Key Points at a Glance
- Hydrogen sulfide, or H₂S, is produced by certain intestinal bacteria and in the body’s own cells. It is not inherently harmful; it also performs important signaling functions.
- Elevated H₂S levels in exhaled breath are associated particularly with diarrhea. However, a rotten-egg smell does not prove that small intestinal bacterial overgrowth is present.
- Conventional hydrogen and methane breath tests do not measure H₂S. A three-gas breath test, such as the Trio-SmartTM test, also measures hydrogen sulfide. A flatline on a conventional breath test is not sufficient on its own to reliably diagnose H₂S-SIBO.
- There are currently no sufficiently validated, standardized treatment protocols for specifically treating excess H₂S production. Treatment and dietary measures should be tailored to the individual.
Scientific basis: medical guidelines, peer-reviewed clinical studies and scientific reviews. Relationships that remain uncertain are identified accordingly.
Hydrogen Sulfide-Producing Gut Bacteria:
Symptoms, Diagnosis and Treatment of H₂S-SIBO
Hydrogen sulfide-producing gut bacteria are part of the natural intestinal microbiota. However, increased production of this gas has been linked to certain digestive symptoms.
The term “hydrogen sulfide SIBO,” or “H₂S-SIBO,” is often used in this context. Research is still evolving, and important questions remain open, particularly regarding diagnosis and treatment.
Medical disclaimer: This article is for general information only and does not replace medical examination, diagnosis or treatment. Do not start antibiotic treatment or a highly restrictive diet on your own.
1. What is SIBO, and how do digestive symptoms develop?
SIBO stands for 
“Small Intestinal Bacterial Overgrowth”, meaning an excessive bacterial population in the small intestine that causes symptoms. Under normal conditions, the small intestine contains far fewer microorganisms than the large intestine. When bacteria process more food components in the small intestine, they can produce gases, among other things. Possible symptoms include:
- Gas and a
bloated abdomen 
Abdominal pain and cramps- A feeling of fullness
- Diarrhea (also called diarrhoea)
- Constipation (obstipation)
In more severe cases, nutrient absorption may also be impaired. Possible consequences include vitamin B₁₂ deficiency or impaired fat absorption. These complications do not affect everyone with SIBO.
Finally Understand SIBO
Your SIBO Compass explains in simple terms what may be behind chronic abdominal symptoms.
It helps you understand which next steps may be useful so your gut can start feeling better.
How are SIBO, gut flora and irritable bowel syndrome related?
The microorganisms living in the gut are called the intestinal microbiota, or informally the gut flora. The broader term microbiome is also commonly used. Changes in the composition or function of a microbial community are described as dysbiosis.
SIBO and irritable bowel syndrome (IBS) may cause similar symptoms and may occur together, but they are not the same condition. Having IBS does not automatically mean that small intestinal bacterial overgrowth is present.
1.1 Which breath tests are used for SIBO?
For SIBO diagnosis, glucose or lactulose breath tests are mainly used. After drinking a test solution, breath samples are collected at specified intervals. Hydrogen and methane are usually measured.
These microbially produced gases enter the bloodstream and then reach exhaled breath through the lungs.
Breath tests provide indirect evidence. Preparation, the test substrate and intestinal transit can affect the result. Findings must therefore always be assessed in conjunction with symptoms and medical history. A three-gas breath test adds hydrogen sulfide to the measurements. For more information, see Section 3 on diagnosis.
1.2 How is SIBO generally treated?
Treatment depends on symptoms, test findings and potential underlying causes. Options may include physician-prescribed antibiotics, treatment of an underlying condition, and individually adapted dietary measures.
Not all interventions have been studied to the same extent for every gas profile. Find out more in Section 6 on treatment.
2. How do the different gas profiles compare?
SIBO is often simplified into three forms: hydrogen, methane and hydrogen sulfide. Strictly speaking, this classification is not entirely accurate. Methane is produced by archaea, not bacteria.
