39. Why Does Your SIBO Keep Coming Back? (And What Most Treatments Miss)

Is SIBO (Small Intestinal Bacterial Overgrowth) really the root cause of your bloating and food intolerances — or is it a downstream effect of deeper dysfunction?

In this episode of The Histamine Well Podcast, Joanne explains why SIBO rarely develops in isolation and why antibiotics or herbal antimicrobials alone often fail to prevent relapse.

If you’ve been stuck in the cycle of treating SIBO repeatedly without lasting improvement, this episode explores the underlying mechanisms that may be driving bacterial overgrowth in the first place.

Joanne unpacks how impaired gut motility, nervous system dysregulation, low stomach acid, sluggish bile flow, estrogen dominance, mold toxicity, thyroid dysfunction, and histamine intolerance all contribute to creating the perfect environment for SIBO to thrive.

Rather than focusing solely on eliminating bacteria, this episode highlights a terrain-based, root-cause approach to restoring long-term digestive health.

In This Episode, We Discuss:

• What SIBO (Small Intestinal Bacterial Overgrowth) actually is
• Why SIBO often returns after antibiotics
• The migrating motor complex (MMC) and gut motility
• The vagus nerve and nervous system regulation
• Bile flow and its antimicrobial role
• Estrogen dominance and SIBO
• Mold toxicity and mitochondrial dysfunction
• The connection between SIBO and histamine intolerance
• Why relapse happens — and how to prevent it

If you found this episode helpful, please subscribe, leave a review, and share it with someone navigating SIBO or chronic gut issues.

For worldwide online consultations via Zoom, visit: www.joannekennedynaturopathy.com

