Hydrogen Sulfide SIBO: How to Test and Treat

If you’ve ever been told your SIBO test was “normal” but still feel bloated, foggy, and nothing you eat seems to sit right—this post is for you.

Hydrogen sulfide SIBO is one of the most overlooked and under-tested forms of bacterial overgrowth. And unfortunately, most doctors aren’t trained to look for it.

As a functional medicine dietitian, I work with people every day who have been dismissed or misdiagnosed—people who’ve followed strict low FODMAP diets, taken rounds of rifaximin, and done “everything right” but still don’t feel well.

It’s not in your head. You may simply have a form of SIBO that’s rarely screened for and poorly understood in conventional care. But we’re learning more—and there are answers.

In this article, we’ll explore what hydrogen sulfide SIBO is, how it affects your gut and whole-body health, and why it’s been missed in testing and treatment for so long. We’ll also cover the most up-to-date research and the tools I use in clinical practice to help people recover—even if everything else has failed.

What Is Hydrogen Sulfide SIBO?

SIBO stands for small intestinal bacterial overgrowth. It occurs when bacteria that normally live in the large intestine begin growing where they don’t belong—in the small intestine, where they disrupt digestion and cause a wide range of symptoms.

Understanding the SIBO Subtypes

There are three main types of SIBO, defined by the gas they produce.

• Hydrogen-dominant SIBO is the most common and is usually associated with diarrhea, bloating, and nutrient malabsorption.
  
• Methane-dominant SIBO is caused by archaea (not bacteria) and tends to cause constipation and slowed gut motility.
  
• Hydrogen sulfide SIBO is the newest and least understood. It’s associated with loose stools, foul-smelling gas, sulfur intolerance, and a variety of hard-to-pin-down symptoms like fatigue, brain fog, and skin reactions.

How Hydrogen Sulfide Is Produced in the Gut

Hydrogen sulfide is a gas produced by specific bacteria that feed on sulfur-rich compounds. When these bacteria overgrow in the small intestine, they convert dietary sulfur into hydrogen sulfide gas.

At low levels, hydrogen sulfide plays a role in gut health and cell signaling. But in excess, it becomes toxic to the gut lining. It can damage epithelial cells, suppress beneficial hormones like GLP-1, and lead to systemic inflammation (1).

Why It’s Often Overlooked in Conventional Testing

Most conventional SIBO tests only measure hydrogen and methane gas. Hydrogen sulfide wasn’t even measurable on breath tests until recently.

As a result, many people who test negative for SIBO on standard breath tests are told they’re fine—even when they clearly aren’t. It’s not uncommon for people with hydrogen sulfide overgrowth to bounce from provider to provider with no clear answers.

The good news is that newer testing options now measure all three gases—including hydrogen sulfide—and give us a much clearer picture of what’s going on.

Symptoms of Hydrogen Sulfide SIBO

Hydrogen sulfide SIBO doesn’t always present the same way as other forms of SIBO. While some symptoms overlap, this subtype has a few unique features that can make it easier to spot once you know what to look for.

Digestive Symptoms

The most common digestive symptoms include:

• Loose stools or diarrhea
  
• Excessive bloating, especially after meals
  
• Gas with a strong sulfur or “rotten egg” smell
  

Many people also report feeling uncomfortable with high-sulfur foods like garlic, onions, eggs, or cruciferous vegetables. These foods can feed hydrogen sulfide–producing bacteria and trigger noticeable symptoms.

Systemic Symptoms

Because hydrogen sulfide gas affects more than just digestion, symptoms often go beyond the gut. Some of the most common systemic issues include:

• Brain fog or difficulty concentrating
  
• Fatigue that doesn’t improve with rest
  
• Bad breath with a sulfur-like odor
  
• Histamine intolerance (flushing, hives, headaches, or food reactions)
  
• Sensitivity to supplements containing sulfur or NAC
  

These symptoms are often brushed off or treated in isolation, but when they occur alongside gut issues, hydrogen sulfide overgrowth should be considered.

Common Misdiagnoses

Hydrogen sulfide SIBO is frequently misdiagnosed—or completely missed. Because the symptoms are non-specific, it’s often confused with:

• IBS-D (Irritable Bowel Syndrome with Diarrhea)
  
• Food sensitivities or “leaky gut”
  
• Histamine intolerance
  
• Anxiety or chronic fatigue
  
• Parasitic infections or mold toxicity
  

In many cases, the root issue is microbial—but the wrong microbes are being targeted, or none at all. That’s why proper testing and an individualized plan make all the difference.

