Hydrogen Sulfide SIBO Treatment & Natural Protocols (2025 Guide)
Hydrogen sulfide SIBO is newly discovered and possibly the most misunderstood form of small intestinal bacterial overgrowth. It can trigger persistent and often debilitating symptoms, ranging from the unmistakable ‘rotten egg’ smelling gas, to relentless abdominal pain to chronic fatigue and even neurological symptoms.
While many SIBO treatment protocols focus on hydrogen or methane-dominant SIBO, hydrogen sulfide SIBO requires a more nuanced, multi-faceted natural approach that addresses its unique challenges. Thankfully, with the right guidance, support, and understanding, lasting relief is entirely possible.
Here is what we are going to cover in this guide:
What Is Hydrogen Sulfide SIBO?
Hydrogen sulfide SIBO (H2S SIBO) occurs when bacteria producing hydrogen sulfide, a gas known for its 'rotten egg' odor, overgrow in the small intestine. This excessive bacterial growth, and the hydrogen sulfide gas it produces, can disrupt various functions of the body, causing symptoms like bloating, abdominal pain, diarrhea or constipation, fatigue and brain fog.
Small Intestinal Bacterial Overgrowth (SIBO) develops when normal gut bacteria overgrow in the small intestine, a region where only a limited number of microbes should live. In hydrogen sulfide SIBO, the overgrowth is dominated by bacteria that produce hydrogen sulfide gas (H2S). It is commonly referred to as H2S SIBO, and more recently been referred to as Intestinal Sulfide Overproduction (ISO) to acknowledge that hydrogen sulfide gas can occur throughout both the small and large intestine.
So how does Hydrogen Sulfide SIBO differ from other forms of SIBO?:
Hydrogen SIBO often manifests with symptoms like bloating and diarrhea.
Methane SIBO is commonly linked to constipation.
Hydrogen Sulfide SIBO (ISO) can cause variable bowel habits, such as a mix of diarrhea and constipation, along with more intense abdominal pain and fatigue. It doesn’t always present with the rotten-egg smelling gas symptom. Its systemic impact is known to trigger neurological symptoms, like brain fog, fatigue, dizziness and headaches.
Understanding these differences and knowing the type of SIBO you have will help guide the right natural eradication strategy to achieve lasting gut health.
Symptoms of Hydrogen Sulfide SIBO
Hydrogen sulfide SIBO has a distinct symptom profile. Key signs of H2S SIBO include:
Digestive issues:
Bloating and distension: Persistent swelling and discomfort caused by gas in the GI tract.
Abdominal pain: Cramping that may be persistent or intermittent.
Bowel irregularity: Many clients experience diarrhea, but we often see an alternating pattern with constipation.
‘Rotten egg’ odor: A hallmark of hydrogen sulfide production, this odor is often noticeable on the breath or in flatulence. Not all clients experience this symptom.
Food intolerances: Sensitivity to high-sulfur foods, such as eggs, garlic, onions, cruciferous vegetables like kale and protein powders which contain the amino acids cysteine and methionine.
Supplement intolerances: Low tolerance to sulfur-based supplements, such as NAC, glutathione, MSM, alpha-lipoic acid and garlic based antimicrobials that contain the whole garlic bulb (not Allimax/Allimed).
Systemic symptoms:
Fatigue and brain fog: Likely resulting from reduced mitochondrial function and systemic inflammation from H2s gas, which can act as a neurotoxin in the body.
Headaches and mood disturbances: Neurological symptoms that may be linked to the neurotoxic effects of elevated H2S gas.
Because these symptoms can overlap with other gastrointestinal and systemic conditions, lab testing and careful clinical correlation are essential.
How Hydrogen Sulfide SIBO Causes Symptoms
Hydrogen sulfide SIBO doesn’t just cause gut discomfort, it can affect your whole body. This section is for those who want to know more about how this specific type of SIBO leads to symptoms like bloating, fatigue, and brain fog.
