Which Probiotics to Rebuild Gut Diversity and how to rotate them

Which Probiotics are Best to Rebuild Gut Diversity and How to Rotate Them

Megan Essential Oils & Supplements, Healing Diets, Health & Nutrition 26 Comments

I’ve had clients ask me recently which probiotics we use and how to rotate them. Whether you’re on a healing protocol or a wellness diet, gut diversity is the precedent.

It’s easy for many of us to choose one trustworthy probiotic supplement and stay on it, especially if it’s a probiotic with multiple strains. However, a healthy baby is born with an unimaginably diverse ecosystem of living flora.

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The best we can do to recreate this ideal complexity involves seeking out a variety of high-quality probiotics.

This fact also holds true for probiotic-rich foods. For example, certain brands of store-bought probiotics rely on only one or a few strains of flora, so the company may predictably inoculate their ferments, without variation. It’s better for their business to know what they’re getting (which strains) and have the ferment be predictable. But this means store-bought, even locally made probiotics, can be lacking in diversity. (What’s best for the success of food businesses isn’t usually what’s best for our bodies.)

Store-bought sauerkrauts are still helpful, yet may not provide enough variety (or volume of probiotics).

Pre-existing conditions also affect which probiotics to choose. For example, certain strains are safe for those recovering from SIBO (small intestinal bacteria overgrowth). Other strains are recommended for IBS (irritable bowel syndrome). And all the brands I share here are ideal for families with children: kid-safe.

This probiotic is SIBO-safe, great for those who experience bloating with more common strains of probiotics. But it’s also an excellent soil bacteria that I use with our family. It’s popular on the GAPS Diet, contains 29 strains of flora and is recommended by Dr. Natasha Campbell McBride, the diet’s creator. It’s called Prescript Assist, and I first learned about it from Chris Kresser when working to heal my own SIBO. Prescript Assist also helps to reduce inflammation. (If you purchase from the above source you can use the code BEAUTIFUL10 at check-out for a 10% off discount.)

This unique soil bacteria probiotic is excellent for helping to heal food sensitivities and improve the immune system as well as colon health. It can provide relief for those struggling with chronic constipation and even bladder issues. It’s a great price, which is one more reason to include it in a rotation. (Use the code BEAUTIFUL10 at check-out for a 10% off discount.)

Just Thrive is another probiotic of excellent quality and highly recommended for GAPS. It’s hard to say enough good things about this choice. Just Thrive is undergoing ongoing clinical trials for its effectiveness. It’s showing itself to colonize, heal leaky gut and exclude pathogenic organisms. One of the strains in Just Thrive also produces antioxidants. Many who take this probiotic notice an improvement in bowels, sleep or overall energy. It’s a great choice for the entire family. (Use the code BEAUTIFUL10 at check-out for a 10% off discount.)

I use this one to heal my histamine sensitivity, and I first learned about it from the GAPS website. It also contains a prebiotic. (Histamine allergic responses are increasingly common among those with leaky gut, but avoiding all triggers is not the key to wellness; rather, gradual re-introduction of foods and the right probiotics helps to heal.) This probiotic blend is naturally found in the mucosal lining of the human gut. These strains also crowd out pathogenic bacteria. The supplement was created by Ben Lynch, the country’s leading expert on the MTHFR gene mutation.

While most recommended probiotics contain many different strains, this supplement does not. There are two leading brands that can be used to obtain Saccharomyces boulardii, a nonpathogenic, probiotic, beneficial yeast. It’s excellent for many GI conditions including C. Difficile, Crohn’s and chronic IBS problems like diarrhea and constipation. It’s safe for children and does not cause bloating for those with SIBO. This is the brand I have always used, and this is the brand most medical doctors recommend to their patients.

And, last but not least, widely used and loved, is BioKult. With 14 strains including high-quality soil bacteria, this probiotic is common to those on traditional or healing diets and of reliable quality. Dr. Natasha Campbell-McBride actually helped to formulate this product. It can help those with constipation. Conversely, as with many high-quality probiotics, use caution when you start taking the supplement. Too much too fast can result in feeling sick, fatigue, bloating, constipation, or whatever symptoms the patient may be prone to: anxiety, depression, headaches, joint pain, rashes, dyslexia etc. Start this supplement slowly, especially if you’re also starting a healing diet. Capsules can be opened, to start with a smaller amount, and put directly into the mouth. (I discuss dosage more below.)

None of these brands require refrigeration.

For my kids, who are mostly healthy and well, I use one product for anywhere from 1-6 months, and then switch to the next.  There’s no exact rule on the time frame, and sources vary. We also eat various ferments to add diversity. Dr. Natasha has stricter guidelines about how long to stay on one group of strains for those who are sick and healing. I discuss those specifics below.

