Probiotic Protocols to Heal IBS and SIBO Naturally
Introduction
As many of my readers know, I have stayed drug free and surgery free from widespread Crohn’s disease for over 25 years. In this series, I interview my long‑time colleague, Natasha Trenev. She is the founder and owner of Natren Probiotics. Many people call her the mother of probiotics.
She had probiotic standards read into the U.S. Congressional Record. If our industry followed those standards, probiotic supplements would be far better today.
I asked Natasha to join me for a series of deep‑dive calls. I want to bring her knowledge into the mainstream. She has worked in this field for 60 years. She is 77 and still working because she sees so many chronically ill adults and children. We both care deeply. We also use critical thinking. We test ideas. We keep what works. We discard what does not.
This blog is based on my in-depth interview with Natasha Trenev, the Mother of Probiotics.
You can watch the complete episode in this video:
Or you can listen to the podcast:
In this post, I share what we discussed about irritable bowel syndrome and small intestinal bacterial overgrowth.
I also share the exact protocol I use, with probiotic species and herbal antimicrobials.
IBS and SIBO: What They Are and Why They Matter
What is Irritable Bowel Syndrome
Irritable bowel syndrome is a functional gastrointestinal disorder. Doctors use this term when the digestive tract looks normal on tests. Yet symptoms persist. IBS symptoms include abdominal pain, bloating, gas, diarrhea, constipation, or a mix. These symptoms affect quality of life. Work, school, travel, and relationships suffer.
IBS does not always get labeled as inflammatory. But inflammation often plays a role. The gut microbiota becomes imbalanced. Gut motility slows or speeds up. The immune system overreacts or underreacts. Food breaks down into particle sizes that feed bad bacteria. The result is discomfort and distress.
What is Small Intestinal Bacterial Overgrowth
Small intestinal bacterial overgrowth means too many bacteria live in the small intestine. Bacteria should be dense in the large intestine. The small intestine should hold fewer microbes. In SIBO, fermentation happens too early. This triggers gas, distention, abdominal pain, diarrhea, or constipation.
Nutrient absorption suffers. Fatty acids may not get absorbed well. Fat‑soluble vitamins can drop. Many people labeled with IBS also have SIBO. Breath tests try to detect it. These tests can help. They can also miss cases. Clinical trials use them with a placebo group to measure change, but real life is messier.
Root causes and risk factors
Root causes differ by person. Common risk factors include low stomach acid, chronic stress, past antibiotic therapy, use of proton pump inhibitors, slowed gut motility, food poisoning, and abdominal surgery.
Leaky gut, also called increased intestinal permeability, can add to the load. The gut microbiome shifts. The immune response becomes confused. I aim my protocol at these causes.
Why I Trust Natasha Trenev’s Perspective
Natasha’s standards focus on strain specificity, potency through expiry, and proper delivery. She warns against vague labels like “probiotic blend.” She rejects soil‑based probiotics for most people with IBS or SIBO. She focuses on traditional probiotics with documented safety and clear strain IDs.
She has watched the industry change. She has also seen misinformation explode. She and I agree. A colon cleanse is not what most IBS patients need. A careful, staged plan is needed instead.
Natasha also reminds us that the intestinal lining is only one cell thick. Those cells turn over every three to five days. Attached bacteria shed with those cells. So regular intake of live microorganisms is needed.
This is why daily probiotic supplementation matters.
How IBS Feels Day to Day
IBS with diarrhea can rule a person’s life. Natasha shared how many people plan routes by bathrooms. The urge hits fast. Accidents happen. Fear grows. IBS with constipation is also miserable. Gas builds. Pain increases. The digestive tract feels stuck. Either pattern hurts.
Pain often comes from trapped gas and nerve irritation. When food does not fully digest, the wrong bacteria feast on it. They make excess gas. Neurons in the gut wall get irritated. Abdominal pain follows. Post‑meal discomfort can appear minutes after eating.