Too much gas in the wrong place:
Sulfate-reducing bacteria produce hydrogen sulfide gas when they feed on sulfur-containing foods. A little H2S is normal and even helpful for the body, but in hydrogen sulfide SIBO there’s way too much, and it's in the wrong place - your small intestine. The gas build-up can cause bloating, distension, abdominal pain, and diarrhea and/or constipation.Disrupted energy production:
Hydrogen sulfide gas can interfere with how mitochondria, the energy producers in our cells, work. This is especially a problem in the gut lining, which needs a lot of energy to stay healthy and absorb nutrients. When energy production breaks down, the gut lining can become weak and inflamed. As a result, your body struggles to absorb key nutrients like iron and B12, which are essential for energy. These low nutrient levels can lead to symptoms like fatigue and brain fog. At the same time, inflammation in the gut puts an extra drain on your energy reserves. Together, these issues create a cycle of exhaustion that’s hard to break.Weakened gut lining and inflammation:
Too much hydrogen sulfide can also damage the gut barrier and lead to what’s commonly known as ‘leaky gut’. That means things that aren’t supposed to pass through the gut wall, like toxins or bacteria, can leak into your bloodstream. When this happens, it can trigger the immune system and lead to systemic inflammation. The disrupted environment in the gut may also encourage harmful bacteria to grow, making symptoms worse. Over time, this process can contribute to more widespread symptoms such as joint pain, headaches, mood changes, and even neurological issues.Impaired sulfur metabolism and detoxification pathways:
While not specific to hydrogen sulfide SIBO, impaired sulfur detoxification is an important contributor and deserves a spot on this list because we have found it relevant for many of our clients. Some individuals have trouble breaking down and clearing sulfur compounds due to genetic or functional issues in their sulfur and sulfite detox pathways. Specifically, some clients have variations in the CBS gene or low levels of the mineral molybdenum, which supports sulfur metabolism. When these pathways aren’t working properly, sulfur compounds, including hydrogen sulfide, can build up in the body faster than they can be cleared. This overload can lead to symptoms like fatigue, brain fog, headaches, sensitivity to sulfur-rich foods or supplements, irritability, and skin issues such as rashes or hives. We often need to address impaired sulfur metabolism when we address hydrogen sulfide SIBO so have added this to our list of how it causes symptoms.
These interrelated processes explain why hydrogen sulfide SIBO not only causes gut symptoms but also contributes to systemic issues such as fatigue, brain fog, and even neurological disturbances.
Bacteria Responsible for Hydrogen Sulfide SIBO
Hydrogen sulfide gas is primarily produced by a group of bacteria known as sulfate-reducing bacteria (SRB), which use sulfur compounds as fuel. Some of the key SRB involved in H2S SIBO include:
Desulfovibrio: most well-known SRB genus in the gut.
Bilophila wadsworthia: often linked to high-fat, high-sulfur diets.
Fusobacterium: can contribute under certain conditions.
Clostridia species: some can reduce sulfur as part of their metabolism.
E. coli: not a classical SRB, but can produce H2S under certain conditions.
Root Causes of Hydrogen Sulfide SIBO
Let’s start with understanding how bacteria actually end up overgrown in the small intestine.
Three routes of bacteriaL overgrowth
Retrograde migration of bacteria from the large intestine:
Bacteria that produce H2S gas are more common in the large intestine, where they normally belong. But if gut motility slows down or the ileocecal valve (the one-way gate between the small and large intestines) isn’t working properly, these bacteria can migrate back up into the small intestine. Once there, they can start to overgrow and produce hydrogen sulfide gas.Overgrowth of existing bacteria (in-situ bloom):
Some hydrogen sulfide-producing bacteria already live in the small intestine in small amounts. But factors like a diet high in sulfur-rich foods, stress, or antibiotics can wipe out the normal bacteria and give these microbes the chance to take over. When the balance of your gut bacteria shifts like this, it creates the perfect environment for hydrogen sulfide SIBO to develop.Exposure to harmful bacteria in food and water (ingested):
In some cases, hydrogen sulfide-producing bacteria may be introduced from outside of the body, through contaminated food or water. If your stomach acid is low, from things like PPI use and stress, these harmful bacteria can survive the stomach and make their way down into the small intestine, where they can cause problems.
The two underlying causes of SIBO
Now that we’ve discussed how bacteria can overgrow in the small intestine, let’s dive into SIBO root causes - the underlying factors that, when working properly, should actually prevent SIBO. We’re going to look at two key areas agreed upon by most SIBO experts as our current framework for SIBO root causes.
1. Impaired gut motility
The number one reason why SIBO develops is a slow or dysfunctional migrating motor complex, also known as the MMC. The MMC is a cleansing wave-like motion that sweeps bacteria and food out of the small intestine between meals. When the MMC doesn't function properly bacteria can stay in the small intestine and multiply. The most common causes of disrupted MMC function that we currently understand are as follows:
Post-infectious IBS and food poisoning: One of the most well-documented causes of SIBO is a condition called post-infectious IBS, which often develops after a bout of food poisoning, gastroenteritis or traveler’s diarrhea.
