducing the spread of P. copri in the gut could delay or prevent the onset of this disease (Scher JU, 2013).
  • TYPE 1 DIABETES (T1D): Multiple studies have shown dysbiosis in individuals with preclinical T1D (Bo Li, 2018). Issues include a sharp decrease in microbiome diversity, low community stability, an abundance of the Bacteroides strain of bacteria, fewer Bifidobacterium species and a lack of butyrate-producing and lactate-producing species (Bo Li, 2018).
  • MULTIPLE SCLEROSIS (MS): Studies suggest a distinct alteration in the MS gut microbiome compared with healthy controls (Bo Li, 2018). A study of 60 MS cases has reported an increased abundance of Methanobrevibacter (Archaea) and Akkermansia and a reduction in Butyricimonas (Bo Li, 2018). These MS-associated bacteria in the gut predispose the body towards a pro-inflammatory profile (Bo Li, 2018).

In short, pathogenic bacteria can be highly problematic to overall gut health. In certain people with a genetic disposition, they can contribute to the development of autoimmunity. This is why is extremely advisable to be mindful of your gut health and consistently work on supporting a healthy gut.


Once the AI disease process is activated, it does not have to be forever. It can be managed or even reversed by stopping the interaction between genes and the environment.

It is critical to reduce inflammation and calm the overactive immune response. Two steps are necessary:


  • Address gut health with Functional Medicine. An experienced FM practitioner can order a stool test for you. A stool test can indicate the balance of bacteria in your gut microbiome and identify the good bacteria, the neutral bacteria and the bad. This tells if you have dysbiosis or not. Then you can work on reducing the bad bacteria and supporting the growth of good bacteria in your gut. Finding a good FM practitioner is crucial in achieving this.
  • SIBO or small intestinal bacteria overgrowth, alongside dysbiosis, is often a factor in leaky gut and in AI. With your FM practitioner, you can test for SIBO and address it if you have it.
  • Once you have treated any gut infections or overgrowths, it is critical to address leaky gut. There are therapeutic strategies aimed at re-establishing the intestinal barrier function and restoring leaky gut. These will downregulate or decrease the actions of zonulin and offer a way to manage AI diseases (Fasano, 2012).
  • Probiotics: Several trials show that the microbial changes caused by probiotics may improve gastrointestinal symptoms and inflammation in rheumatoid arthritis, ulcerative colitis, and multiple sclerosis (Liu Y, 2018). Probiotics are likely to be used in autoimmune diseases as a component of the treatment (Liu Y, 2018). However, one size will not fit all. The choice of optimal probiotic strains will differ for each AI disease (Liu Y, 2018). Work with an experienced FM practitioner to identify which probiotic strains will help improve your particular AI condition.
  • Prebiotics: Prebiotics are certain foods that feed the good bacteria of the gut. They are an important part of supporting overall gut health. Please see our dietary recommendations here for info on prebiotic foods.


  • If you can identify the environmental trigger of your AI disease, you can eliminate or minimize your exposure to that trigger. A trigger is a specific antigen, or protein, that the immune system recognizes as a threat (real or not), that sets off the cascade of over-activation.
  • In the case of celiac disease, the trigger is gluten for example. However, in the vast majority of autoimmune diseases the trigger remains unknown.
  • It can be challenging to identify your trigger. The key autoimmune drivers usually fall into these six areas:
    • Diet
    • Leaky Gut & Dysbiosis
    • Infections
    • Toxins
    • Stress
    • Hormonal Imbalances

Your plan to manage and reduce AI symptoms should also include the following:

  • IMPROVE DIET: A few successful dietary approaches are being used to address AI. The two most common are the AutoImmune Paleo (AIP) diet and the Dr. Terry Wahls diet. The AIP diet was developed by Dr. Sarah Ballantyne. It does eliminate many foods and mainly focuses on meats and vegetables. Dr. Terry Wahls developed her Wahls diet which she used to greatly improve her MS. It focuses on high amounts of vegetables and other anti-inflammatory foods. Both diets support and improve gut health, reduce inflammation and remove problematic foods from the diet. Try one or both of these diets. You can work with your FM practitioner for more detail on the best diet for you.
  • RESOLVE INFECTIONS: Infections, bacterial or other, can be a trigger for AI. It is important to test for and address any infections. This could be bacterial like some of the overgrowths mentioned above that contribute to AI, viral like Epstein-Barr Virus, mycotoxin-related like Lyme disease or mold illness or other. Use an FM approach to resolve any infection you may have.
  • DECREASE EXPOSURES TO TOXINS: Pollution, chemicals, environmental toxins of all sorts are everywhere. We cannot escape exposure completely, but we can work to minimize our exposure to toxins. Eat a clean organic diet. Use clean, green household cleaning and other products. Switch to natural, non-chemical personal care products and use the EWG’s Skin Deep website ( to rate your products. Minimize EMFs from your phone and WIFI. Get an air filter for your home and a good water purification system. Avoid spending time in heavily-polluted areas or areas where chemicals are heavily used. Don’t smoke or drink excessive amounts of alcohol. Don’t use plastic containers for food or water storage. Switch to glass or stainless steel. Cook in clean safe cookware.
  • REDUCE / MANAGE STRESS: Stress can contribute to the development of leaky gut so reduce it wherever you can. Take on less commitments. Manage your stress through meditation, yoga, tai chi and time spent in nature.
  • ADDRESS HORMONAL IMBALANCES: Hormonal imbalances can also be an issue with AI. Address these with the help of your FM practitioner.

If you or someone you know is suffering from an autoimmune disease, get in touch with our clinic today. Book a free 15-min discovery call to see how we can help you with your symptoms. We can answer your questions and help you book an initial consult with one of the functional medicine doctors in our clinic.

—-    Please follow our next article in the Autoimmune-Microbiome series    —-

We will provide more evidence of the effects that the microbiome has on autoimmunity.


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November 5, 2019

Autoimmunity & the Gut Part 1, The Gut-Brain Axis Series, The Microbiome-Autoimmune Connection

by Nicola Schuler, CNTP, MNT and Dr. Miles Nichols


Gut health is closely involved in autoimmunity (AI). In fact, there are three elements necessary for an autoimmune disease to develop. These are a genetic predisposition, a leaky gut and an environmental trigger (Fasano, 2012). This is commonly referred to as the triad of AI. Through intestinal permeability, or leaky gut, the gut becomes a critical factor in AI.

AI diseases are typically chronic and can require lifelong treatment. Conventional medicine says there is no cure for most AI diseases. But Functional Medicine has developed different approaches that can help to manage or improve an AI disease, and in some cases, to reverse an AI disease.

There are more than 100 different autoimmune diseases. Forty other additional diseases are thought to have an autoimmune component (The American Autoimmune Related Diseases Association, 2019). We cannot list them all here but common ones include multiple sclerosis, lupus, celiac disease, Crohn’s, Hashimoto’s, rheumatoid arthritis, fibromyalgia, type 1 diabetes, ulcerative colitis, vitiligo, Meniere’s disease and others.

AI diseases are becoming more and more common in our modern society.

• The National Institute of Health (NIH) estimates up to 23.5 million Americans suffer from autoimmune disease and that the prevalence is rising (The American Autoimmune Related Diseases Association, 2019). The NIH numbers only include 24 diseases for which good epidemiology studies were available (The American Autoimmune Related Diseases Association, 2019).
• The American Autoimmune Related Diseases Association (AARDA) says that 50 million Americans suffer from autoimmune disease when all AI diseases are included (The American Autoimmune Related Diseases Association, 2019).
• Autoimmune diseases are more common in women, and they often run in families.


Autoimmunity (AI) occurs when the body’s immune system attacks itself. The immune system protects the body by responding to invading microorganisms, such as viruses or bacteria, by producing antibodies or other types of immune cells. Normally, an immune response cannot be triggered against the cells of one’s own body. In some cases, however, immune cells make a mistake and attack the cells that they are meant to protect. Essentially, the person’s immune system attacks its own tissue. This can lead to a variety of autoimmune diseases.

Factors such as genetics, the environment, infections, and the gut microbiota all play a role in autoimmune disorders. The microbiome, meaning the specific bacteria in the gut, has a very important and long-term effect on the immune system, starting at birth. It also plays a significant role in autoimmune disease (Campbell, 2014).

It is not fully understood how the microbiome interacts with the immune system in either the development or the absence of an autoimmune condition (Thomas S, 2017). Microbial dysbiosis in early life can negatively affect how the immune system develops and provide the basis for allergic disorders or other health problems in later life (Thomas S, 2017). Dysbiosis may trigger intestinal permeability (or leaky gut) and consequently may trigger autoimmune diseases, given the right circumstances (Thomas S, 2017).