My Core Philosophy: Reduce, Rebuild, Repeat
I recommend a simple cycle. Reduce harmful microbes. Rebuild beneficial bacteria. Repeat as needed. I learned this the hard way with my own gut. I then tested it with hundreds of readers.
Step 1. Reduce pathogens during the day
In my protocol, I use a powerful herbal antimicrobial approach. Wild oregano oil works well for many people. It is taken up to five times per day during a defined “kill phase.” This is not used forever, but in pulses.
Some people also rotate in other herbal antimicrobials such as olive leaf extract, garlic extract, or grapefruit seed extract. These are options, but it’s best to choose one primary tool for each round.
Step 2. Rebuild at night with targeted probiotics
Before bed, I recommend a high dose of therapeutic probiotic strains. Natren probiotics are my choice because I trust their strain integrity and delivery system. The bacteria need to survive stomach acid, attach to the intestinal wall, and communicate with the immune system.
The probiotics species in Natren probiotics include Bifidobacterium bifidum, Bifidobacterium infantis, Lactobacillus acidophilus and Lactobacillus bulgaricus. These species support both the small intestine and the large intestine.
They help reduce bloating, improve gut motility, calm the immune response, and stabilize the digestive lining.
Step 3. Repeat the cycle until stable
This treatment cycle is repeated based on symptoms. For chronic conditions, it may be repeated every few months. For inflammatory bowel disease, longer cycles may be needed.
Symptom tracking is important here: bowel movements, gas, abdominal pain, mood, and energy all provide guidance. When symptoms return, repeat the protocol. When stability is reached, continue with a maintenance dose of probiotics.
Healthy Trinity: Where It Fits and How It Helps
Natasha recommends starting with Natren’s Healthy Trinity, a three-in-one probiotic system. It delivers specific strains to the areas of the gastrointestinal tract where they are most effective. Many people with IBS begin with two capsules per day, taken away from food.
However, if you’re having more than 3 bowel movements per day, I don’t recommend you swallow any capsules (or pills) as the transit time is too fast for them to dissolve properly. In that case, use Natren’s powdered probiotics and mix in filtered water.
Healthy Trinity can be helpful whether IBS shows up as spastic colon, or constipation:
For spastic IBS, the bifidobacteria in Healthy Trinity support the large intestine. They can reduce urgency, improve stool formation, and ease abdominal pain.For constipation-predominant IBS (IBS-C), the lactobacilli support gut motility. Natasha often recommends adding additional Digest-Lac alongside meals, since it naturally stimulates peristalsis. While none of her probiotics are harmful, taking very high doses too quickly can cause an intense die-off (Herxheimer reaction). This happens when yeast or bad bacteria die and release toxins.
Symptoms can include fatigue, headaches, rashes, or flu-like feelings. Starting slow and increasing gradually works better.
How I Pair Antimicrobials and Probiotics
We learned this through experience. Early on, some of my readers tried to only kill pathogens. They felt awful. They took longer to recover. When we paired killing during the day with rebuilding at night, we saw faster, gentler progress.
In our informal reader study with over 250 participants, this paired approach gave better results. People reported significant improvements in gas, bloating, and abdominal pain. Many also noted better sleep and calmer moods. The gut‑brain axis responded!
Food Strategy During Treatment
Food choices can either support or slow recovery. Both Natasha and I recommend keeping the diet simple during treatment.
Foods to avoid
Raw vegetables and salads
Sugar and sweetened drinks
Processed and packaged foodsGrains, especially those exposed to glyphosateAlcoholAny foods that clearly trigger symptomsFoods to include
Cooked vegetables, broths, and slow-cooked stewsPasture-raised meatsGrass-fed beef, which Natasha notes may stimulate the growth of healthy bifidobacteria in the large intestineCarefully tested dairy: many people react to cow dairy, but raw sheep’s milk yogurt is often better tolerated. I’ve found that adding Natren probiotic powders to sheep yogurt can help build tolerance over time. Always start with a very small amount and increase slowly.
