The Best Probiotic Protocol? The “Triple Therapy” Approach - Dr. Michael Ruscio, DC

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Do you want to start feeling better?

Yes, Where Do I Start?

The Best Probiotic Protocol? The “Triple Therapy” Approach

This Multi-Category Method Ensures You Don’t Miss Out on Any Benefits and Cuts Through the Strain-Specificity Noise

Key Takeaways:

  • Probiotics can be divided into three categories: Lactobacillus with Bifidobacterium, Saccharomyces boulardii, and soil-based probiotics.
  • Instead of focusing on specifics like best time, strain, or capsule type, triple therapy uses all probiotic categories at once for a synergistic (and simpler) approach.
  • Research supports the use of multi-category and multi-species probiotics over single-species or single-strain.
  • If you don’t experience symptom relief in three to four weeks, a more comprehensive gut reset might be necessary.
  • Probiotics have been shown to improve autoimmune conditions, gut health, food intolerances, brain fog, seasonal allergies, fungal infections, and parasites.
  • Probiotics benefit general wellness and health maintenance by promoting a healthy and balanced gut microbiota.

The verdict is in. Gut health is unequivocally a key foundational factor in overall health and well-being. Without a strong, semipermeable gut wall and diverse microbiota (beneficial bacteria and fungi in your gut), your health will likely suffer in one way or another. The best way to ensure your gut stays healthy is to support your digestive system with adequate nutrient intake, proper sleep, stress reduction, exercise, and a probiotic supplement [1, 2].

When it comes to probiotics, the scientific community has learned a great deal about how to use them to maintain overall health and speed the recovery of serious illnesses like helicobacter pylori (H. pylori) [3]. Additionally, chronic inflammatory conditions like autoimmune diseases, leaky gut, inflammatory bowel disease, irritable bowel syndrome (IBS), gastritis, constipation, and other health conditions of the digestive tract may all benefit from the use of probiotics [4, 5, 6, 7, 8, 9, 10].



There are three different categories of probiotics available on the market, and when you combine all three, you’re using a triple therapy probiotic. This is the best way to take probiotics, in my clinical experience.

It’s thought that a combination probiotic treatment like this may help restore balance in the gut microbiome, especially if trying one category alone isn’t leading to improvement.In this article, I will share what the science says and what I’ve witnessed in my clinical practice with patients who’ve used a triple therapy probiotic protocol to address their gut health issues. I will start with some definitions and key terms so that we’re all speaking the same language, and then I’ll get into the science and a case study from our clinic.

Probiotics: Making Sense of the Labels

When you pick up a probiotic supplement at a grocery store, you’ll see the same handful of things on every label, even if the details vary. On the front, you’ll see a big number written out with the letters “CFU,” along with a number, usually in the billions, such as “15 billion CFU”. CFU stands for colony-forming units. Those big numbers are essentially the total number of microscopic organisms living in each capsule—usually bacterial, but sometimes fungal.

When you look at the back label, you’ll see exactly what’s in the bottle—a list of italicized Latin words, sometimes a series of letters or numbers after that, and the CFU (in the millions or billions).

The first Latin words will either be Lactobacillus (or just an “L.”), Bifidobacterium (or just a B.), Saccharomyces (or just an “S.”), or Bacillus (usually not abbreviated, to avoid confusion). Those words denote the category of the probiotic. When it comes to Triple Therapy, category is the main focus. 

The second word, for example, rhamnosus or reuteri, is the species of the organism.

The series of numbers and letters (for example, MM53 or RC-14) are the specific probiotic strain of the species. The strain may or may not be listed on the label, but is almost always listed in scientific research. The strain can help us understand the unique benefits that the probiotic provides. Think about it like dog breeds: all dogs are the same species, but each breed has its own unique characteristics.

The ingredient line on your probiotic label might look like this:

L. reuteri MM53 ……………………30 million

or

Lactobacillus reuteri MM53 ……………………30 million

or

L. reuteri ……………………30 million

or

Lactobacillus reuteri ……………………30 million

Regardless of how it’s listed, this probiotic is part of Category 1, which I’ll explain in the next section. This contradicts much of what you may read or hear, but for general health purposes, you don’t need to know the strain. It’s not integral to specify the strain to benefit from a probiotic protocol. Remember, what’s more important is categories.

Triple Therapy: Combining All Three Categories

As I mentioned in the introduction, using all three categories simultaneously constitutes a triple therapy probiotic regimen—the best probiotic regimen, in my opinion. Let’s define the three categories of probiotics.

Category 1: Lactobacillus and Bifidobacterium species.