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Transcript

0:00

Hi, it's Joanne. If you've treated SIBO before, maybe with antibiotics, herbal medicines, or strict diets, but the symptoms keep coming back. You are not alone. This is something I see constantly in clinic. Patients come to me after trying multiple SIBO protocols, sometimes for years, and the relief is always temporary. The reason is that SIBO is very rarely the primary problem. In most cases, it's actually a downstream consequence of deeper dysfunction in the gut environment. So today we're going to talk about why SIBO keeps coming back, and the underlying drivers that most treatment approaches completely miss. Welcome to the Histamine Well Podcast. Designed for practitioners and patients alike. This is your trusted source for insights on histamine intolerance, methylation, gut health, women's hormones, and much more. I'm Joanne Kennedy. Your host, naturopath, author, and educator. Passionate about breaking down complex science into clear, accessible knowledge. Whether you are a health professional or navigating your personal wellness journey, the Histamine Well Podcast bridges the gap between cutting edge research and practical understanding to empower you with the tools to thrive. Hi everyone. Welcome back to the histamine well. Today I'm gonna talk about something I see constantly in clinic, and that is sibo. Small intestinal bacterial overgrowth. But this isn't going to be an episode about which antibiotic to use, which antimicrobial protocol works best. This is about something much deeper. It's about why SIBO rarely occurs on its own. Because in my experience, SIBO is almost never the primary problem. It's a downstream consequence of a disrupted gut terrain. And if we don't address that terrain, the relapse cycle continues. So what exactly is sibo? SIBO simply means that there is an excessive amount of bacteria in the small intestine, and these bacteria ferment carbohydrates known as FODMAPs, and they produce gas. Hydrogen, methane, and sometimes hydrogen sulfide gas. And that fermentation leads to the classic symptoms of sibo. Bloating, distension, altered bowel patterns, pain reflux, and we also get the knock on effect of histamine flares and food intolerances. But when I see a SIBO patient, I'm always thinking, why those bacteria there in the first place? The small intestine is not designed to house large amounts of bacteria. It has built in protective mechanisms to prevent that. And when those mechanisms fail, the bacteria can accumulate. So instead of asking how do we kill off the bacteria, we need to ask why is the small intestine inhabitable for these bacteria? And this is where the discussion on terrain comes in. Under normal physiology, the small intestine stays relatively low in bacterial load because of adequate stomach acid, effective bile flow, pancreatic enzymes, migrating motor complex activity, a healthy vagus nerve signaling, adequate secretory IGA levels, and a really coordinated immune system. If any of those systems weaken, then stagnation develops. And stagnation allows this fermentation. SIBO is, it's essentially not just a overgrowth of bacteria problem, it's a stagnation problem. So let's unpack exactly what disrupts the terrain. Now, one of the most overlooked and common drivers is the nervous system. And if I had to pick one that I see clinically all the time, it would have to be this. Nervous system dysregulation from chronic stress, trauma, overworking, hypervigilance, perfectionism, long-term sympathetic nervous system dominance. When someone leaves in chronic fight or flight digestion is really compromised. The vagus nerve that controls motility and enzyme secretions and it coordinates the migrating motor complex. It becomes underactive. Now, the migrating motor complex is like this cleaning wave in the small intestine, and it sweeps out undigested food and bad bacteria. It only works properly when you're in a parasympathetic nervous system state, which is rest and digest. Now, if that cleaning wave weakens, then the food and bacteria linger. It causes delayed gastric emptying, reduced bile flow, impaired pancreatic enzyme output, and really sluggish motility. And that stagnation creates a perfect environment for this bacteria to grow. So this is where people often give prokinetics trying to get it all to work. But if the nervous system remains dysregulating, then the underlying signaling problem is going to persist. And this is why things like breath work, somatic therapy, nervous system retraining, trauma resolution and sleep regulation aren't just adjuncts. So actually foundational to SIBO treatment. Let's move on to bile flow. 'cause bile flow is profoundly antimicrobial. It suppresses bacterial overgrowth. It keeps the microbes moving along. It emulsifies fats, so it actually regulates microbial balance. And if bile becomes sluggish, thick, or insufficient, bacterial populations will start to grow causing sibo. Now things that really impair bile flow are chronic stress, mold mycotoxins, estrogen dominance, endometriosis, low thyroid function, gallbladder issues, gallbladder removal, liver issues, rapid weight loss, or a long term restrictive dieting. Now estrogen in particular actually thickens bile. So high estrogen states, including in endometriosis, will frequently slow bile flow. And bile stagnation doesn't just affect sibo, it also increases beta glucuronidase activity in the gut, which recirculates estrogen. So now you have a feedback loop. You have high estrogen, thick bile, microbial imbalance, increased beta glucuronidase enzyme, and more estrogen recirculating. So this cycle just goes round and round and round. Before we go any further, I want to speak directly to the practitioners and students listening. If you're intrigued by histamine and methylation and eager to expand your knowledge in this fascinating area, we offer the Histamine and Methylation online group coaching course. The only program of its kind. It covers everything you need to know about histamine and methylation, providing both the theory and guidance you need to treat these issues effectively in clinical practice. We cover sibo, hormonal imbalances, oxalates, M-T-H-F-R. The four pathways of methylation, including the folate pathway, methionine pathway, tetra hydro biopterin pathway, and the all important transsulfuration pathway and much more. The program is delivered by detailed online webinars and handouts for you to keep. And for eight weeks you'll meet with me for live coaching calls in a private community space with other practitioners from all over the world dealing with histamine and methylation issues in their patients every day. Together we learn so much. To learn and apply, visit joanne kennedy naturopathy com. Now, another huge issue that we see clinically and is so often missed is mold mycotoxins. Okay, so we've got mold. They produce these microscopic mycotoxins that get into your body and cause havoc. They impair mitochondrial function. They suppress immune signaling. They disrupt the vagal tone, the vagus nerve tone. That's a big problem. They thicken bile. Another big problem. They also activate mast cells. They increase histamine amongst many other things. And so mold patients, all the time, they also present with sibo. They often come to me thinking that they have sibo and that fixing SIBO will fix the laundry list of all their quite chronic and serious health symptoms, conditions. They've tried to see treat SIBO many times and it never goes away and they don't actually feel that much better when they're treating it. It's actually because they do have a mold problem. So again, SIBO is really the root cause. When the mitochondria is impaired, motility weakens. When immune function is suppressed, we have the microbial surveillance in the gut declines. Then mast cells are activated and they cause so much inflammation that it disrupts gut barrier. And the gut barrier function deteriorates. So I touched on endometriosis before. So, you know, there is research on this, but it's clinically goes hand in hand. Like, when I see a girl with endometriosis. I will presume that she's got SIBO until otherwise it's that common. So endometriosis, it's inflammatory. It's estrogen driven. It is actually an immune dysregulation issue on in itself. It's associated with pelvic congestion and it's associated with adhesions. And so these adhesions can impair motility. So this is what happens with endometriosis. We've got the estrogen, the thickening, the bile. We've got the adhesions, which means that we just can't sweep out undigested food and bad bacteria. The motility is slow. So it's a really, really vicious cycle with endometriosis. This constant inflammation, hormone disruption, motility impairment, and bowel stagnation. No wonder these girls always, present with SIBO as well as endometriosis. So with histamine, I mean, you would've heard me say this, SIBO itself is a major cause of histamine. So just the gases cause inflammation. The gut inflammation releases histamine. The inflammation reduces Dao enzyme synthesis. So the net result is too much histamine. It's sort of like a chicken and egg situation because when there's so much histamine, it influences gut motility. It alters intestinal permeability, it modulates immune activity. It can also affect gastric acid secretion. So the more histamine you have, the worse it is for sibo. And that's actually why my sibo, low histamine diet is so efficacious at getting this firestorm down really, really quickly. If you're interested in that diet, it is available on my e bundle, which you can purchase on my website. So this is why we see just treatment with antibiotics alone, or even herbal antimicrobials alone, often just don't work. Because it's not restoring vagal tone, bile flow, hormone balance. Immune resilience. It's not looking at mold mycotoxins, mitochondrial output, estrogen dominance. So the environment remains the same, and if the environment that caused the SIBO remains the same, well, it's simply not going to go. And we see this clinically all of the time. So in my clinical experience, long-term SIBO improvement requires nervous system regulation, restored bile flow, addressing mold if present. We also can look at thyroid physiology for thyroids out. That's also gonna affect your gut motility and your digestive enzyme secretions. We need optimal stomach acid. People are so low on hydrochloric acid from stress. We need to make sure the migrating motor complex is working properly. That's a real clinical skill to pick that up in your patients. We need to get the histamines down because of that chicken and egg issue with histamine, sibo, driving up histamine. Histamine, then causing gut damage. And we need to balance estrogen. We need to detoxify estrogen. So there's so much when it comes to sibo. It's not just an overgrowth of bacteria. So if you are struggling with sibo, we are here to help. We see patients online via Zoom globally. You can easily book yourself in for an appointment via my website, which is joanne kennedy naturopathy.com. So thank you for joining me. I hope you found this episode beneficial. Be sure to subscribe to the histamine well so you don't miss an episode. Leave a review and you can also share this episode with someone who could benefit. If you have any questions you'd like answered or have a topic you'd like me to discuss, please go to my website, joanne kennedy naturopathy.com, where you can provide us with that information. Until next time, take care and be well.