Other dietary tools
Some people find short-term relief with a modified low FODMAP diet or an elemental diet during the antimicrobial phase. These reduce fermentable substrates in the small intestine. However, they are temporary tools.
The long-term goal is always a diverse, whole-food diet that supports a healthy gut microbiome.
The Immune System and Your Gut
Your immune system listens to your gut microbes. When the right bacteria attach to the gut lining, they send calming signals. They can down-regulate an overactive response. They can also increase defenses when needed.
Natasha uses a simple image. Think of the immune system as a scanner. Think of food and bacteria as QR codes. If the code is wrong, the immune system overreacts. If the code is right, it lets food and good microbes pass. Probiotic species help set the code.
This is one reason probiotic supplementation improves more than bowel habits. People often report fewer food reactions. Skin clears. Joints ache less. Energy rises. The entire body benefits when the digestive system calms down.
Gut‑Brain Axis and Mental Health
I see strong links between gut health and mood. The digestive tract produces serotonin and dopamine. The vagus nerve carries signals between the gut and the brain. When dysbiosis dominates, anxiety and depression can increase. People may even feel wired and tired.
Natasha and I have seen young people on multiple psychotropic drugs while their gastrointestinal tract is in distress. She has also seen how hard some drugs are to taper.
She notes that certain medications, like some SSRIs and benzodiazepines, can be difficult. This is not medical advice. It is a call to look at the gut first. When the gut microbiota improves, the brain often follows. Better sleep, steadier mood, and clearer thinking show up as the gut heals.
Testing: Helpful, But Not the Whole Story
Breath tests for SIBO can guide treatment. Stool tests can find pathogens. But both have limits. Stool only shows what leaves the body. It does not prove dominance in the gut. Breath tests miss cases and can be affected by diet and motility.
I do not wait on perfect tests. I use symptoms to guide action. I start the protocol. I adjust based on response. I save money for quality probiotics and whole food instead of many rounds of testing.
Traditional Probiotics vs Soil‑Based Probiotics
People ask me about soil‑based probiotics. I do not use them for IBS or SIBO. Natasha has long warned about this category. Traditional probiotics, with lactobacilli and bifidobacteria, work in symbiosis with the human GI tract. They have 100 years of clinical studies. They offer predictable, beneficial effects. Soil organisms can behave differently. Many IBS patients report flares after taking them. I choose the safer path.
Managing Die‑Off and Herxheimer Reactions
When pathogens die, they release toxins. Candida overgrowth is a good example. As it dies, up to 168 toxic compounds flood the system. This can create a “die-off” or Herxheimer reaction, where symptoms temporarily worsen before improving. Common die-off effects include headaches, joint pain, skin eruptions, fatigue, and flu-like feelings.
To manage this stage, it helps to:
Slow down the antimicrobial phase if symptoms are too strongDrink plenty of filtered waterUse binders such as ColonEaze, bentonite clay or activated charcoal (taken away from food and supplements)Rest and reduce stress where possibleUse gentle detox tools like infrared saunas, if availableThese steps allow the body to continue clearing harmful microbes while keeping the die-off reaction at a manageable level.
Daily Habits That Protect Gut Health
Water & microplastics: Natasha said she once spent two weeks looking for water in glass bottles. She explained that microplastics encourage infections and kill beneficial bacteria. So yes, the part about avoiding plastic water and preferring glass is true.Organic food & additives: Both Natasha and I emphasized how pesticides, chemicals, and additives damage gut flora. So this is consistent.Wi-Fi and radiation: I specifically mentioned that Wi-Fi and microwave radiation damage cellular structure and add to the toxic burden. So reducing screen time and exposure at night fits.
