4 Ways to Help Re-inoculate Your Gut

Joy Cutrone, Wellness & Certified AIP Coach, FMCHC-Candidate
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A quick intro to the Repopulate step of the 5Rs

Repopulating the gut microbiome is an important step in the 5Rs protocol for healing the gut to support wellness in all forms of autoimmune disease. So how do we do that, especially in the large intestine?

Once you’ve removed toxins and any stealth infection (in the “Remove” phase of the 5Rs), and ensured that you’ve replaced any missing elements of your digestive process (in the “Replace” phase of the 5Rs), then “Repopulate” is the next step in the 5Rs cycle. Keep in mind you’ve still got the Repair phase and the Rebalance phase of the 5Rs for best results. Repopulating and helping to sustain healthy gut flora is one important step in the 5R process – and a good way of living to help keep systemic inflammation at bay.

4 ways to support a healthy gut

Here are 4 good ways to repopulate or “reinoculate” the gut: a clean diet, fermented foods, pre- and probiotic foods and supplements and, when necessary or available, clean FMT. We’ve engaged all 4 of these tactics to tackle serious gut dysbiosis in our family (an imbalance of the bad guys vs. good guys in the microbiome). These are BIG topics and you can read more about this in other articles. Meantime, here are some excerpts from those articles, including several written by Christine Stubbe, ND, who is a gut-health specialist, and other experts we cite:

1. Clean diet

Experts like Dr. David Perlmutter, MD and Dr. Alessio Fasano, MD, stress the importance of diet in the health and diversity of the microbiome. Dr. Fasano tells us, “Nutrition, among all the influential elements that can change the microbiota composition, is the key element.”

2. Fermented foods

Foods that have been fermented, such as “sauerkraut, lacto-fermented vegetables like carrots, broccoli, cauliflower, sweet potatoes and pickled cucumbers, beet kvass, fermented fruit, kombucha, and water kefir.” These are the true fermented foods you make or find in your whole grocer, not vinegar-based substitutes. Check out this guest post by Sarah Ramsden in AutoimmuneWellness.

3. Pre- and probiotic foods and supplements

Dr. Gerry Mullin, MD advises to, “Choose nutrient dense prebiotic foods that help the growth of a biodiverse gut microbiome. A few examples are apples, asparagus, artichokes, beans, garlic, leeks, root vegetables, and other foods rich in fiber. Foods that contain live bacteria also bolster the friendly gut flora. Examples of fermented foods that contain healthy friendly bacteria include; kefir, yogurt, miso, sauerkraut, pickled vegetables, kimchi, and more.” Note that we avoid beans, dairy, and soy (miso) in an AIP diet.

For probiotics, you’ll be hard-pressed to get beneficial bacteria from a bottle that colonize, but you’ll definitely feed the good guys that you’ve got. I like UltraFlora Spectrum by Metagenix because it has a broad spectrum of bacteria, including Saccharomyces Boulardi, which safely combats a Candida imbalance, which can be common. Note also that you’ll want to choose an option that excludes Lactobacillus if SIBO is suspected.

4. FMT

In the U.S., Fecal Microbiota Transplant (FMT) is available for patients who have refractory C-Dif infection; otherwise, it’s only available through trials. We went to The Taymount Clinic in the UK, because this was a vital necessity for our loved one fighting severe pancolitis. We learned from a functional medicine assessment that the fact that they were born via C-section was a contributing factor: they’d never had a proper microbiome in the first place. Taymount seems to be the most experienced in the world; they are definitely expert, systematized — and kind, to boot. Best of all, the process was effective: our family member has not had a flare since, where this, in combination with other factors, played a key role in that success.

How to get started with the 5Rs

If you’re not familiar with the 5Rs process as a whole, there is a fair bit of discussion about it on the internet. I comb through that in our Introduction to Gut Health. Or you can see this brief intro by Dr. Jill Carnahan for a shorter summary or, for deeper insight, the series of three articles by Christine Stubbe on the Remove, Replace, Repopulate steps of the 5Rs. I recommend that you pursue a 5Rs approach with the guidance of a certified functional medicine practitioner: there are some diagnostics and associated interpretation needed to do this process effectively — and if you’re going to pursue a 5R cycle, which typically takes about 3 months, you’ll want to know that you’re hitting your targets and likely to get the best results.

See Also

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