These are the most well-researched types of probiotics, with over 500 trials assessing their validity. These live microorganisms are also known as lactic-acid-producing probiotic bacteria, and they are a natural part of the human microbiota. They typically do not colonize your gut, but they do improve overall health [11, 12, 13, 14, 15]. 

Category 2: Saccharomyces boulardii

These are the second-most researched probiotics, with over 100 studies to support their efficacy. This category is a beneficial fungus that is not a natural part of human microbiota but has been shown to improve human health [16, 17].

A 2023 randomized pilot study showed that taking a strain of S. boulardii led to a decrease in small intestine bacterial overgrowth (SIBO), IBS, abdominal pain, and diarrhea after just two weeks. These beneficial results are likely because this probiotic fungus is antibacterial and antimicrobial. These qualities help fight off pathogens (bad microbes) that can cause symptoms  [18]. 

Category 3: Soil-Based Probiotics

Also known as spore-forming bacteria, the third category is the least researched, with fewer than 100 trials to evaluate their effectiveness [19, 20, 21]. This is the only category of the three capable of colonizing the large intestine long-term [22]. You will know you have a soil-based probiotic if the bacteria on the bottle says “Bacillus”. 

Why Use All Three Categories?

Years ago, I started seeing a pattern in the research: multi-species formulas were imparting the most benefits of probiotics. I began to wonder whether treating people with multiple categories might be even more advantageous.

So, I put my hypothesis to the test in the clinic. I began with patients who weren’t seeing substantial improvements using single-category, multi-species formulas. I added a formula from a different category, and the patient would begin to improve

Then, when we’d add in the third, the patient would improve even more. I saw this over and over again in my clinic.

The best way I’ve found to describe using a triple therapy probiotic protocol is to use an analogy of legs on a stool. A stool with one or two legs is wobbly and unstable, but when you add a third leg, it’s sturdy enough to stand on. 

The synergistic effects of three instead of one or two dramatically increase the efficacy of probiotics.

Case Study

A patient named Phyllis had been suffering from symptoms of SIBO for three years. 

When she came to me, she had already been on a Paleo, low-FODMAP diet for nearly two years without seeing much change in her condition. She’d also tried several different single-category, multi-strain probiotic formulas** over that year and a half and had experienced some negative side effects from them. Bloating was a big one. Despite her nearly perfect diet for addressing SIBO symptoms, she hadn’t seen much improvement.

When she came to me, the only change we made was to switch her probiotic plan to a triple therapy probiotic protocol. After one month on the new treatment plan, Phyllis began to see marked improvements in her symptoms—better energy, better stool regularity, better bowel movements generally, and improved overall gut health. The comprehensive approach of the triple therapy seemed to make the biggest difference in her gut recovery.

**Probiotic dietary supplements range in quality and ingredients. It’s really important that you choose a high-quality product with the specifics on the back of the label that I mentioned above and one that has Good Manufacturing Practices (GMP) certification and notes that it’s been tested by an independent lab. In the specific case of SIBO or other types of gut dysbiosis, you DO NOT WANT PREBIOTICS in your formula, as that type of fiber can lead to flare-ups. I don’t know exactly what Phyllis took in the years she was taking probiotics before she came to me, so it’s possible that some of her relief also came from taking a higher-quality product.

How to Implement a Triple Therapy Probiotic Protocol

As is the case with virtually any health intervention, it’s important to monitor how the probiotics affect you over time and talk to your healthcare provider before starting if you have questions or concerns. I mentioned above that you should start with one type of probiotic at a time to ensure that no category causes a reaction before proceeding with all three. Once you’ve established that you can tolerate all three, follow these steps:

  1. Find a high-quality probiotic from each of the three categories and take all three together. To save a few dollars and avoid having to store some probiotics in the fridge and others on the counter, consider my Triple Therapy Probiotic Powder Sticks. I created these to make sticking to this regimen a lot easier.
  2. Monitor your symptoms for three to four weeks. It’s a good idea to write them down in a journal. If you’re improving, stay on the triple therapy protocol until your improvements have plateaued.
  3. Once you’ve seen your maximum improvement (you’ve plateaued), stay here for about a month to allow your system to calibrate to these new improvements. Then reduce your dose (possibly start by taking half a packet instead of a whole one), and find your minimal effective dose. Stay on your minimal effective dose.

It’s important to note that for those with severe reactivity or gut dysbiosis, you might find that one of the three causes bloating, discomfort, or other undesirable side effects at first. In that case, you’d leave that category out until your gut begins to heal, and then you can eventually add it in to experience the benefits of triple therapy.