Increased H₂S production also does not necessarily occur exclusively in the small intestine.
| Condition | Characteristic gas | Symptoms and associations | Microorganisms involved |
|---|---|---|---|
| Hydrogen SIBO | Hydrogen, H₂ | Gas, bloating, abdominal pain; diarrhea is common | Including Escherichia coli and Klebsiella pneumoniae |
| Intestinal Methanogen Overgrowth (IMO) | Methane, CH₄ | Especially associated with constipation; bloating and gas are also possible | Methanogenic archaea, particularly Methanobrevibacter smithii |
| H₂S overproduction, often called “H₂S-SIBO” | Hydrogen sulfide, H₂S | Elevated breath levels are primarily associated with diarrhea; urgent bowel movements, a sulfur-like odor, brain fog, burning pain and joint symptoms are possible | Intestinal H₂S producers include Desulfovibrio and Bilophila wadsworthia; newer small intestinal data also show associations with Proteus mirabilis |
This table is intended as a guide. Symptoms overlap and cannot reliably distinguish between conditions. A breath test also does not directly identify a specific bacterial species.
2.1 What characterizes hydrogen SIBO?
Hydrogen is produced during bacterial fermentation of carbohydrates. In hydrogen SIBO, this activity occurs to a greater extent in the small intestine. Bacteria associated with this condition include certain E.-coli and Klebsiella strains.
2.2 Why is “methane SIBO” actually called IMO?
Methane-producing microorganisms belong to the archaea. Because they are not bacteria and can occur in both the small and large intestine, “Intestinal Methanogen Overgrowth,” abbreviated IMO, is the more appropriate term. Elevated methane levels are particularly associated with constipation.
2.3 What does hydrogen sulfide SIBO, or ISO, mean?
“Hydrogen sulfide SIBO” usually refers to suspected or documented increased H₂S production associated with digestive symptoms. Certain bacteria can produce H₂S, for example, by reducing sulfate or breaking down sulfur-containing compounds.
The more recent term “Intestinal Sulfide Overproduction” (ISO) is also used in the scientific literature. It describes excessive intestinal sulfide production without automatically restricting it to the small intestine. Its diagnostic and therapeutic interpretation is still developing.
What roles do Desulfovibrio, Bilophila wadsworthia and Proteus mirabilis play in H₂S-SIBO?
Bacteria being studied in connection with intestinal hydrogen sulfide production include Desulfovibrio, Bilophila wadsworthia and Proteus mirabilis. They can contribute to H₂S production through different metabolic pathways:
- Desulfovibrio: This genus includes sulfate-reducing bacteria that can produce hydrogen sulfide when metabolizing sulfate.
- Bilophila wadsworthia: This bacterium can metabolize taurine, among other compounds. This produces sulfite, which is reduced to hydrogen sulfide. It should therefore not simply be classified together with sulfate-reducing bacteria.
- Proteus mirabilis: Recent analyses of human small intestinal samples show associations between the presence of this H₂S-producing bacterium and elevated hydrogen sulfide levels in breath.
A breath test—ideally a three-gas breath test, which is not available in Germany—measures gases rather than identifying individual bacterial species. Conversely, finding a particular bacterium alone establishes neither an H₂S-SIBO diagnosis nor a reason for treatment with rifaximin. Diagnosis and treatment therefore involve different levels of assessment.
3. How can hydrogen sulfide SIBO be investigated?
A conventional hydrogen and methane breath test cannot directly detect H₂S. A method that explicitly measures hydrogen sulfide is required.
What does a three-gas breath test such as the Trio-SmartTM test measure?
A three-gas breath test measures hydrogen (H₂), methane (CH₄) and hydrogen sulfide (H₂S) in exhaled breath. One example is the Trio-SmartTM test. The additional H₂S measurement may provide evidence of elevated intestinal hydrogen sulfide production that a conventional two-gas breath test cannot directly detect.
However, this test does not directly identify Desulfovibrio, Bilophila wadsworthia or Proteus mirabilis. Elevated breath H₂S levels alone also cannot reliably determine how much of the gas originated in the small intestine versus the large intestine. Questions concerning thresholds, standardization and clinical interpretation remain unresolved.
Before being tested in Germany, ask which gases the medical practice or laboratory actually analyzes and whether H₂S measurement is offered. The term “SIBO breath test” alone does not indicate whether hydrogen sulfide is included.
Can a flatline on a breath test suggest H₂S production?
