When I was first searching for a healing plan for Chronic Disease, I learned about the important role of gut health in autoimmune disorders and chronic disease — and how replenishing it with probiotics and fermented foods can help bring gut health back into balance.
According to research, every person with a chronic disease or an autoimmune disorder has something called intestinal permeability, also known as a “leaky gut.” This made a lot of sense to me, because my clients had many of the symptoms of intestinal permeability — including bloating, stomach pains, irritable bowel syndrome (IBS), and acid reflux — as do many people with Chronic Disease.
However, not everyone with intestinal permeability will have these symptoms. Some may have no apparent gut symptoms at all.
Chronic Disease and Autoimmunity has been determined to be a three-legged stool, requiring a combination of the right genes, the right triggers, and intestinal permeability, to manifest itself.

Our gut barrier has the important job of letting nutrients into the body while keeping bacteria, viruses, parasites, and toxins out. When the gut barrier is impaired, these harmful organisms can leak into the body. We call this intestinal permeability, or “leaky gut.”
A leaky gut has gaps in the gut lining that allow irritating molecules and substances to escape from the digestive system, and enter into the bloodstream. This irritation can interrupt the immune system’s ability to regulate itself and put the body into a perpetual “attack mode” that is counterproductive to healing.
There are various reasons why a person may have intestinal permeability.
Gluten, which is the protein found in wheat products, has become a well-known cause of intestinal permeability, and many individuals with autoimmune conditions have been able to find relief in symptoms by following a gluten free diet, the Paleo diet, or another elimination diet such as the Autoimmune Paleo diet (AIP). Some people have even seen a complete remission in their autoimmune condition after removing gluten from their diet.
Other common reasons a person may experience a leaky gut include stress, food sensitivities, nutrient deficiencies, and intestinal infections.
A gut may also be more permeable due to an imbalance of probiotic (good) vs. opportunistic (bad) gut bacteria, also known as dysbiosis. E. coli and Proteus bacterial species are often referred to as “opportunistic pathogens” because they only become pathogenic when the opportunity is just right. If they are outnumbered by probiotic bacteria, they behave like good citizens of the gut and may add value. When they outnumber the probiotics, they may start to bore into the gut wall, leading to intestinal permeability.
People with autoimmunity have been found to have lower amounts of the probiotic bacteria Lactobacillus and Bifidus, and higher amounts of the opportunistic E. coli and Proteus bacteria.
I’ve seen this pattern of low levels of probiotic bacteria with high levels of opportunistic bacteria on my lab tests, as well as the tests of many clients with Chronic Disease or autoimmune disorders that have had stool testing to quantify microbial flora. (You can have your functional medicine doctor order this test for you, or you can self-order the GI-MAP or GI Effects test.)
When I first took a stool test, I was shocked to see that I had zero growth of Lactobacillus bacteria, even though I was eating yogurt on a daily basis. I didn’t realize at the time that the problem with most commercial probiotics and yogurts, is that they don’t have enough beneficial bacteria to make a difference.
I started to eat fermented foods and added high doses of probiotics… and began to feel better and better. (I had already been gluten and dairy free and had hit a “healing wall.”)
I retested myself with the same test when all of my GI symptoms were gone, and found that my probiotic bacteria were in the optimal range, and the E. coli and Proteus species were no longer dominating my gut flora.
Thus, one of the very first recommendations I make for EVERYONE with Chronic Disease or Autoimmune disorder is to be sure to get enough probiotics on board.

One of the easiest ways to introduce more beneficial bacteria to your microbiome is to eat fermented foods.
Here’s a one of my favorite recipes. I love making this coconut milk yogurt to add a dose of probiotics to my weekly diet.
Coconut Yogurt
Prep time: 30 minutes
Cook time: 8 to 24 hours
Serves: 4
Coconut yogurt is a delicious way to restore balance to your gut. This creamy homemade coconut yogurt provides all of the gut-healing benefits of yogurt, without the extra sugar and other additives that can complicate your health journey. I love using this in salad dressings and smoothies, or enjoying it topped with shaved coconut, pumpkin seeds, nuts, berries or a splash of maple syrup. 
Ingredients:
14 ounces creamed coconut
½ cup water (omit if using canned coconut cream)
2 teaspoons collagen
1 tablespoon maple syrup
Dairy free yogurt starter, 2-4 high-quality probiotic capsules, ¼ cup yogurt starter, or ¼ cup yogurt from previous batch.
Directions:

1. Blend the creamed coconut with water in a high-powered blender. Alternately, if you can find an organic canned cream coconut product without additives, you may also use that (omit the water as you will not be blending the coconut cream). Heat the coconut milk to 180ºF, then cool to 110ºF.
2. Add the yogurt starter, and then add the collagen and maple syrup. Mix to combine.
3. Place the mixture in a yogurt maker or tightly sealed Mason jar at room temperature for 8 to 24 hours.
4. If using a yogurt maker, remove and put into sealed containers, such as glass Mason jars.
5. Store in the fridge for up to 2 weeks.

