21. How to Treat SIBO Naturally: Diet, Herbs, Testing & the Clinical Approach That Works

Struggling with persistent SIBO symptoms or unsure where to start with natural treatment? In this episode, I break down exactly how I treat SIBO in clinic — from diet and herbs to overlooked factors like biofilm, enzymes, histamine, and oxalates.

Whether you're a health practitioner, student, or someone personally dealing with SIBO, you'll walk away with a deep understanding of the step-by-step process required for real, lasting results — not just temporary relief.

What I Cover:

✔️ Why a low FODMAP diet is non-negotiable if you're treating SIBO naturally
✔️ How to use testing — and retesting — to guide effective treatment
✔️ The best herbs for hydrogen and methane SIBO (and why they differ)
✔️ The role of SIFO (Small Intestinal Fungal Overgrowth) and how to spot it
✔️ Why addressing biofilm is essential for treatment success
✔️ How digestive enzymes (including brush border support) accelerate healing
✔️ The hidden role of histamine intolerance in stubborn cases
✔️ Why oxalates can spike on a low FODMAP diet — and what to do about it
✔️ What to do when the migrating motor complex (MMC) isn’t working
✔️ The best prokinetics, binders, and enzyme supplements I use in practice
✔️ When and how to safely reintroduce foods after treatment
✔️ What recurring SIBO is trying to tell you

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Transcript

Joanne Kennedy: 0:02

Practitioners and students. Enrollment is now open for the next cohort of my histamine and methylation online group coaching course. Kicking off on Monday the 18th of August. This is the only program of its kind. Designed to give you both the theory and clinical application you need to confidently treat histamine and methylation issues In clinical practice. We'll cover things like histamine intolerance, the methylation pathways, including the folate pathway, methionine pathway, tetra hydro biopterin pathway, and the all important transsulfuration pathway. As well as SIBO, Hormonal Imbalances, oxalates, M-T-H-F-R, and much more. You'll get detailed webinar content and handouts for you to keep, plus 8-weeks of live coaching calls with me inside a private practitioner community where we dive deep into real clinical cases and challenges practitioners are facing every day. And just a heads up. If you enroll by the 3rd of August, you can save up to$500. Together, we learn so much. To learn more and apply, visit joannekennedynaturopathy.com. Hi everyone and welcome back to the show. Today, I'm going to share my tips on how to treat SIBO Naturally. These are insights based on what I do clinically to get real lasting results. So whether you are a practitioner new to SIBO, a student learning the ropes, or someone personally dealing with SIBO, I hope that you'll get a lot out of this episode. I'm going to teach you why following a low FODMAP diet is essential. If you're going to treat SIBO naturally. Why testing and then retesting following treatment really matters. The herbs are used for hydrogen and methane SIBO. My thoughts on SIFO, small intestinal fungal overgrowth and why it often shows up alongside SIBO and what to do about it. While we must address biofilm if we want the treatment to work. The importance of digestive enzymes. How histamine issues can be a hidden part of the puzzle. And how oxalates can rear their ugly head on a low FODMAP diet. So here we go. First of all, we must follow a low FODMAP diet if you're going to treat SIBO naturally. You cannot get rid of SIBO just with herbal medicine without doing a low FODMAP diet. If you go allopathy and take antibiotics, then yes. You don't have to do a low FODMAP diet. But if you're gonna treat it naturally, you absolutely do. And this is why.. FODMAPs are fermented by the SIBO bacteria. And essentially, that's what causes the gases. The hydrogen and methane gas. But it's essentially feeding the bacteria. It's a food source. They're gonna proliferate and grow and grow and grow and grow. So you do need to reduce the FODMAPs and reduce their food source. It's very simple. This is why when you do a low FODMAP diet that it really, really helps with your symptoms really, really quickly. It's also starting to change the environment in the small intestines. So when you are reducing the bacteria, you are actually reducing the acidity and the inflammation in the small intestine. And so that is going to allow your digestive enzymes to work properly'cause they need more of an alkaline environment. Histamine people, the inflammation that the FODMAPs is causing is driving up your histamines. So removing the FODMAPs is gonna really, really help calm down the inflammation, reduce the acidity. Then we can layer in with herbs. It's very, very hard