When creating our own ferments at home, (sauerkraut, kvass or yogurt for example), probiotic diversity is often present on the vegetable or in the raw milk already. Nature is ready to go. All we have to do is provide the right temperature and setting for that life to proliferate. You can also use any of the above probiotics to jump-start a ferment. This approach is safe and fun, but you may end up with variations in flavor! However, it allows you to maintain certain strains in your diet without buying a lot of expensive supplements.

What is a therapeutic dose?

Dr. Natasha Campbell-McBride teaches us in her book Gut and Psychology Syndrome how to safely dose probiotics, how we’ll feel when we’re healing and being affected by that dose, and how to safely increase the dose over time.

A therapeutic dose refers to the amount of probiotic needed to make and maintain a positive change in our bodies, and it’s highly individual. This dose often must be worked up to, starting with a lower amount that can produce die-off symptoms in patients. The symptoms we experience during this process are often unpleasant, but shouldn’t discourage us from persisting with the regimen, gently. Our bodies will adjust and improve with the presence of probiotics; and then we are to increase our dosage, to, in a sense, continue the onslaught of the good army. When we finally reach the therapeutic dose and no longer have die-off symptoms, we are told by Dr. Natasha to maintain that high dose for 6 months, and then to gradually decrease the dose by half long-term (for years).

Which Probiotics to Rebuild Gut Diversity and how to rotate them

Here’s an example from my own life: Two years ago I started a therapeutic dose of Prescript Assist with no symptoms. I took 2 each morning and 2 each evening for 6 months. Now I take 1 Prescript Assist each morning with a low-maintenance dose of another probiotic- Saccharomyces Boulardii. After reducing both of these probiotics to 1 each morning, I began a new probiotic. When I first started it, (ProBiota Bifido), I got a terrible headache. I was taking it to heal my histamine intolerance and started with 1/2 a capsule. That was too much. So I backed off to just a few specks, which was fine and left me symptom-free. I increased to an 1/8 of a capsule and got a mild headache. I learned that I needed to start with just a teeny amount, maybe 1/16 of the capsule and increase from there. Gradually I’ll continue to increase this probiotic until I reach a therapeutic dose. This will feel like quite an accomplishment and an encouraging step for my body. I’ll maintain that therapeutic dose for 6 months, then reduce it by half and choose another probiotic to gradually add. At some point, I can inoculate a ferment with these probiotics so I’m not taking so many pills.

While my kids are mostly well and can tolerate any probiotics without symptoms, my progress is slower. I am systematically looking for strains that give me symptoms as a clue that my body needs those flora.

To review and clarify, a flare-up of symptoms is usually not a sign to stop taking a certain probiotic altogether. Rather it is a good sign that the body needs that strain of probiotic, and a green light to proceed slowly. We are actually looking for the strains that need to be built in our bodies. If we find a probiotic or probiotic blend that increases or brings on our symptoms, that is a strain our bodies lack. What we more commonly call die-off (also called the Herxheimer reaction) does, however, cause inflammation, something not to perpetuate without a strategy. We experience mild symptoms with the goal of greater gut diversity and overall wellness.

As mentioned earlier, homemade ferments can be inoculated with whatever strain of probiotic you feel your body needs.

Many, of course, will not experience die-off. Recolonizing and/or supporting a diverse gut ecosystem is still being achieved by rotating probiotics.

Finding your dosage

For those on a healing journey, find your dosage by increasing it (this may be food-sourced, such as a teaspoon of sauerkraut juice) until you feel a die-off symptom, then pull back to just below that for at least one week, before trying to increase your dosage just slightly.

What is your experience with probiotics, die-off, relief of symptoms and creating greater gut diversity?

  • Renee Kohley

    This is fantastic Megan! I just tried Just Thrive for the first time this summer and funnily enough I have Hashimoto’s and I found that my body really responded well to it. This is such an easy list to follow! Thank you!

  • Melissa

    Just taking my Prescription Assist when I found this article. Thanks again, Megan, for such thoroughly researched and well-written information. My mother-in-law has Hashi’s, and I can’t wait to show her this article!

  • thefoodhunter

    sharing with a friend who always has questions I can’t answer. Thanks!

  • I have to quit certain probiotics since they caused a lot of digestional issues. I use a refridgerated one.

  • Emily @ Recipes to Nourish

    This is so helpful! I really appreciate you breaking it down so we know which ones to turn to first. I know I have struggled with which ones to use.

  • Carol

    Great post with so much information–there isn’t a one size fits all! I’ve been taking probiotics for years now and have noticed a difference. Thanks for sharing.

  • Thanks for this! I love how you broke it down by concern…we love our Biokult!