If you don’t want to make your own fermented foods, I’ve listed some tried and trusted brands below that I’ve incorporated in my own diet before I started making my own.

• Fermented coconut yogurt: CoYo Coconut Milk Yogurt and So Delicious Dairy Free are two options sold in the United States.
• Fermented coconut water: CocoBiotic by Body Ecology
• Fermented cabbage: Check your organic grocery store and make sure you get the kind that is refrigerated, as the probiotic bacteria only survive for a couple of weeks at room temperature. To order online, try Superkrauts, which is a great brand that ships its products, chilled to your home, through Amazon.

Probiotic Supplements

Probiotics have been widely researched for a variety of conditions, including irritable bowel syndrome, constipation, anxiety, depression, and even skin disorders. They can help improve digestion and nutrient extraction from the foods we eat, and can also balance the immune system. Additionally, probiotics can help with many types of gut disorders, including small intestinal bacterial overgrowth (SIBO), which is present in over 50 percent of people with Chronic Disease and Autoimmune disorder.

Types of Probiotics That I Have Used Successfully

Beneficial Yeast Probiotics

Saccharomyces boulardii (S. boulardii) is a beneficial yeast that helps to clear out dysbiosis such as the pathogenic bacteria, Candida, and some parasites (including Blastocystis hominis). It also helps to clear out H. pylori, an infection that has been implicated in ulcers and has been linked to Chronic Disease and Autoimmunity. ​S. boulardii does not colonize the gut wall, but instead, it causes an increase of secretory IgA, which supports our own body’s natural defense against infections and opportunistic gut bacteria.
This beneficial yeast is generally safe for SIBO, and should be used whenever you are taking a course of antibiotics (or after their use), to help re-balance the gut flora. While the label of the product recommends taking 2 capsules per day, I used higher doses, building up to 4 capsules, three times per day.
I really love this probiotic because it’s so broad-spectrum and actually assists our own gut with working better on its own. I’ve been recommending S. boulardii for many years, and some versions are stable at room temperature, while others need to be kept in the fridge. As a pharmacist, I’m always looking for ways to make taking supplements easier, so I always recommend a heat-stable version of S. boulardii from Designs for Health, so that my clients don’t forget to take it. (Remember, getting the supplement and keeping it in your home is the first step, but getting benefits from it actually requires taking it! )

Lactobacillus-Based High Dose Multi-Strain Probiotics

Most grocery stores and health food stores sell Lactobacillus-based probiotics that contain 10 billion colony forming units (CFU’s) of one probiotic strain. While this seems like a really big number, in reality, we have one trillion bacteria in our gut, and that small amount is not likely to make a difference. In fact, most probiotic supplements only contain enough probiotics to maintain an already healthy gut, not to restore gut microbe balance. I, personally, haven’t seen major benefits from using Lactobacillus probiotics — unless taken in very high doses.
Furthermore, research is showing that probiotic diversity is associated with greater health and improved gut function. I prefer probiotic blends containing Lactobacillus strains in addition to other probiotics, instead of single strain probiotics that only contain one type of Lactobacillus. Probiotic blends generally contain various strains of Lactobacillus, Bifidobacteria, and in some cases, beneficial Streptococcus bacteria. Thus, I recommend taking higher doses of multi-strain probiotics.
If you’ve never taken probiotics, you will want to start with the 10 billion CFU probiotic, but work your way up to a higher dose over time.
Rather than taking multiple pills, numerous companies have created high dose probiotic blends.
Designs for Health 50B CFU probiotic, which contains 50 billion colony forming units, is a great high dose probiotic to start with as you work your way up. (This version also has the benefit of being stable at room temperature).
Another high dose Lactobacillus-based probiotic that I have used with great success, and that has the most research behind it, is known as VSL #3, which contains 450 billion CFU of probiotics per dose. This particular probiotic has been clinically studied for ulcerative colitis and irritable bowel syndrome. The probiotic has been so successful in inducing remission, it has been labeled as a “medical food.” Please note, this is a very expensive probiotic, but you may be able to get it covered by your insurance if you have the right diagnosis.
While this used to be my go-to probiotic, in the last few years, I’ve had some negative experiences with it… Namely, a family member with new onset ulcerative colitis seemed to have a flare-up after using it. The word on the street in functional nutrition circles is that the probiotic can exacerbate inflammatory bowel conditions, which I also learned the hard way. (It was surprising, as all of the studies about this probiotic actually reported that it helped those conditions.)
Additionally, there was some recent controversy between the inventor and manufacturer of this probiotic. Allegedly, the inventor left the company, along with his proprietary recipe, and the product that the VSL-3 manufacturer has been making is different than the clinically tested product. According to the website of Visbiome, the inventor’s new company:
“Claudio De Simone, inventor of high-potency probiotic, sued pharmaceutical companies for making false advertising claims, ownership rights to the product formula and unpaid royalties.”
I have since stayed away from VSL-3 and have not yet tried Visbiome, but I also learned about a less expensive yet equally effective brand of high dose multi-strain probiotics from my brilliant nutritionist friend, called Probiomed 250 also from Designs for Health. 
High dose, multi-strain probiotics can be very helpful for people with Chronic Disease and Autoimmunity in general, and especially for those who often show low levels of them on gut lab tests. However, they may be problematic for people with SIBO, which can be caused by an overgrowth of various bacteria, including Lactobacillus and Streptococcus bacteria — often found in probiotics.