Neurological disorders: The MMC is regulated by the enteric nervous system, the gut’s built-in ‘second brain’, so any condition that affects the brain, spinal cord, or vagus nerve can impair gut motility. The most common neurological conditions we see that are linked to SIBO are Parkinson’s Disease, Diabetes, Traumatic Brain Injury, Autonomic Nervous System Dysfunction like POTS and Dysautonomia, and very importantly Vagus Nerve Dysfunction.
Chronic infections: Often an overlooked cause of impaired gut motility and SIBO relapse. Conditions like Lyme disease, Epstein-Barr virus, parasites and mold exposure can disrupt the nervous system, vagus nerve function and the MMC, making it difficult for the small intestine to clear bacteria effectively.
Chronic stress and HPA axis dysregulation: Your gut is highly sensitive to stress, and chronic activation of the stress response can significantly reduce MMC function.
Hypothyroidism: Hypothyroidism reduces gut motility because thyroid hormones T3 and T4 stimulate the MMC. When thyroid function is low, these signals weaken, and we are more likely to have slower gut clearance. Constipation is also common in hypothyroid clients, increasing fermentation and slowed motility in the small intestine.
Medications: Certain medications have the unfortunate side-effect of significantly suppressing gut motility, which can lead to bacteria hanging around in the small intestine. Common MMC-suppressing medications include opioids like Oxycodone, Morphine and Codeine, Proton Pump Inhibitors and H2 Blockers, antibiotics and anticholinergic medications such as some antidepressants, antihistamines and bladder medications.
2. Structural issues
Even with a fully functional MMC, bacteria can still overgrow if they get stuck in the small intestine or if they migrate backward from the large intestine. Structural issues create physical roadblocks that prevent bacteria from being cleared out properly, making SIBO more likely to develop and harder to resolve. Common structural causes of SIBO include:
Adhesions: Adhesions are bands of scar tissue that form between organs and tissues after surgery and abdominal infections. The most common surgeries our clients have had prior to testing positive for SIBO are c-sections, endometriosis surgeries and appendix removal surgery. Adhesions from these can create kinks or narrow areas, restricting normal flow of food and waste and trap bacteria in the small intestine.
Blind loops: A blind loop is a section of the intestine where bacteria accumulate and multiply instead of being cleared out. This can happen because of past surgeries that changed the intestinal shape like gastric bypass and bowel resections, diverticula or small pouches in the intestine, as well as intestinal kinking or narrowing from chronic inflammation or scar tissue.
Ileocecal valve dysfunction: We touched on this earlier when talking about retrograde migration. The ileocecal (ICV) is a one-way ‘door’ between the small and large intestine that prevents bacteria from moving backward. When this valve isn’t working properly the door remains open, so large intestine bacteria can backflow into the small intestine, increasing the risk of SIBO.
Ehlers-Danlos Syndrome and other connective tissue disorders: EDS weakens the structure of the intestines. This can lead to loose, uncoordinated gut movement which slows digestion, weakened ICV function allowing bacteria to migrate backward and prolapsed or stretched-out intestines, creating pockets where organisms can get stuck.
Other risk factors that contribute to SIBO
Beyond our two SIBO root causes, impaired motility and structural issues, there are other risk factors that weaken your gut’s ability to prevent bacterial overgrowth. These factors don’t directly cause SIBO but increase the likelihood of overgrowth if motility or structure are already compromised.
Changes to the microbiome: These can occur following antibiotics that wipe out beneficial bacteria, a diet high in sugar and processed foods and chronic stress.
Weakened gut defenses: Low stomach acid, bile and enzyme deficiency, age and weakened immunity help create the perfect environment for bacterial overgrowth.
Sulfur deficiency: There’s also a theory that your body may increase hydrogen sulfide production, by supporting sulfate-reducing bacteria (SRB), if it senses it’s not getting enough usable sulfur. This may be an attempt to support detoxification and other important processes that rely on sulfur.
Testing for Hydrogen Sulfide SIBO
Testing for hydrogen sulfide SIBO can be a little trickier than testing for other types of SIBO, but it's still possible with the right tools and clinical insight. Breath testing is the most common method, and with careful interpretation, it can give us valuable clues about what's happening in the gut that might be contributing to symptoms.