Why Standard SIBO Testing Falls Short

Hydrogen sulfide SIBO is a classic example of how outdated testing methods can leave people suffering without answers. Most providers still rely on traditional breath tests that simply weren’t designed to detect this subtype.

The Problem with Lactulose Breath Tests

For years, the lactulose breath test has been the gold standard for diagnosing SIBO. This test measures the levels of hydrogen and methane gases produced by bacteria in your small intestine after you drink a sugar solution.

The problem? It doesn’t measure hydrogen sulfide.

If you have hydrogen sulfide–producing bacteria in your gut, they may actually consume the hydrogen gas that would otherwise show up on the test—resulting in a flat-line or falsely negative result. This is why so many people with hydrogen sulfide overgrowth are told their test is normal, even when their symptoms are anything but.

The Trio-Smart Test and Other Emerging Tools

The Trio-Smart test is currently the only breath test on the market that measures all three SIBO gases: hydrogen, methane, and hydrogen sulfide. It’s a major step forward in helping us catch cases that would otherwise be missed.

Other tools, like GI-MAP or stool analysis, may suggest an overgrowth of hydrogen sulfide–producing bacteria (like Desulfovibrio, Fusobacterium, or Bilophila), but these are indirect clues rather than diagnostic tools.

Even with these newer options, many conventional providers don’t know how to interpret the results or aren’t aware the test exists.

Clinical Clues When Testing Fails

In my practice, I’ve worked with many clients who have textbook hydrogen sulfide symptoms but have never received a diagnosis. That’s because while testing is helpful, it isn’t everything.

If you have:

• Rotten-egg smelling gas
  
• Worsening symptoms with sulfur-rich foods
  
• Loose stools + fatigue + brain fog
  
• A history of IBS-D or unexplained bloating
  
• A flat-line or “normal” SIBO test with unresolved symptoms
  

…then it’s worth exploring the possibility of hydrogen sulfide overgrowth, even if your tests haven’t confirmed it.

In these cases, a personalized, evidence-informed approach to diet, supplementation, and microbiome support can often bring more clarity than the test results ever did.

What the Research Says About Hydrogen Sulfide SIBO

We’re still in the early stages of understanding hydrogen sulfide SIBO, but the research that does exist paints a compelling picture. While it’s far from complete, the studies we have so far are helping us connect the dots between symptoms, root causes, and potential treatment options.

Disrupted Metabolism and GLP-1 Suppression (2)

One of the more interesting developments in the research is the link between hydrogen sulfide gas and GLP-1 suppression. GLP-1 is a hormone that helps regulate appetite, blood sugar, and insulin sensitivity. In a recent animal study, bacteria like Desulfovibrio were shown to reduce GLP-1 production and impair metabolic function.

While the study was done in mice, the implications are worth considering. If hydrogen sulfide–producing bacteria can interfere with metabolic signaling, it could help explain why so many people with SIBO experience stubborn weight gain, blood sugar crashes, or cravings that don’t respond to a typical “healthy” diet.

I break this down further in my article on SIBO and weight gain. If you’ve been doing everything right and are still gaining weight or feeling inflamed, this connection is worth exploring.

H2S Bacteria and IBS-D Correlation

Another study looked at individuals with IBS and found something interesting. Those with diarrhea-predominant IBS had significantly higher levels of hydrogen sulfide on breath tests, along with a higher abundance of Fusobacterium and Desulfovibrio species. (3)

These bacteria are known hydrogen sulfide producers. Their presence may not only drive the gas itself but also trigger inflammation and loose stools. 

This offers a potential explanation for why some people with “IBS” never respond to fiber or gut-soothing diets. People with diarrhea-predominant IBS should look into hydrogen sulfide SIBO as a potential cause of their symptoms.

Bismuth and Botanical Therapies in Early Studies

There is no gold-standard treatment for hydrogen sulfide SIBO yet, but some early studies and clinical strategies are showing promise. These include a mix of herbal antimicrobials, gas-binding agents, and sulfur-modulating compounds that are already in use in functional care settings.

Biocidin and Binder Protocols (4)

One open-label study tested a protocol using a combination of Biocidin, a broad-spectrum herbal antimicrobial, and a GI binder to help trap hydrogen sulfide gas. The results were encouraging: nearly 67 percent of participants had resolution or significant improvement in symptoms and gas levels.

This protocol may work well because it doesn’t rely on sulfur-containing compounds, and it takes a two-pronged approach—reducing the bacteria while also binding up the excess gas they produce. It’s a relatively gentle option that many people tolerate better than antibiotics or high-dose herbals.