to get rid of SIBO just with low FODMAP diet. We also need the herbs and the combination of that is what's gonna work. It's gonna give you the best results. Another thing that is really important with FODMAPs is that you really do need to follow the serving size. So you'll notice that there are certain foods that you need to completely avoid, and then there are others that you can have in only limited amounts. That's where the serving size really matter. For high FODMAP foods, it's not just about what you eat, it's about how much you eat. So even a food that's considered low FODMAP can become high FODMAP if you go over the recommended portion. Too much is simply gonna feed the bacteria and it's gonna trigger a symptom. It is really important to stick to the serving sizes. I will often have patients come back to me where they're not really adhering to the serving size and I don't know. I get it. It's'cause it's healthy food. It's broccoli and asparagus and cauliflower. And it's your vegetables and I know people just can get a bit bored and they end up eating too much but I can tell the symptoms will not be going down quick enough. So this is the thing guys, with SIBO, you should be getting really, really good results in your symptoms. A really significant reduction in your symptoms really, really quickly. If you're not, there's something wrong. And sometimes, and I'm gonna talk all about that and why. But sometimes it's actually because you're not really following the diet to the tea. And you know, it's like you can go and eat a whole lot of junk food. And it's probably not gonna make, it's gonna make you feel terrible and it, well, it's not good for SIBO because it's causing more inflammation and acidity in the gut, but it's not feeding the bacteria. So that's not the problem. The problem is actually these healthy plant foods that are continually feeding the bacteria. And if you just don't get them down, it's very, very hard for you to get on top of the SIBO bacteria even with herbal medicine. Another really important thing is that you need to test for SIBO. I can't tell you how many people have come to me. They've done a stool test and the practitioners told them that they've probably got SIBO from the stool test. It's like you can't extrapolate if someone has SIBO from a stool test. Also the classic hydrogen SIBO is loose stools diarrhea. The classic methane SIBO is constipated. But clinically, that's not what we see all the time. So someone can have hydrogen SIBO and still be really constipated because of other issues. They might be gluten intolerant. It might be hormonal. They might have digestive enzyme insufficiency. A sluggish thyroid, et cetera. So you could think, oh, they're methane dominant. Because they're constipated, but they've actually got hydrogen and constipated from other reasons. The other reason we need to test is that we need to understand the hydrogen and methane levels and the balance between them. As this was gonna help guide treatment, especially choosing the right antimicrobials. So some people are hydrogen dominant, meaning the bacteria in their small intestine produce mostly hydrogen gas. And others are methane dominant, which is actually caused by a different type of organism called methanogens, and these feed off hydrogen and convert it into methane. Sometimes you'll see both gases on a test. Someone might have high hydrogen, so they're hydrogen dominant, but are still producing some methane because of that conversion is happening. The hydrogen is being converted into the methane. And then there are people that just show high methane and almost no hydrogen. That can mean that the methanogens are using up all the hydrogen and converting into methane. The hydrogen levels look flat, but the methane is high. Understanding which gas is dominant, or if both are present really matters because we use different herbs to different organisms, the different bacteria. We also need to understand that methanes, methanogens are stubborn, okay? And they need a different approach to hydrogen. Without testing, we are really flying blind, and this is where I see a lot of patients come to me where they haven't tested and they're flying blind, and it's just a complete and utter waste of time and money. For hydrogen dominant, the best herb I find is berberine. Berberine is not a herb. It's actually an active constituent of different plants. Philodendron, Golden Seal, hydrastis canadensis, and berberis vulgaris. I think is the botanical name of the Barberry. Philodendron, is by far the strongest. So in Australia it's very easy to get Philodendron. It's medi herb do Philodendron Forte. So I'll always use that for my Australian patients. Overseas patients, I think Philodendron's hard to get so the Golden Seal or a lot of