SIBO breath testing
SIBO breath testing is a simple, non-invasive test that measures gas production in the digestive tract. During the test, you consume a sugar solution - typically lactulose, glucose or fructose - that isn’t fully absorbed in the small intestine. Overgrown bacteria then ferment this sugar, producing gases like hydrogen, methane and hydrogen sulfide. Breath samples are collected at regular intervals, every 15-20 minutes over 2-3 hours, to track gas levels.
The hydrogen sulfide challenge
Hydrogen sulfide is harder to test for than the other gases. Many breath tests only measure hydrogen and methane, so hydrogen sulfide overgrowth can sometimes be missed. In these cases, we often see a ‘flatline’ pattern, where hydrogen and methane levels stay low for the full duration of the test (typically 120 minutes), even when the person has clear SIBO symptoms. This happens because some bacteria convert hydrogen into hydrogen sulfide, hiding them on standard testing.
The TrioSmart test by Gemelli Labs is currently the only breath test on the market that measures all three gases, including hydrogen sulfide directly. It can provide a more complete picture, especially when symptoms strongly suggest H2S SIBO.
What to look for on standard hydrogen and methane SIBO testing
Gas patterns: A minimal rise (1-4ppm) or flatline in hydrogen and methane levels despite significant symptoms can be a clue.
Clinical correlation: The presence of symptoms that correlate, such as bloating, distention, abdominal pain, constipation, diarrhea, a distinctive “rotten egg” odor on the breath or in flatulence and more systemic symptoms we have listed above.
Our approach to interpretation
While breath testing is helpful, gas readings don’t always match up perfectly with how someone feels. That’s why we don’t rely on numbers alone. Instead, we combine test results with a client's symptoms, health history and lifestyle factors to get a thorough understanding of what is going on.
This holistic approach means we are less likely to miss an imbalance and ensures that if hydrogen sulfide SIBO is part of the picture, it’s identified and addressed with a tailored protocol of recommendations.
E.g., Flatline of hydrogen and methane gases on SIBO breath testing is used as a clue for hydrogen sulfide SIBO.
Trio-Smart testing includes hydrogen sulfide gas. A level above 2.5-3ppm is indicative of hydrogen sulfide SIBO.
Natural Treatment Protocols for Hydrogen Sulfide SIBO
At The Functional Gut Health Clinic, we've guided hundreds of clients through successful hydrogen sulfide SIBO protocols using our comprehensive and individualized approach. Our multi-phase protocol targets the bacterial overgrowth, supports overall gut function, and addresses underlying imbalances so clients can clear their symptoms without suffering relapse.
The 6 key steps to natural hydrogen sulfide SIBO eradication are:
Follow a low-sulfur, low-fermentation diet: Reduce fermentable carbohydrates and high-sulfur foods (like garlic, eggs, kale and onions) to limit bacterial fuel for gas production.
Use targeted herbal antimicrobials: Use single-herb antimicrobials such as emulsified oregano and bismuth-based formulas to reduce hydrogen sulfide-producing bacteria.
Support sulfur detox pathways: Enhance sulfur clearance and reduce symptom flares with nutrients like molybdenum.
Break down biofilms: Incorporate a biofilm disruptor, often combined with bismuth, to help antimicrobials reach and clear bacteria more effectively.
Address impaired motility: Use natural prokinetics such as ginger or Iberogast to stimulate the migrating motor complex and prevent relapse.
Rebuild the gut microbiome: Introduce prebiotics like GOS and probiotics such as Lactobacillus plantarum when tolerated to restore microbial balance and support gut lining health.
Here is an diagram overview of our approach to addressing hydrogen sulfide SIBO naturally, with each step discussed in detail below:
1. Diet for Hydrogen Sulfide SIBO
When it comes to managing hydrogen sulfide SIBO, diet is one of the most effective ways to get your symptoms under control quickly. While it won’t fix the root cause or eliminate the bacterial overgrowth on its own, making the right changes to what you eat can reduce symptoms by 60–90%, depending on the approach you choose to take.
The overgrown bacteria in SIBO feed on fermentable carbohydrates, turning them into gas. For hydrogen sulfide SIBO, that gas is hydrogen and hydrogen sulfide. By reducing the bacteria’s food supply, we can minimize gas production and relieve symptoms. But here’s the key; restrictive diets should only be followed for a short time, just long enough to bring relief while we work on addressing the root cause. Long-term restriction can harm your gut microbiome and slow your healing.