When hydrogen and methane values remain consistently low throughout a breath test, this is often called a “flatline.” One possible explanation is that certain microorganisms consume hydrogen to produce hydrogen sulfide.
A flatline may be a reason to consider increased H₂S production as a possible explanation. However, it cannot reliably establish hydrogen sulfide SIBO. A conventional hydrogen and methane breath test does not measure H₂S directly.
Intestinal transit, test preparation and other factors can also affect the result. A flatline should therefore be evaluated by a physician together with symptoms and other diagnostic findings. It is too simplistic to assume that lactulose must reach the large intestine after exactly 120 minutes in everyone. The absence of a gas increase after 180 minutes does not prove that H₂S-producing bacteria in the small intestine have already broken down the test solution. Slow intestinal transit is also possible, meaning the lactulose may not yet have reached the large intestine.
Are symptoms or stool tests sufficient for a diagnosis?
No. Diarrhea, gas and abdominal pain have many potential causes. A rotten-egg smell does not reliably indicate where in the intestine the gas originated. A stool sample also cannot directly reveal bacterial colonization of the small intestine. Stool testing therefore does not replace reliable evidence of small intestinal bacterial overgrowth.
4. What does hydrogen sulfide do in the gastrointestinal tract?
Hydrogen sulfide is not inherently harmful. Along with nitric oxide and carbon monoxide, it belongs to a group of gaseous signaling molecules called gasotransmitters. These gases help cells communicate with one another.
In the gastrointestinal tract, H₂S is involved in:
- regulating intestinal motility,
- the function of the mucosal barrier,
- the processing of pain signals,
- inflammation and protective mechanisms in tissues.
Its effects depend, among other things, on its concentration, where it is produced and how it is broken down. Experimental studies show both protective and harmful effects. These findings cannot directly establish what amount of H₂S causes symptoms in a particular individual. However, H₂S can contribute to inflammation and is suspected of promoting colorectal cancer.
5. Could hydrogen sulfide SIBO be linked to brain fog?
A connection between intestinal H₂S overproduction and brain fog has been described in clinical observations. However, a direct causal relationship has not yet been sufficiently established.
What role does the gut–brain axis play?
The gut, microbiome and brain communicate through various pathways, including the nervous and immune systems and microbial metabolic products. These interactions are referred to as the microbiota–gut–brain axis. Research in this field helps explain possible links between intestinal processes and brain function. However, it remains unclear whether H₂S-SIBO directly causes brain fog through gases absorbed into the bloodstream or through neuroinflammation.
6. What helps when hydrogen sulfide SIBO is suspected?
The first step is to determine which explanation for the symptoms best fits the overall findings. This includes looking for contributing factors such as impaired intestinal motility or anatomical changes after surgery. Treatment should not be based on a suspected gas profile alone.
6.1 What roles do rifaximin and bismuth play in H₂S-SIBO?
Rifaximin is an antibiotic that acts mainly in the intestine and is used for SIBO. There are no sufficiently validated, standardized protocols for specifically treating H₂S overproduction. Findings from SIBO in general cannot automatically be applied to this situation. In international treatment discussions, bismuth—particularly bismuth subsalicylate—is also considered as a possible H₂S binder or “sulfide binder.” Bismuth can bind sulfide in a poorly soluble form. An older human study found a marked reduction in H₂S released from stool samples following bismuth subsalicylate use. However, this is not sufficient proof that it reliably treats or eliminates H₂S-SIBO. There are also no sufficiently validated, standardized protocols specifically for combining bismuth with rifaximin in H₂S-SIBO.
Single-ingredient bismuth products are not officially available in Germany and are not appropriate for unsupervised self-treatment. With bismuth subsalicylate in particular, contraindications and drug interactions must be considered, including salicylate allergy or the use of anticoagulant medications. Whether such a preparation is appropriate should be carefully assessed by a physician.
6.2 Can a low-FODMAP diet relieve symptoms?
A low-FODMAP diet reduces certain fermentable carbohydrates and sugar alcohols. It may relieve symptoms such as bloating, particularly in people with IBS. The strict elimination phase is not intended to be a permanent diet. Foods are then gradually reintroduced to assess individual tolerance. Support from a qualified nutrition professional can help prevent unnecessary restrictions.