  • Megan Stevens

    That’s so good to know, Renee! They’re still doing testing with Hashi’s, so it’s great to have firsthand feedback. 🙂

  • Megan Stevens

    You’re welcome. Wonderful. 🙂

  • Megan Stevens

    Haha, perfect. Thank you!

  • Megan Stevens

    Anna, I’m not sure if you read above that sometimes symptoms are an indication that our bodies need those or that strain? But that we must start with teeny amounts…

  • Megan Stevens

    I’m so glad it was helpful. I was helpful for me, too, to write them all down in one place! 😉

  • Megan Stevens

    Thanks, Carol. They really do make a difference.

  • Megan Stevens

    Yes, BioKult is so great. You’re welcome and thanks!

  • K Ann Richman

    Thanks…helpful info. I like homemade probiotics because they provide other vitamins and nutrients .I’ve noticed a difference when consuming them.

  • Jessica S

    I was diagnosed with sibo and began treatment before I became pregnant. Now, a year into nursing, I still suffer from symptoms and don’t quite know how best to handle it at this time in my life. The thought of tackling it myself is overwhelming… I was wondering if you have any recommendations for trusted holistic/healthcare professionals well-versed on the subject in or around Sandy, OR?

  • Missy

    I have been battling c diff since this last summer, from taking antibiotics for a sinus infection. I have been taking probiotics the whole time with no results, and then recently started taking S. boulardi. The problem with the Jarrows brand I’m having is I don’t know how much to take. Any suggestions would be greatly appreciated, as I am fighting a losing battle. Thank you.

  • Sarahx3

    What are your thoughts on rotating probiotics throughout the week? For instance, taking Prescript Assist 2x week, and Just Thrive 3x week, while using kefir or kombucha or sauerkraut as well?

  • Megan Stevens

    Hi Jessica, sorry to have missed your message until now. I don’t know anyone in Sandy. But I do consulting and have a lot of experience with SIBO. Please feel free to see my Consulting page if I can be of help: http://eatbeautiful.net/consulting/ Blessings!

  • Megan Stevens

    So sorry, Missy. C Diff is difficult for everyone! I’m not a practitioner, so I can’t help with dosage. I do recommend finding a functional practitioner. I do have clients with C Diff, and they usually take more than one kind of probiotic at the same time, increasing dosage for results, based on their practitioner’s advice. Blessings as you figure it out. Hang in there!

  • Megan Stevens

    Certain probiotics like Prescript Assist will never colonize. By nature they pass through and bless along the way. So, in that sense, you can take them but also switch around a bit. Other probiotics will colonize, if given the right environment over time. Those are the probiotics to be more mindful about taking every day for many months, so they can repopulate the gut. Off the top of my head I know that some of the probiotics in Just Thrive are also transient. You can look up each one to see about all of them. Using kefir, sauerkraut etc. daily is ideal.

  • Monika Courtney

    I was wondering, while I was eating clean & healthy unprocessed food (paleo-lowcarbhighfat), I started eating probiotics, sauerkraut & turmeric/ginger in small amounts. I started getting reflux & the area under my ribs where the liver lies was very tender/throbbed. As these were the increases in intake I cut them out to relieve symptoms. I kept using biocult. I’m on xarelto a blood thinner & thought maybe turmeric acted as a blood thinner & upset the liver. Symptoms have settled. After reading blog, I’ll follow the instructions to reintroduce probiotics.

  • Raia Torn

    Wondering if you know the difference between the Bio-Kult Protexin (the one you link to), and the Bio-Kult Advanced Probiotic, which is what I have been taking. I tried to look at the packaging image on Amazon, but I couldn’t tell the difference. Thanks. 🙂

  • Megan Stevens

    Hi Raia, good question. The labels of the two products have the exact same ingredients listed: Bacillus subtilis PXN 21
    Bifidobacterium bifidum PXN 23
    Bifidobacterium breve PXN 25
    Bifidobacterium infantis PXN 27
    Bifidobacterium longum PXN 30
    Lactobacillus acidophilus PXN 35
    Lactobacillus delbrueckii ssp. bulgaricus PXN 39
    Lactobacillus casei PXN 37
    Lactobacillus plantarum PXN 47
    Lactobacillus rhamnosus PXN 54
    Lactobacillus helveticus PXN 45
    Lactobacillus salivarius PXN 57
    Lactococcus lactis ssp. lactis PXN 63
    Streptococcus thermophilus PXN 66
    I’m not sure why they have different names… 🙂

  • Raia Torn

    Thanks! 🙂

  • Jason T

    Can you recommend a probiotic if one is TH2 immune dominant? I would really like to start Prescript Assist,but am unsure if it would be appropriate for Th2 dominance? As i have read that some probiotic strains can increase Th2 cells.