Our dietary approach
Our diet recommendations are always tailored to the individual, but in general, our approach for hydrogen sulfide SIBO is very similar to what we use for hydrogen SIBO. The focus is on reducing fermentable carbs while supporting digestion with easy-to-absorb nutrients from well-cooked vegetables, healthy fats, and quality protein.
For clients with more intense symptoms, we may suggest structured diets like:
The SIBO BiPhasic Diet
The SIBO Specific Food Guide
These diets are especially helpful because they give guidance on both which foods to eat and how much, which can make a big difference. For example, a small portion of sweet potato might be tolerated, while a larger serving could trigger symptoms, depending on what else you've eaten that day.
If you’ve already done a strict SIBO diet and are feeling better but want more flexibility, we may shift toward a Paleo-style diet, which is still low in processed carbs but less restrictive overall.
Other less strict options include:
Low-FODMAP Diet
Specific Carbohydrate Diet (SCD)
GAPS Diet
Fast Tract Diet
Cedars-Sinai Low Fermentation Diet
No one-size-fits-all diet works for every case, so we always customize based on your symptoms, lifestyle and stage of healing.
Special diet considerations for hydrogen sulfide SIBO
While not everyone with hydrogen sulfide SIBO reacts to sulfur-rich foods, many do, especially during the early stages of healing. For this reason we may consider a lower sulfur diet. Low-sulfur doesn’t mean ‘sulfur-free’, and as such we only remove foods clients have found to be problematic, such as:
Onion and garlic
Kale and other cruciferous veggies
Eggs
Chicken (especially leftovers)
If these foods are making symptoms worse, we often recommend temporarily removing them during Phase 1, and then reintroducing slowly once antimicrobials are complete.
Practical diet tips for SIBO
Here are a few additional recommendations we give all of our clients starting Phase 1 of our SIBO framework:
70% cooked / 30% raw: Cooking breaks down fiber and resistant starch, making vegetables easier to digest and less likely to trigger symptoms.
Ripe fruits: Unripe fruit is higher in resistant starch, which can be irritating to the gut.
Meal spacing: Leave at least 4 hours between meals to give your migrating motor complex (MMC) time to sweep bacteria and food remnants out of the small intestine.
Avoid MMC disruptors: Alcohol, caffeine and artificial sweeteners can interfere with this cleansing wave, so it’s best to limit or avoid them during healing.
Diet is a powerful tool for managing hydrogen sulfide SIBO, but it's only one piece of the puzzle. When combined with the right testing, supplements and lifestyle strategies, it can help you move from symptom relief to long-term healing.
2. Natural Antimicrobials for Hydrogen Sulfide SIBO
Once you've laid the foundation with diet changes, the next step in our SIBO framework is targeting the overgrowth itself, and that's where herbal antimicrobials come in. These plant-based supplements act like nature’s antibiotics. They help reduce harmful bacteria without wiping out your beneficial microbes, and they’re often gentler on the gut than prescription options. That’s why they’re our go-to for hydrogen sulfide SIBO.
While research is still evolving, our clinical experience shows that single herb antimicrobials, taken for 4 weeks, are currently the most effective option for hydrogen sulfide SIBO. In most cases, one round is enough. Only a small number of clients have needed a second month of eradication.
As always, the exact supplement and dosage should be guided by a qualified practitioner, but here’s what we’re currently seeing the best results with:
Bismuth
Bismuth is an antimicrobial that helps reduce sulfate-reducing bacteria (the ones responsible for hydrogen sulfide gas). It also binds to hydrogen sulfide itself, which can provide fast symptom relief. In our clinic, bismuth has been the most consistently effective option so far. We typically recommend bismuth subnitrate, Found in Priority One’s Biofilm Phase 2 Advanced, which also helps break down biofilms that protect bacteria. An alternative is bismuth subsalicylate, the active ingredient in Pepto Bismol. This product does contain salicylates, which can be difficult to tolerate.Oregano
High-dose oregano is another powerful antimicrobial that specifically targets hydrogen sulfide-producing bacteria. We often pair it with bismuth because oregano reduces bacterial overgrowth, while bismuth binds the gas and reduces symptoms. Oregano is a strong herbal antimicrobial, best used in rotation with other antimicrobials so you can use a lower dose, which will help to prevent bacterial resistance and damage to the native gut flora. We prefer an emulsified formulation such as Biotics, ADP Oregano, since this emulsified form of oregano is gentler on the gut and better tolerated than many other options.Uva Ursi and Silver Hydrosol
Both Uva Ursi and silver can be effective in some cases, but they come with more risks and require close monitoring. We only recommend them under practitioner supervision after thoroughly reviewing any contraindications.