You may have noticed a lack of details in these probiotic instructions, and that’s intentional. The research simply doesn’t substantiate all the parameters you hear about probiotics. It doesn’t matter what time of day you take your probiotic supplement. It doesn’t matter whether you take it on a full or empty stomach. It doesn’t even matter if the probiotic is alive. It just matters that you take it and notice whether or not you improve within a month.

Why Take A Daily Probiotic

Taking a high-quality daily probiotic has been shown to improve a wide array of chronic health issues and acute infections, and support overall health and wellness. You may also want to add probiotic foods to your daily diet. These foods also support gut health, providing good bacteria and digestive enzymes to aid digestion. 

There are some caveats to using probiotic foods as a therapeutic dose of probiotics. Probiotic foods have beneficial bacteria but don’t always contain all three categories. They also need to be consumed every single day to maintain benefits. For this reason, supplements are often a better daily staple with probiotic foods layered on top for added gut benefits.

Kimchi is usually eaten at the beginning and throughout a Korean meal, and miso at the beginning of a Japanese meal, for example. Other probiotic foods include sauerkraut, kefir, miso, kombucha, yogurt, and tempeh. 

If you have a GI condition or a sensitive gut, you should make sure you can tolerate these foods before adding them to your diet because they may contain prebiotics that may be irritating before you heal. For example, cabbage is a prebiotic food that can be irritating. This is another reason why it may be better to opt for a probiotic supplement over-relying on probiotic foods alone.

The following conditions have all improved from the use of probiotics in placebo-controlled trials and meta-analyses of the available research:

  • Autoimmune conditions, including type 1 diabetes, multiple sclerosis, and rheumatoid arthritis [4, 23, 24, 25, 26]
  • Digestive conditions, such as  bloating, constipation*, diarrhea, and diverticulitis [27, 28, 29, 30, 31

*there is less conclusive research on pediatric constipation [32, 33]

  • Brain fog associated with Alzheimer’s disease, bipolar disorder, and fibromyalgia [34, 35, 36, 37]
  • Food intolerances, like intolerance to gluten and dairy [38, 39, 40]
  • Seasonal allergies and hay fever [41, 42]
  • Fungal infections, such as Candida albicans [43]
  • Parasites like Blastocystis hominis and Giardia lamblia infections [44, 45]

Probiotics have also been instrumental in treating acute gastrointestinal tract infections, like Helicobacter pylori infections, which can cause peptic ulcers [23]. When combined with the standard triple therapy (a coincidentally similar name for the antibiotic therapy given to treat this infection), probiotics have reduced antibiotic-associated diarrhea, vomiting, nausea, and other side effects of the antibiotic treatment. Probiotics also had a positive effect when combined with antibiotic therapy for Helicobacter pylori infection in clinical trials. The probiotics helped patients recover more quickly than they would with conventional treatment alone [28, 46, 47]. 

General Wellness and Digestive Health

Multiple systematic reviews of randomized controlled trials offer consistent and clear insights supporting the health benefits of taking probiotics. Probiotics can:

  • Increase the bacterial diversity, or health, of your bacterial community [48, 49, 50]
  • Fight pathogens (harmful bugs) and their toxins [48, 49, 51, 52, 53]
  • Promote a more rapid recovery from imbalanced gut microbes [48, 49]
  • Promote a healthy immune response in your gut [48, 49, 54, 55, 56]
  • Reduce gut inflammation (remember, excessive inflammation is part of an overzealous immune response) [48, 49, 50]
  • Encourage the growth of healthier microbes in your gut [48, 49, 54]
  • Reduce leaky gut (intestinal permeability), a condition that has been linked to inflammatory disease [48, 49, 57, 58, 59]

The bottom line is that probiotics can help improve the balance of gut bacteria and other organisms in your intestinal tract, reduce an overactive immune system, and reduce the inflammation that can lead to undesirable symptoms. 

Try Triple Therapy

Probiotics are antibacterial, antifungal, and antiparasitic. These properties help promote a healthier, more supportive, and balanced community of organisms in your gut to support overall wellness and address serious health concerns. 

If you’re experiencing intestinal issues or chronic conditions like autoimmunity, and the probiotics you’re on aren’t helping, it might be time to try a triple therapy approach to probiotics.

The science and my experience with patients in my clinic support the synergistic effects of using all three categories together rather than a single strain on its own. 

We would love to help you get started on your gut health journey. Reach out to our clinic to set up an appointment, or for a more self-paced approach, check out my book, Healthy Gut, Healthy You.

The Ruscio Institute has developed a range of high-quality formulations to help our patients and audience. If you’re interested in learning more about these products, please click here. Note that there are many other options available, and we encourage you to research which products may be right for you.

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