Bismuth Compounds (5)

Bismuth is a mineral known for its ability to bind hydrogen sulfide gas in the gut, making it especially useful for symptom relief in hydrogen sulfide SIBO. Some studies suggest it may also enhance the effectiveness of antibiotics by disrupting bacterial iron metabolism.

Another important reason bismuth is often used is its potential to break down biofilms—the sticky layers that bacteria create to protect themselves from treatment. If you’re unfamiliar with how biofilms make SIBO harder to treat, I cover that in more detail in my article on how to approach biofilms.

Bismuth isn’t a standalone treatment, but when used properly, it can support better outcomes and improve tolerance to antimicrobials.

Allicin (Used with Caution)

Allicin, a compound derived from garlic, is widely considered one of the most effective herbal treatments for SIBO. It has strong antimicrobial activity and can help reduce gram-negative bacteria like E. coli and Klebsiella.

However, it may not be the best option for hydrogen sulfide SIBO. Because allicin breaks down into sulfur-containing compounds, it can sometimes worsen symptoms in sensitive individuals.

In some cases, allicin can still be helpful when used alongside bismuth to offset gas production, but it should be used with caution. You can learn more about how allicin works in my full article on allicin and SIBO.

Limitations of Current Research and What We Still Don’t Know

Here’s the honest truth. Hydrogen sulfide SIBO is understudied. There are no large-scale randomized controlled trials. There are no formal guidelines on how to test for or treat it. And many of the studies we do have are in animal models or small, open-label trials.

But that doesn’t mean it’s not real.

If anything, the lack of research reflects the gap between conventional medicine and real-world experience. Patients are experiencing very real symptoms. Functional providers are observing consistent patterns. And the research, though limited, is beginning to back it up.

This is where functional nutrition shines. It doesn’t wait for perfect data before taking action. It looks at symptoms, patterns, clinical evidence, and lived experience. And it builds a plan around you—not a textbook.

Natural Treatment Options for Hydrogen Sulfide SIBO

There is no one-size-fits-all approach to treating hydrogen sulfide SIBO.

In functional nutrition, we focus on reducing bacterial overgrowth, supporting gut healing, and restoring balance without overly restricting the diet.

Many people do best with a combination of targeted antimicrobials, gentle symptom support, and simple nutrition strategies that reduce fermentation without starving the body.

Low-sulfur diets: When to use and when to stop

Low-sulfur diets are often recommended for hydrogen sulfide SIBO, but there’s no clinical research supporting their effectiveness. Most of what we know about them is anecdotal.

In theory, removing sulfur-rich foods might reduce symptoms by limiting fuel for hydrogen sulfide–producing bacteria. But in practice, this approach is overly restrictive and potentially counterproductive.

Sulfur-containing foods—like cruciferous vegetables, onions, garlic, and eggs—are some of the healthiest foods on the planet. They support detoxification, feed beneficial bacteria, and protect the gut lining.

Rather than eliminating them across the board, it’s more useful to identify whether someone has a true sulfur intolerance or simply a dysbiosis that needs correction.

In most cases, symptoms improve not by removing sulfur, but by restoring balance to the microbiome and supporting the pathways that process sulfur in the body.

If someone is extremely reactive, I may reduce sulfur foods temporarily, but my goal is always to bring them back in. Long-term avoidance is neither necessary nor helpful in most cases.

Supporting the gut without triggering symptoms

Instead of cutting out entire food groups, the goal should be nourishment without aggravation. For many people with SIBO, symptoms are more about bacterial imbalance than the food itself.

When needed, a short-term Low FODMAP diet may help reduce fermentation and calm symptoms. It is the most rigorously studied dietary intervention for both SIBO and IBS and can be a helpful bridge during treatment. That said, I always aim to reintroduce foods and liberalize the diet as soon as possible.

What matters more than restriction is personalization. Supporting digestion, encouraging motility, using appropriate antimicrobials, and addressing microbial imbalances directly tends to lead to much better results than simply avoiding food.

Antimicrobials and Supplement Options

Supplements can make a big difference in hydrogen sulfide SIBO when used strategically.

Rather than pushing high doses of herbs or antimicrobials, I prefer a targeted and supported approach that lowers symptoms while restoring balance.

Here are a few of the tools I use in practice:

Biocidin and GI binders

Biocidin is a broad-spectrum botanical blend that targets a wide range of bacteria, including hydrogen sulfide–producing species.

It works well for people who are sensitive or unable to tolerate antibiotics.

When paired with a GI binder, it can help mop up hydrogen sulfide gas as the bacteria die off.

This two-step method reduces bloating, gas, and flare-ups during treatment.