the commercial products like Thorne, pure encapsulations, et cetera. They'll use their own specific types of berberine. It's very specific for hydrogen and definitely a herb I would always use for hydrogen dominant. Oregano also works on hydrogen. So if you've got a bit of a stubborn case, you can also go in with a some oregano. And when you see the methane with the hydrogen, using herbs that are specific for methane like Allicin at the same time is really important. So, so often I'm using a combination of Berberine and allicin for hydrogen dominant SIBO with some methane. When it comes to methane dominant, which can be a bit more stubborn. I will always use Allicin. It is probably the most effective herb for methane. And I'll use that alongside oregano and neem. Or there is a commercial product called Atrantil, which is very good at reducing the methane bacteria. methane will take longer. It's stubborn. It can take four or five months to get rid of, whereas hydrogen is more like three to four months. So what about sifo? Small intestinal fungal overgrowth? It's actually really common in people that have SIBO. So whether it's hydrogen dominant or methane dominant. Even though there's no reliable test for sifo, we often suspect it as the same environment that allows bacterial overgrowth will also create the perfect conditions for the fungal overgrowth. Some of the more specific symptoms of SIFO are going to be intense sugar cravings or carbohydrate cravings. Oral thrush, or a coated white tongue. Itchy ears, skin, yeast infection, recurring vaginal thrush. Feeling worse on antibiotics but potentially better on antifungals. Alcohol intolerance. So feeling drunk really easily, and a worsening of symptoms with high sugar or fermented foods. I'll also put oxalates onto that list.'Cause when you've got a lot of fungal overgrowth it can make oxalates worse. I'd also put mold onto that list. Mold disrupts bile flow, which is a major cause of SIBO. When you've got mold, you are more inclined to grow fungus in the gut, and some of those fungal species contain oxalate. So if you're interested to learn more about oxalates, I think it's my third episode where I interview my colleague Melanie peers all about oxalates. SIFO can often also cause symptoms that overlap with SIBO. Including bloating and distension, gas, burping, brain fog, fatigue, constipation, diarrhea, skin rashes, breakouts, as well as all of the histamine reactions. Because SIFO often coexists with SIBO, it can be really tricky to separate them. But when you see those specific fungal signs, like the sugar cravings, the thrash, the yeast infections, oxalate symptoms. That to me is a really strong clue that yeast is a big part of the picture. But the good news is that if you have sifo, the approach to treating it really overlaps with how we treat SIBO. So you're removing the foods that feed both the bacteria and the yeast. Things like sugar, refined carbohydrates, excess starch, and high FODMAP foods. This is gonna help starve off the fungal overgrowth. And some of the herbs that we use for SIBO are also strong antifungals. Including the Berberine, the oregano, and the Allicin. So you actually don't need a whole separate protocol for sifo. It is kind of the same protocol, but if someone is not improving the way I'd like them to, then I might look at doing some extra specific antifungals. So caprylic acid or pau d'arco is also a really great product from research nutritionals called Elim a Cand, which is a really potent antifungal. Another thing we really need to address is biofilm. If you dunno what biofilm is, it's like this protective coating that surrounds the bacteria and the yeast. And it allows them to colonize, proliferate, and grow. It actually provides them with a really lovely environment to live in. And to make it, it uses our iron and our calcium and magnesium amongst other things. So it's bad as it can cause these nutrient deficiencies. Also it's bad because like herbal medicine and antibiotics can't actually get through that biofilm to actually kill off the bacteria that's underneath. So we need to break down that biofilm. And there are really great supplements to help do that. Like N-Acetylcysteine is a biofilm disruptor. Commercial products like Kirkman's Biofilm Disrupt, or I think it's called Biofilm Defense, and then Research Nutritionals, bio Disrupt. There are quite a few other commercial products available. So that it is important to deal with biofilm, but you can't do it too quickly. So how I would do it is you go in with a low FODMAP diet, the specific antimicrobials that you need. You need to also make sure your bowels moving just to clear it all out. And then after you've been doing that. It depends on how sensitive someone is, but I'd definitely be, making