When leaky gut occurs, there are essentially small holes in the gut lining. Through these holes, various large protein molecules of undigested food can get into the bloodstream and travel all around the body. As this undigested food continues to pass through the holes of the gut lining, food intolerances will occur and the immune system will be triggered over and over into attacking these particles. Eventually, the immune system becomes excessively activated and goes into overdrive. Certain body tissue can look like undigested food molecules. This is called molecular mimicry.

The immune system can start to confuse a food or other foreign molecule with a particular body tissue, and start to attack its own tissue. This self-attack is what happens in an autoimmune disease. For example, Hashimoto’s is when the immune system attacks the thyroid. In MS, the attack is on the myelin sheath surrounding nerves.


Several factors can lead to leaky gut:

DYSBIOSIS: Increased intestinal permeability is influenced by the make-up of the gut microbiota (Fasano, 2012). An unbalanced gut flora or dysbiosis, when more bad bacteria exist vs. good bacteria, can contribute to leaky gut. Dysbiosis has been associated with autoimmune diseases, particularly, rheumatoid arthritis (RA), type 1 diabetes (T1D), multiple sclerosis (MS) and autoimmune liver disease (AILD) (Li, 2018).

ZONULIN: Zonulin is a protein that regulates intestinal permeability by modulating the tight junctions of the gut lining (Fasano, 2012). Zonulin has been found to be higher in autoimmune conditions associated with a dysfunction of the tight junctions, including celiac disease (CD) and T1D (Fasano, 2012). Both animal studies and human trials have established that zonulin is involved in the development of autoimmune diseases (Fasano, 2012).

Zonulin is triggered or increased by small intestinal exposure to bacteria, as in the case of SIBO or small intestinal bacterial overgrowth, and gluten (Fasano, 2012). These have been identified as the two more powerful triggers (Fasano, 2012) for higher zonulin, which will lead to leaky gut. In the small intestine, when exposed to excessive bacteria, zonulin is secreted in genetically susceptible individuals (Fasano, 2012). This affects the intestinal barrier function by releasing zonulin and can cause leaky gut (Fasano, 2012).

POOR DIET: Diet dramatically affects gut health and the specific strains of gut bacteria. The US diet has changed dramatically since the 1950’s. We have new strains of grains, especially in wheat, rice, soy, and corn. The food supply contains GMO’s, chemicals, pesticides, fungicides, insecticides, antibiotics, heavy metals, such as arsenic, chemical ingredients such as artificial preservatives, colorings, and flavorings and plasticizers such as bisphenol A. Animal products contain the hormones and antibiotics given to the animals. In addition, antibiotics, antacids, proton pump inhibitors, histamine 2 blockers, and other drugs are widely used.

In line with these dietary changes, there has been a significant increase in autoimmune diseases, linking the quality of diet and autoimmune problems (Campbell, 2014).

The specific elements of our diet that contribute to leaky gut are:

• Refined and processed sugars
• Refined carbohydrates
• Genetically modified foods
• Vegetable oils
• Alcohol: Data indicate that alcohol is associated with dysbiotic changes in the gut microbiota, meaning that balance of good vs. bad bacteria tips into dysbiosis (Engen PA, 2015). Alcohol may also be associated with increased gastrointestinal tract inflammation and intestinal permeability resulting in systemic inflammation and tissue damage (Engen PA, 2015).
• Gluten: Gluten triggers the release of zonulin. Zonulin is a key factor in regulating tight junctions of the gut lining. Zonulin’s increase in genetically susceptible individuals may lead to immune-mediated diseases, i.e. autoimmunity (Fasano, Intestinal permeability and its regulation by zonulin: diagnostic and therapeutic implications., 2012).
• Dairy
• Packaged, processed, and junk foods: Glucose, salt, emulsifiers, organic solvents, gluten and nanoparticles are increasingly used by the food industry, allegedly to improve the quality of food. All of these additives are known to increase intestinal permeability by breaking down the tight junctions of the gut lining (Lerner A, 2015).
• Any food to which a person has a sensitivity or allergy

STRESS: Stress is a factor and can disturb the make-up of the microbiome and increase permeability (Camilleri, 2019).

MEDICATIONS: Certain medications can increase intestinal permeability. Non-steroidal anti-inflammatory drugs (NSAIDs) such as ibuprofen (Motrin, Advil), aspirin, Celebrex and others increase permeability (Camilleri, 2019). Other drugs, such as antibiotics and oral contraceptives disrupt the intestinal barrier (Bischoff SC, 2014).