Accessing high-quality supplements
Finding trustworthy supplements can be tricky. That’s why we’ve set up a Supplement Dispensary for our clients in the US, with 20% off all recommended products. It’s an easy way to access professional-grade antimicrobials. Access our dispensary here: https://us.fullscript.com/welcome/blindemann
Herbal antimicrobials are powerful tools and they’re not one-size-fits-all. Always check in with your practitioner before starting any new supplement to make sure it’s right for you.
Elemental Diet for Hydrogen Sulfide SIBO
The Elemental Diet is a liquid formula made of pre-digested nutrients that are absorbed high up in the small intestine. It’s designed to starve bacteria in the small intestine while still nourishing the body with easily-absorbed nutrients, and it's often used as an alternative to herbal antimicrobials for SIBO.
But here’s the problem, most Elemental Diet formulas contain sulfur-rich amino acids like methionine, cysteine and taurine. For people with hydrogen sulfide SIBO, these sulfur compounds can actually feed the problem, giving the bacteria more fuel to produce hydrogen sulfide gas and worsening symptoms like bloating, diarrhea or abdominal pain.
Because of this, we don’t recommend the Elemental Diet for our clients with hydrogen sulfide SIBO. Instead, we’ve seen better results with a low-sulfur diet combined with herbal antimicrobials. Supporting detox pathways, especially with nutrients like molybdenum, can also help the body clear hydrogen sulfide more effectively.
Bottom line: while the Elemental Diet can be helpful for other types of SIBO, it’s not our preferred approach for hydrogen sulfide SIBO due to the risk of symptom flare-ups.
SIBO Biofilm Disruption
Around 75% of bacterial infections involve biofilms. These are protective layers that bacteria build around themselves that make them much harder to get rid of. Bacteria inside biofilms can be up to 1000 times more resistant to antibiotics and herbal antimicrobials. That’s why including a biofilm disruptor in your hydrogen sulfide SIBO protocol can make a big difference. Breaking down these protective layers allows your antimicrobials to work more effectively and helps ensure the overgrowth doesn’t come back as easily.
One of our go-to products is Biofilm Phase-2 Advanced by Priority One. It’s a powerful 2-in-1 formula that combines bismuth, which binds hydrogen sulfide gas and reduces symptoms, with a blend of ingredients designed to break down biofilms. Many of our clients have seen great results using it alongside their antimicrobial protocol.
3. Microbiome Support for Hydrogen Sulfide SIBO
When it comes to supporting the microbiome in hydrogen sulfide SIBO, we’re still in the early days. There’s limited research and clinical experience to guide us, so much of what we know is based on trial, error and emerging studies. That said, there are some promising tools we consider, especially when clients need help managing symptoms or when beneficial bacteria are trending low.
In our SIBO Framework, microbiome support is the third piece of Phase 1, and it includes both prebiotics and probiotics. Let’s break those down.
Prebiotics for H2S SIBO:
Most prebiotic fiber isn’t well tolerated with SIBO, especially in the early stages. That’s because they can feed both good and opportunistic bacteria, and when you’re dealing with bacterial overgrowth, this often leads to more gas, bloating and discomfort. But there’s one exception we make and it is to Galactooligosaccharides (GOS).
GOS is a specific type of prebiotic that has actually been shown in research to reduce hydrogen sulfide gas production. When we use it in practice, we usually recommend starting it about 2 weeks into an antimicrobial protocol, and then slowly increasing the dose over a few weeks, up to 5.5g daily, depending on how well it’s tolerated.
Probiotics for H2S SIBO:
Probiotics are another tool we sometimes use to support the microbiome and ease symptoms, but again, there’s not much research yet specific to hydrogen sulfide SIBO.
One standout study from 2014 looked at a probiotic strain called Lactobacillus plantarum LP-8. After just 4 weeks of daily use, participants showed an increase in beneficial bacteria like Bifidobacterium and a decrease in Desulfovibrio, one of the main hydrogen sulfide-producing bacteria. Unfortunately, this exact LP-8 strain isn’t available in supplement form yet.
That said, our clients have reported symptom improvements when using other Lactobacillus plantarum strains. So while the research is still catching up, this may be a useful tool for managing symptoms and gently supporting microbiome balance.