sure your bowels are moving. And I'd go in maybe like three or four weeks after doing low FODMAP diet and the herbs. And just start breaking down that biofilm slowly. I'd just be upping the dose like every week. Just so that you don't get massive die-off reactions. And if you do get die-off reactions, which is just like a worsening of any of your symptoms, fatigue, headache, nausea. You can take a binder, something like activated charcoal, which will help reduce those die off symptoms. The big problem with biofilm is that it does cause the reduction in these minerals. Iron, calcium, or magnesium. You so often see women with SIBO having really low iron. We see it in men as well. Men's ferritin is usually up well over 150 if they're eating enough animal protein. But if you're seeing a man with ferritin levels down at like 50. There's definitely something wrong and clinically, I've seen it often SIBO. Women, it's a disaster'cause of menstrual blood and the lower your iron gets the heavier your bleeding gets and your iron gets lower and lower and lower. So one of the main causes of this is actually SIBO. Now the problem is if you go in and supplement with iron it creates more biofilm. So this is a bit of a clinical dilemma for me where I see a patient that's got really low iron and it's causing her to feel really tired, depressed. It's causing her to have very heavy periods. It's like, wow, like you so need iron to just get your mood and your energy up, but it's gonna feed the biofilm. It just depends clinically when some women are just that they can't function, you know They can't actually even prepare the meals that they need to do for the low FODMAPs and go grocery shopping and work. I will sometimes just do a little bit of iron, but I'll always make sure that they're eating. Ray, way more red meat than before and taking hydrochloric acid to really, really help absorb it and try and get the iron up. You'll find a lot of people that have had iron infusions that feel terrible from iron infusions that can often be due to it feeding all the biofilm and creating havoc with SIBO. Also when you have calcium magnesium deficiency, that's gonna cause havoc with your acid-based balance. If you are interested in that I've done an episode all on acidity and how we need these alkalizing minerals and also oxalate people. Calcium and magnesium. You need it to bind up your oxalates. This is why we really need to be dealing with the biofilm not just for SIBO, but to get our iron levels restored and our calcium magnesium levels restored. Moving on to bowels. Guys, this to me is a no brainer. And I dunno why other practitioners aren't really checking this. You have to get your bowels moving. You can't get rid of SIBO if your bowels aren't complete emptying daily. So I'll always check in with my patients after starting a protocol just to hone in on the bowel. Basically, if you're not pooping out the undigested food and bad bacteria, you're not gonna clear your SIBO. Supplements that I love.. laxatone. Metagenic laxatone is a supplement that you can buy on I Herb. It's called Cleanse More. It works extremely well. For really stubborn patients, I will get them to do abdominal massage. You can find resources online for that. Castor oil packs. Sometimes people need to do enemas. Also nervous system dysfunction is such a massive contributed chronic constipation. So the Nerva hypnotherapy App. if you do that in the morning I see it work wonders for stubborn constipation. If you're getting incomplete emptying, that to me is a real sign of digestive enzyme insufficiency particularly hydrochloric acid and pancreatic enzymes. So you might need to start supplementing with some digestive enzymes. Getting bowels moving is essential. Like you're not even on the starting blocks until your bowels are moving. Another really important part of SIBO treatment is getting the digestive enzymes right. Digestive enzymes are disrupted with SIBO. It's like a chicken and egg situation. This is what happens. Hydrochloric acid is released when you chew and it causes an acidic environment in the stomach, which you absolutely need to digest and break down your food. At the same time, your brain when it recognizes that your chewing releases hydrochloric acid, it actually gets a hormone message sent to the pancreas. That then triggers the pancreas to send pancreatic juice into the small intestine that alkalizes the small intestine. You need an alkaline environment for the pancreatic enzymes to work. The pancreatic juice and the pancreatic enzymes will go into the small intestine. The brush border enzymes that really break down your food at the sort of the end point. They need an alkaline environment to work as well. So you need the alkaline environment. Also when you chew your