Spore-Based Probiotics

Spore-based probiotics came on my radar after some colleagues reported seeing excellent results while using them with their clients. Soil-based probiotics are naturally occurring, spore-based, and have a unique mechanism of action, which allows them to directly modulate the gut microbiome.
Spore-based probiotics have shown promise in various autoimmune diseases, as well as in reducing allergies and asthma. They also have an ability to boost Lactobacillus colonies, so they can be used concurrently with Lactobacillus probiotics, as well as in place of them. Unlike the Lactobacillus probiotics, spore-based probiotics can reduce SIBO and increase gut diversity by boosting the growth of other beneficial flora.
Clients and colleagues with Chronic Disease or Autoimmune disorder have reported the following after using them for 30 to 90 days:

• Improved mood
• Less pain
• Better bowel movements
• More energy
• A reduction or complete elimination of food sensitivities

I have had clients use Probiospore by Designs for Health with great success. The starting dose for Probiospore probiotics is one capsule every other day, and the therapeutic dose is two capsules per day. Once the desired effect has been seen (generally three to six months in people with Chronic Disease or Autoimmune disorder), I recommend dropping down to a maintenance dose of one capsule per day.

Tips for Using Probiotics

If you’ve never taken probiotics before, you will want to start low and go slow, as you may have increased symptoms if your gut flora changes too rapidly. For example, if your target dose is 50 billion CFU, then you may want to start off at a dose of 10 billion CFU, until your gut has adjusted. If you’ve found that you can tolerate that dose, but have not reached your gut health goals, you can work your way up to your target dose.
To boost the effect of probiotic supplements, I recommend making sure you are getting plenty of prebiotics in your diet. Prebiotics are the foods your microbiota feed on, and are necessary to ensure that the population of healthy bacteria in your gut grows and flourishes. Foods rich in prebiotics include: chicory root, Jerusalem artichoke, dandelion, garlic, leek, onion, bananas, apples, konjac root, cocoa, burdock root, flax seeds, yacon root, jicama, and asparagus.
Additionally, those with SIBO (small intestine bacterial overgrowth) will need to avoid many probiotics, especially those containing prebiotics, as they will just be adding fuel to the fire. Soil-based probiotics have been found to be effective for those with SIBO, and S. boulardii is generally safe as well.
One more thing to note when you first start taking a high-quality probiotic: the “good” bacteria will begin to colonize your gut and crowd out the “bad” bacteria that had taken up residence there. When these bad bacteria are crowded out and attacked, they may start to release toxins that build up faster than your body can get rid of them. This will cause your body to begin an immune response to clear them out, with symptoms that may include digestive discomfort, changes in bowel movements, muscle aches, headaches, and skin sensitivity. This is oftentimes referred to as a healing crisis or a Jarisch-Herxheimer reaction. While uncomfortable, this type of reaction is an indication that your probiotics are working and that you are eliminating the bad bacteria! However, this highlights the importance of starting low and going slow when you begin taking a new probiotic, so that you can minimize the unpleasant symptoms. Staying hydrated and moving your body as much as possible will also help your body clear out the toxins more rapidly.

The Takeaway

Gut healing is a journey; you may need various interventions like removing reactive foods and infections, taking enzymes and probiotics, and balancing nutrients. In some cases, such as after a bout of food poisoning, antibiotic treatment, or a stressful life period, you may need to start the healing process from scratch. Remember, be kind to yourself — and learn to listen to your body — so that you can support and feed it properly. You are worth it!