As always, we recommend introducing pre- and probiotics carefully, and only when the time is right in your healing journey. When used strategically, they can help shift your gut back toward balance without making symptoms worse.
4. Supporting Digestion, Detoxification and Motility
Digestive support:
When hydrogen sulfide SIBO throws your gut off balance, it doesn’t just cause uncomfortable symptoms, it can also disrupt how well you digest your food. That’s why we include digestive supports as a key part of Phase 1 in our SIBO Framework. While it’s listed as step 4, we actually layer these in alongside diet and antimicrobials to help restore normal gut function from the start.
SIBO often interferes with your body’s ability to produce digestive enzymes, especially those made in the brush border of the small intestine. Without enough enzymes, food doesn’t break down properly, leading to fermentation, gas and more symptoms.
To give the digestive system a helping hand, we often recommend using a broad-spectrum enzyme supplement. One of our favourites is Enzymedica’s Digest Gold with ATPro, which many of our clients tolerate well and find effective for reducing bloating and improving digestion.
Good digestion isn’t just about what you eat, it’s also about how calm and relaxed you are when you eat. When your body is stressed, it shifts into ‘fight or flight’ mode, sending blood away from your digestive organs and toward your muscles. That’s why stress can directly impact how well you digest.
To help your gut do its job, try the following:
Taking a few deep breaths before meals.
Slowing down and savoring your food, noticing flavors, textures and chewing thoroughly.
Building in small moments of relaxation during your day to support parasympathetic (rest-and-digest) activity.
These simple habits may seem small, but they can make a big difference in how well your digestive system functions, especially when you’re dealing with SIBO.
Detoxification and managing SIBO die-off symptoms:
As part of our SIBO Framework, detoxification and managing die-off symptoms are essential for keeping your healing process on track. That’s why we include this step as part of the digestive supports element in Phase 1.
When bacteria are killed off, they release toxins into the gut. This can trigger an immune response and lead to what's known as a die-off reaction, or a Herxheimer reaction. Common symptoms include:
Fatigue
Headaches
Body aches
Brain fog
Skin rashes or reactions
Mood changes (e.g. anxiety and depression)
Increased GI upset
These symptoms are usually temporary but can be intense if your body’s detox systems aren’t supported properly.
One mineral we find especially helpful for hydrogen sulfide SIBO is molybdenum. This trace mineral plays a key role in breaking down hydrogen sulfide gas and making it less toxic in the body. For clients experiencing brain fog, fatigue or worsening GI symptoms during die-off, molybdenum can be a game-changer. Short-term dosing up to 1200 mcg daily is generally well tolerated under practitioner supervision, to support detoxification and help ease die-off symptoms.
To make the process more manageable, here are a few go-to recommendations we share with our clients:
Start slow: Introduce diet changes and supplements gradually to avoid overwhelming the system.
Reduce inflammation: Prioritize rest, hydration, and anti-inflammatory foods rich in antioxidants and omega-3s.
Support detox pathways: This is key. Focus on liver-loving foods (like leafy greens, beets, and cruciferous vegetables), consider herbal liver support, and use gentle binders if needed to help mop up released toxins.
Supporting the liver and detox systems helps your body process bacterial toxins more efficiently, reducing the severity of die-off symptoms and helping you feel better, faster.
For more in-depth guidance on managing these symptoms effectively, download our FREE eGuide on Managing Die-Off Symptoms here: eGuide Link
5. Address Root Causes of Hydrogen Sulfide SIBO
We covered the details of this earlier in the blog when discussing the root causes of hydrogen sulfide SIBO. This phase of our approach is about identifying what the underlying root causes are for our clients and then developing a plan to address those. For example, we may incorporate prokinetics to support motility, or recommend visceral manipulation to address adhesions. We may also need to address other chronic infections and support the body's natural immune defenses in the gut (e.g. stomach acid, enzymes, etc.). As motility is the main underlying root cause of hydrogen sulfide SIBO, allowing continued relapse, we will delve into how we address this with our clients.
Motility & prokinetics for hydrogen sulfide SIBO:
The final part of our digestive supports for hydrogen sulfide SIBO is all about supporting motility in the small intestine. This is one of the most important (and often overlooked) pieces of the puzzle, especially when it comes to preventing relapse.
One of the best tools we have to support motility is prokinetics. These supplements stimulate the migrating motor complex (MMC), the wave-like cleansing motion that moves through the small intestine every 90-120 minutes when you're not eating. The MMC helps sweep out leftover food and bacteria, which keeps things moving and prevents bacterial overgrowth from coming back.