food release hydrochloric acid, it sends a message to the gallbladder to take bile into the small intestine, and that helps you digest your fats. It's also antimicrobial and it is also a natural laxative. And this is the thing guys, stress is such a major cause of SIBO. And when you're stressed, you really start reducing your digestive enzymes, particularly hydrochloric acid. I think about hydrochloric acid as the conductor of all of the digestive enzymes. More often than not, I'm ensuring we've got hydrochloric acid in place and pancreatic enzymes. There's a great supplement called pure Encapsulations Digestive enzymes Ultra. I really like that because it's got hydrochloric acid pancreatic enzymes, and it's also got brush border enzymes. It's one of the only supplements that really contains brush border enzymes. There's another supplement called enzyme Science Critical Digestion that's also got the brush border enzymes. I don't think it's got hydrochloric acid. You'll need to take that separately. Now when it comes to bile, what we need to understand about bile is that SIBO bacteria de conjugate bile. They break it. So it renders the bile unavailable to do its job. So in my mind, if you just push more bile. Into a really active SIBO environment, it's gonna keep de conjugating the bile. So I like to go in and reduce the bacteria and start some herbal medicines make sure bowels are moving before I ever give anyone bile support. And a classic symptom of bile insufficiency is gonna be sort of loose stools and diarrhea, but it can also indicate lipase deficiency and lipase is a pancreatic enzyme. If you are interested in learning more about digestive enzymes, I've done an episode all about digestive enzymes, so you can check that out. This next part is really important. And practies, you gotta get this right to really help your patients. People come to me and I highly suspect they have SIBO. I get them to do the test, and then I get them to start the diet at least before I see them in a couple of weeks. I'll also just give them digestive enzymes, get their bowels moving, et cetera. Just sort of start the treatment a little bit. And then they'll come back to me two weeks later and we've got the test result. So I like to do this because it saves money, it saves them an appointment, an extra appointment, and they're gonna start feeling better. And also because of this, if they come back and they're still really bloated and they're doing the diet, got the digestive enzymes in, their bowels are moving. This is a classic sign of issues with the migrating motor complex. Now you can find that the bloating's gone down like 30, 40% usually goes down like nearly a hundred percent. If it's going down, that's good. But some people come back, it's not going down, and they're just eating such healthy foods. Like, you know, a low FODMAP diet is so healthy. You'd think you'd be completely flat tummy. Bloated still. So this can mean one of the reasons is that the migrating motor complex, which is an electrical impulse that kicks in 90 minutes after you eat, it's not, it's not working, and you are not sweeping out the undigested food and the bad bacteria. So it's just, it's just stuck. This is the cause, one of the main causes of their SIBO. So case by case, some people can improve the migrating motor complex with natural prokinetics. These help get the migrating motor complex moving. Iberogast That commercial product, which is available globally is very efficacious along with ginger then natural pro kinetics. Get that in and see how you go. Their bloating causes so much pain from distension and discomfort that I'm like, those natural pro kinetics are not gonna touch the side. They need to take pharmaceutical, pro kinetic. Low dose naltrexone being a really common one because it helps reset that migrating motor complex. So if you've got a patient like that, or if you ask someone like that. You gotta stop and go, we need to fix this because you can never get rid of the SIBO if there's MMC. Migrating motor complex issues. So you're really doing your patients a disservice if you just keep them stuck in that state. I see this all the time. People will go to a doctor. They'll get the rifaximin. Potentially some neomycin for the SIBO. And because they're so strong, it kills it off and you can feel better. But these are the people whereby when they stop literally the next day, all their symptoms are back. Like literally the next day. When it comes back, you know, 6, 7, 8 weeks later, it's not normally an MMC issue. Specifically, it will probably be like poor diet, stress, digestive enzyme insufficiency, constipation, creeping back in, et cetera. But when it's that quick, it's, I think about that as a migrating motor complex issue. Moving on to histamines. If