Once a leaky gut is established in a genetically susceptible person, an AI disease may potentially develop.


Dysbiosis should be identified, monitored and treated because it can contribute to autoimmunity. Most infectious agents, such as viruses, bacteria and parasites, can induce autoimmunity via different mechanisms (Kivity S, 2009). Bacterial infections in particular are associated with many autoimmune diseases involving chronic inflammation (Sherbet, 2009).

In many cases, it is not a single infection but rather the ‘burden of infections’ from childhood that is responsible for the development of autoimmunity. The development of an autoimmune disease after infection tends to occur in genetically susceptible individuals, often with intestinal permeability or gut dysbiosis (Kivity S, 2009).

ENTEROCOCCUS GALLINARUM: One study has linked autoimmune reactions to a bacterium in the gut called Enterococcus gallinarum (Manfredo Vieira S, 2018). The autoimmune response can be triggered when the bacterium spontaneously migrates from the gut to other organs in the body, such as the spleen, liver, and lymph nodes (Manfredo Vieira S, 2018). The results were confirmed when researchers compared cultured liver cells of healthy people versus those of people with an autoimmune disease and found traces of Enterococcus gallinarum in the autoimmune group (Manfredo Vieira S, 2018).

BACTEROIDES FRAGILIS: Another study has identified the bacteria Bacteroides fragilis to be involved in AI (Stewart L, 2018). A protein produced by this common gut bacteria may trigger the onset of autoimmune disease through the concept of molecular mimicry. Researchers found that patients with autoimmune disorders display higher-than-normal levels of a “mimic protein” produced by Bacteroides fragilis (Stewart L, 2018). This specific microbe in the gut produces protein molecules that mimic a human protein, which can cause the immune system to attack its own cells by mistake through molecular mimicry and this can contribute to autoimmunity (Stewart L, 2018).

KLEBSIELLA PNEUMONIAE: It has been known for some time that the pathogenic bacteria, Klebsiella pneumoniae, is linked to certain AI diseases (Rashid T, 2013). Studies have found that Klebsiella is the most likely triggering factor involved in the initiation and development of two autoimmune diseases; ankylosing spondylitis (AS) and Crohn’s disease (CD) (Rashid T, 2013). It appears that Klebsiella microbes can grow and thrive in the bowel of genetically susceptible people.

MYCOBACTERIUM AVIUM SUBSPECIES PARATUBERCULOSIS or MAP: MAP is a bacterium that is the known infectious cause of Johne’s disease, a chronic inflammatory bowel disease (IBD) in cattle (Dow, 2012). MAP is also involved in Crohn’s disease, which is very similar to Johne’s. MAP acts as a trigger of autoimmune disease and is associated with autoimmune diabetes, autoimmune thyroiditis and multiple sclerosis (Dow, 2012).

PREVOTELLA COPRI: In a study of 114 people, a bacterium named Prevotella copri was present in the gut of 75% of people with rheumatoid arthritis (RA) compared to only 21% of healthy control subjects (National Institutes of Health (NIH), 2013). In addition, an abundance of Prevotella copri has been identified in patients newly diagnosed with rheumatoid arthritis (Alpizar-Rodriguez D, 2019). The presence of P. copri corresponds to a reduced amount of other beneficial microbes (Scher JU, 2013). This indicates the role of intestinal dysbiosis in the development of RA (Alpizar-Rodriguez D, 2019).

PROTEUS: A strong link exists between Proteus mirabilis microbes and RA (Ebringer A, 2006). It is thought that sub-clinical Proteus urinary tract infections are the main triggering factor (Ebringer A, 2006). In addition, molecular mimicry between these bacteria and the specific tissue under immune attack in RA leads to the continuation of the disease process (Ebringer A, 2006).

In short, pathogenic bacteria can be highly problematic to overall gut health. In certain people with a genetic disposition, they can contribute to the development of autoimmunity. This is why is extremely advisable to be mindful of your gut health and consistently work on supporting a healthy gut.

Please follow us again next week when we will continue with Autoimmunity & the Gut Part 2. We will discuss specific microbiome issues in common AI diseases and we will give you ways to manage and address an autoimmune condition.

If you would like immediate assistance with an autoimmune condition, then get in touch with our clinic today. Book a free 15-min discovery call to see how we can help you with your symptoms. We can answer your questions and help you book an initial consult with one of the functional medicine doctors in our clinic.


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