When the MMC isn’t working properly, it becomes much harder to fully clear SIBO, and even if you do, relapse becomes very likely. Research shows that about two-thirds of SIBO cases relapse, often within 2 - 2.5 months, especially when underlying causes like poor motility aren’t addressed.
Prokinetics don’t replace the MMC, but they enhance its natural function, especially the action of vinculin motor proteins that help coordinate the MMC. If those proteins are severely damaged (for example, from post-infectious IBS or food poisoning), prokinetics might not work as well. But for most people, they’re incredibly helpful and often well tolerated.
We usually introduce prokinetics during the eradication phase to see how clients respond. If they’re well tolerated, we recommend continuing them through the end of Phase 1 and for at least 3 months afterward to get through the critical relapse window. Some clients may need them longer, and that’s completely okay. Personally, I used them for 2 years post-eradication until I felt confident stopping.
There are a lot of prokinetic options out there, but our favorites are ginger root, or blends that include ginger, and Iberogast, a combination of six herbal extracts, which has been shown to support MMC function, great for those who don’t tolerate ginger.
Prokinetics are a powerful part of your SIBO recovery plan. They help maintain momentum, support gut cleansing, and reduce the chance of having to start over again.
Preventing Hydrogen Sulfide SIBO Relapse
Once you’ve gone through the hard work of reducing hydrogen sulfide SIBO, the next goal is to keep it from coming back. Preventing SIBO relapse isn’t one-size-fits-all, it requires an ongoing, personalized strategy based on your lab results, symptoms, and how your body responded to interventions. Here are some of the key tools we use to support long-term recovery and gut resilience:
Diet diversity and food reintroduction:
After a restricted diet during the eradication phase, it’s important to gradually reintroduce a wide variety of whole foods. This helps rebuild a healthy, balanced microbiome, which is key to keeping SIBO at bay.
For hydrogen sulfide SIBO, we pay special attention to sulfur-containing foods. Reintroducing these too quickly can fuel gas production and trigger symptoms like bloating and discomfort. That’s why we take it slow and monitor closely, finding the right balance between diversity and symptom control.
Probiotics and prebiotics:
While these might have been off the table during the early stages of eradication work, prebiotics and probiotics become essential in the recovery phase. Prebiotics and probiotics support beneficial butyrate-producing bacteria, which help suppress SRB and bring back beneficial bacteria, promoting long-term gut health.
Ongoing digestive and motility support:
If poor motility or sluggish digestive function contributed to SIBO, these areas still need attention. We often recommend continuing digestive enzymes, stomach acid support (like HCl) and natural prokinetics to keep the small intestine clear and functioning well. This is especially important in the months following eradication, when your gut is still stabilizing.
Investigating any remaining root causes:
Sometimes hydrogen sulfide levels improve, but symptoms linger. For clients who experience this, it’s worth looking deeper. We may run advanced stool or urine testing or re-evaluate for things like:
Leaky gut
Hidden infections or imbalances
Mold and mycotoxins
Structural or functional digestive issues
Addressing these deeper layers is often what makes the difference between temporary relief and lasting recovery.
Final Thoughts and Next Steps
Healing from hydrogen sulfide SIBO takes more than a quick fix, it requires a comprehensive, natural approach that tackles both the overgrowth itself and the underlying reasons it developed in the first place.
By combining accurate testing, targeted herbal antimicrobials, and personalized support for diet, digestion, detoxification and motility, you can create the conditions your body needs to recover fully, and stay well.
If you're ready to feel better, we’re here to help. You can:
Book an Initial Consultation with one of our experienced SIBO specialists and get started today.
Explore our recommended supplements through our Supplement Dispensary.
Or simply learn more about our process and how we work with clients via a Complimentary 15 Minute Pre-Consultation call with one of our practitioners.
Your journey back to gut health starts with one step, and we’d love to walk it with you because you deserve to heal and feel vibrant and well.
About author: Bella Lindemann, FDN-P
Bella Lindemann is the founder and lead practitioner at The Functional Gut Health Clinic. With her science degree, functional nutrition certification and extensive experience, she is a recognized expert in gut health and the science of SIBO, parasites and other gut infections. With her own personal gut healing experience and having supported thousands of clients across the clinic, Bella is passionate about helping her clients address GI imbalances and take back control of their digestive symptoms.