you are still getting these symptoms, headaches, migraines, vertigo, anxiety, insomnia, inability to regulate your body temperature, heartburn, skin issues, itchy skin hives, eczema if you're getting heart palpitations, shortness of breath, worsening of your symptoms at ovulation of before menstruation. This is a red flag for histamine. So SIBO is a major cause of high histamine. And I've done several episodes on that if you wanna check it out. How that happens is simply the inflammatory environment in a small bowel is causing a release of histamine, and at the same time, reducing DAO enzyme that breaks down histamine. So net result is more histamine. Doing a low FODMAP diet is not a low histamine diet combo. So if this is you, I do have on my website. My e bundle on histamine intolerance has the food list and recipes for SIBO in combination with low histamine. Because I Just do this all the time, I can very easily understand if someone needs to go on a SIBO, low histamine diet straight away. If you're a listener and you're just doing a SIBO diet and you're getting all those symptoms, potentially there's, you need to reduce the histamines and practitioners. This is like a big red flag for histamine issues. So, you know, when I think someone is, just bubbling over, like the histamine bucket is super high, I definitely get them on SIBO low histamine. But if someone just has some very kind of mild sort of histamine symptoms, then often just the SIBO diet will get their histamine bucket down really quickly. So it's just a case by case. It's just e evaluation. Evaluate these patients case by case. Now this is something that also happens. When you go on a SIBO diet, it is definitely not a low oxalate diet. It potentially can head to more of a high oxalate diet because people will do this. They'll remove the grains from their diet and they'll start having almond flour and almond butter. They removing the milk, so they have almond milk or they'll just start eating more buckwheat, which is super high in oxalate amongst other things. If you're getting symptoms like more abdominal pain or you start getting bladder pain, joint pain, malaise, fatigue, raised lymph nodes on a low FODMAP diet, you need to consider oxalates and you need to do that really, really quickly. It's not uncommon for people to have both SIBO and an oxalate problem. Especially if they're more severe presentations because mold is such a cause of SIBO and such a cause of high oxalates. So then we have the double whammy. Just be very careful practitioners on my website, you'll see a list of oxalate symptoms. I'm sure you'll be able to find them online. Make sure that you are asking your question, your patients about all the oxalate symptoms because you've gotta be careful because so often when you go low fodmap, you'll end up eating a lot more oxalate. That's just something that we see in clinic a lot. And if that happens you need to stop and then it becomes a bit of a, well then, then you need to start working out your priorities because you might find that why your patients feel so terrible is actually because of the oxalates, not necessarily the SIBO. Sure. They might have some, the bloating from the SIBO, but their fatigue and their pain symptoms and their really high histamine symptoms can definitely be more due to oxalate than SIBO. If All is going well and probably takes about three to four months for hydrogen SIBO, four to five months for methane SIBO. When my patients are doing well and all their symptoms are gone, and I know they're being compliant, and their bowels are good and they're feeling great, we will always retest. I always retest just to make sure we've got rid of all the bacteria, and then we just start to reintroduce the foods. Not all at once, you can just taper them in relatively well, relatively quickly.'cause if it's gone and you've done all the right things and you've addressed the causes, then usually it follows suit and that person will just start to feel a lot better. And I think you really need to educate them on it doesn't mean that you can go back and have lots of processed foods and, gluten and, sugar and, hydrogenated vegetable oils in excess because, that's going to disrupt the pH and cause SIBO to come back. So a lot of people think, oh, it's gonna be fine for me just to go back to my poor diet. But ultimately those people that get SIBO from poor diet will need to be educated on how to eat a whole foods diet. Everybody i'm here to help. If you are having problems with SIBO. If you haven't been able to get rid of it, if it keeps recurring, I'm here to help. I see patients online via Zoom globally. You can make an appointment with me via my website, joanne kennedy naturopathy.com. 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.