Bismuth-based protocols: Pros and cons

Bismuth helps by directly binding hydrogen sulfide gas in the gut. It can also make certain bacteria more sensitive to antimicrobials and may help break down biofilms.

Bismuth is not for long-term use and may not work for everyone. But for short-term relief, it can be a helpful addition—especially when symptoms are severe.

Learn more about how biofilms impact SIBO in this article.

Supportive Therapies

Treating the bacteria is only part of the picture. To fully recover, we also need to support how the gut moves, clears toxins, and handles stress.

Sulfur detox support (molybdenum, B12, etc.)

If sulfur builds up in the body, symptoms can worsen. In these cases, I may support detox pathways using nutrients like molybdenum, B12, and magnesium.

These help the body process sulfur more efficiently, especially in people with genetic variants affecting sulfur metabolism.

Who Should Be Cautious with Treatment?

While many people respond well to antimicrobials and herbal support, not every supplement is right for every person.

There are a few situations where treatment should be more carefully tailored.

Sulfur Intolerance and CBS Gene Mutations

Some people have trouble processing sulfur compounds.

This can be due to sluggish detox pathways or genetic variants like CBS mutations, which affect how the body breaks down sulfur. In these cases, sulfur-containing supplements or high-sulfur foods may lead to fatigue, headaches, skin breakouts, or irritability.

Instead of removing all sulfur from the diet, I focus on supporting detox with molybdenum, B12, and magnesium, then slowly reintroduce as tolerance improves. Sometimes I will even order a full methylation panel to see if there are any specific bottlenecks in the transulfuration pathway. 

When Allicin and Garlic May Worsen Symptoms

Allicin, the active compound in garlic, is a well-researched treatment for hydrogen-dominant SIBO. But in hydrogen sulfide SIBO, it gets more complicated.

Since allicin contains sulfur, it can sometimes make symptoms worse in sensitive individuals. That doesn’t mean it’s off the table. It just means it should be used cautiously, ideally with a binder or bismuth to help manage the sulfur load.

You can read more about this in my article on Allicin for SIBO.

Patients with Active IBD or Ulcerative Colitis

People with inflammatory bowel diseases—especially ulcerative colitis—tend to have higher levels of hydrogen sulfide–producing bacteria. That doesn’t mean treatment isn’t possible. It just means the gut lining is more vulnerable, and we need to be extra gentle.

I avoid harsh antimicrobials in these cases and focus more on gut repair, immune regulation, and stress management before ramping up antimicrobial support. Healing the terrain often leads to better tolerance and better results.

Functional Care for Hydrogen Sulfide SIBO

Treating hydrogen sulfide SIBO isn’t just about killing off bacteria. It’s about creating the right conditions for your gut to heal—and for those symptoms to actually stay gone.

That’s where functional nutrition makes a big difference.

Why One-Size-Fits-All Doesn’t Work

Hydrogen sulfide SIBO presents differently in each person.

Some people struggle with bloating and brain fog. Others deal with sulfur intolerance, histamine issues, or post-meal fatigue.

No single supplement or diet will work for everyone. What matters is identifying the patterns and building a plan that fits your specific needs, history, and symptoms.

Final Thoughts: You’re Not Broken—You’ve Just Been Missed

If your symptoms don’t make sense, your labs are “normal,” and nothing you try seems to work, it’s not because you’re doing something wrong.

You may just be dealing with something the conventional system isn’t trained to see.

The System Isn’t Set Up for Subtle SIBO Cases

Most providers don’t test for hydrogen sulfide. And even when they do, treatment options are limited to antibiotics or elimination diets.

If you’ve been told there’s nothing wrong—or worse, that it’s all in your head—you’re not alone. Hydrogen sulfide SIBO is real. And it’s more common than we think.

You Deserve Better Answers

Your symptoms are valid. And they’re telling a story that deserves to be heard. With the right approach, it’s possible to feel better—without extreme diets, endless supplements, or living in fear of food. You don’t have to figure this out alone.

Need Help Navigating Hydrogen Sulfide SIBO?

There is no one-size-fits-all approach to hydrogen sulfide SIBO.

Symptoms vary, test results can be misleading, and some treatments can make things worse before they get better.

That’s why functional care matters.

As a functional dietitian, I’ll guide you through the right options—whether it’s breath testing, stool analysis, or functional labs that can actually reveal what’s going on.

I stay in close contact with my clients, often messaging daily to monitor symptoms and make real-time adjustments. No guesswork. No getting lost in a protocol that doesn’t fit.

If you’re tired of trial and error and ready for a personalized plan that works, book a discovery call. I’d love to help you get to the root and finally move forward.