Nature, breathing, vagus nerve: While not word-for-word, I did talk about lifestyle practices like detox, rest, and stress reduction. And I highlighted the gut-brain axis and vagus nerve as essential. So breathwork, acupressure tapping, humming, and gentle movement (walking, restorative yoga, tai chi, qi gong) are all good practices.My Books and How to Use Them
If you want step‑by‑step detail, read my books. Listen to Your Gut and Listen to Your IBS lay out protocols, dosages, and timing. They also cover diet, symptom tracking, and troubleshooting. Many healthcare professionals keep a copy in their waiting rooms.
Some cannot recommend them directly due to regulations. But they use the tools themselves. You can too. If you only want the wild oregano/probiotic protocol mentioned above, then just get my Natural Healing Guide: Gut Infection. It’s a short book, and easy to implement.
Working With Professionals
Partner with a skilled healthcare provider if you can. Choose someone who respects natural care, understands the digestive tract, and will tailor treatment. Share your plan. Ask for help with medication tapers if needed. Combine wisdom. Your body wins when you build a supportive team.
FAQ: Quick Answers From Our Conversation
Question: Does Healthy Trinity help IBS‑D and IBS‑C
Answer: Yes. The bifidobacteria can support IBS‑D. The lactobacilli and Digest‑Lac can support IBS‑C. Start low. Increase slowly. Watch for die‑off. If having more than 3 bowel movements per day, switch to Natren powders.
Question: Can I take probiotics with wild oregano oil?
Answer: Yes. Separate them by two hours. Kill during the day. Rebuild at night.
Question: Do fermented foods replace probiotic supplements?
Answer: No. Fermented foods are functional foods. They support health. But they rarely supply the specific species and potencies needed for IBS and SIBO. Use both if tolerated.
Question: How long will this take?
Answer: Time varies. Some feel better in weeks. Complex cases can take months. Infections like mycobacteria can cycle. I repeat rounds every few months until stable.
Question: What about digestive enzymes?
Answer: Digestive enzymes can help during meals. They reduce the load on the small intestine. They can ease bloating and post‑meal discomfort.
A Note From Natasha
Natasha reminds us that the human body renews itself. About 98 percent of the body rebuilds each year. We also shed vast numbers of bacteria every minute. We must replace them with quality proteins and beneficial bacteria. The body is not defective. It knows how to heal when given the right tools and the right perception of reality. This is hopeful news. It should encourage you to start.
Putting It All Together: A Simple Starter Plan
Choose one primary herbal antimicrobial. For example, wild oregano oil or olive leaf extract. Take it five times per day during the kill phase.Each night, take a high dose of targeted probiotics. Use Natren powdered probiotics or Healthy Trinity.Eat a simple, low‑fermentation diet during the kill phase. Use cooked vegetables, broths, and pasture‑raised meats. Limit grains and sugars. Test dairy carefully. Try raw sheep’s milk yogurt if needed.Support detox with water in glass bottles, rest, binders, and gentle sweating.Track symptoms. Repeat the cycle as needed. Shift to maintenance probiotics when stable.This plan is safe, clear, and effective for many IBS and SIBO patients. It respects the gut microbiome. It respects the immune system. It works with the body.
Why We Are Doing This Series
I invited Natasha because her knowledge is rare. We have few people left with her level of experience. We want to record and share what she knows before it disappears. We want to cut through noise and marketing. We want to give you clear steps that help. In every episode, we will take one topic. We will break it down. We will show you what to do at home.
Healing IBS and SIBO takes time, but it is possible. By reducing harmful microbes, restoring beneficial bacteria, and supporting the gut with diet and lifestyle, you give your digestive system the chance to recover.
Natasha and I share these protocols because we want people to have accurate information, not quick fixes or gimmicks. With the right probiotic supplementation, targeted diet changes, and consistent support, you can improve gut health and quality of life.
For more details, you can explore my books Listen to Your Gut and Listen to Your IBS, or contact Natren directly for guidance on probiotics. My own site also has live chat if you need support in applying these protocols.
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