6.3 Is a low-sulfur diet useful for H₂S-SIBO?
Temporarily reducing dietary sulfur is being discussed as a complementary approach. The rationale is that certain gut bacteria can use sulfur-containing compounds to produce H₂S.
A low-FODMAP diet and a low-sulfur diet are not the same. For example, intolerance to garlic or onions does not necessarily indicate a problem with sulfur: both also contain fermentable carbohydrates. Blanket lists of forbidden foods can therefore be misleading.
How can dietary changes be evaluated systematically?
- Keep a record of symptoms and foods eaten.
- Make changes one at a time wherever possible, rather than all at once.
- Limit restrictions in time and review their effects.
- Reintroduce foods whenever possible.
- Ensure adequate calories, protein and other nutrients.
6.4 Do probiotics and prebiotics help?
The evidence on probiotics is inconsistent and does not support a blanket recommendation for specific products, although there are some indications of potential benefit. Prebiotics should likewise not automatically be used as a necessary way to “rebuild gut flora”; they should be appropriate to the individual treatment situation.
7. Glossary: key terms
Understanding Hydrogen Sulfide and SIBO
- SIBO
- “Small Intestinal Bacterial Overgrowth”: excessive bacterial colonization of the small intestine that causes symptoms.
- Dysbiosis
- A change in the composition or function of a microbial community that may be associated with health problems.
- Gasotransmitter
- A gaseous signaling molecule that helps transmit signals between cells.
- Hydrogen sulfide (H₂S)
- A gas that can be produced by certain microorganisms and by cells in the human body.
- Archaea
- A distinct group of microorganisms that differ from bacteria. Some archaea produce methane.
- IMO
- “Intestinal Methanogen Overgrowth”: excessive growth of methane-producing microorganisms in the intestine.
- ISO
- “Intestinal Sulfide Overproduction”: a newer term for excessive intestinal sulfide production.
- Desulfovibrio
- A bacterial genus that includes sulfate-reducing and H₂S-producing species.
- Bilophila wadsworthia
- A gut bacterium that can produce hydrogen sulfide, among other pathways, by breaking down taurine via sulfite.
- Proteus mirabilis
- An H₂S-producing bacterial species. Recent studies of the small intestine show associations with elevated breath H₂S levels.
- Lactulose breath test
- An indirect test that measures certain gases in exhaled breath after a person drinks a lactulose solution.
- Three-gas breath test
- A breath test that measures hydrogen, methane and hydrogen sulfide. One example is the Trio-SmartTM test. It measures gases, not individual bacterial species.
- Rifaximin
- An antibiotic that acts primarily in the intestine and is used to treat SIBO. Its use must be assessed by a physician on an individual basis.
- Bismuth subsalicylate
- A bismuth compound discussed internationally as a possible sulfide binder in H₂S treatment. There is insufficient reliable evidence of efficacy specifically for H₂S-SIBO.
- FODMAP
- A collective term for certain fermentable carbohydrates and sugar alcohols.
- Gut–brain axis
- Two-way communication between the gut and brain, including via nerves, the immune system and metabolic products.
8. Frequently Asked Questions About Hydrogen Sulfide SIBO
Why does gas smell like rotten eggs with hydrogen sulfide SIBO?
Hydrogen sulfide has a characteristic rotten-egg smell. Certain intestinal bacteria can produce this gas. The odor alone does not prove H₂S-SIBO and does not indicate whether the gas originated in the small or large intestine.
How is hydrogen sulfide SIBO related to brain fog?
A direct causal relationship has not yet been sufficiently established. The gut and brain communicate through the gut–brain axis, but concentration difficulties are not specific evidence of H₂S-SIBO.
Can a standard breath test detect hydrogen sulfide SIBO?
A standard hydrogen and methane breath test does not measure hydrogen sulfide. Additional H₂S measurement is required, as offered by a three-gas breath test. One example is the Trio-SmartTM test. A flatline on a conventional breath test may be a reason to consider increased H₂S production, but it is not enough for a diagnosis. Ask the medical practice or laboratory which gases are measured.
Which bacteria can produce hydrogen sulfide?
Intestinal H₂S-producing bacteria include species from the genus Desulfovibrio, Bilophila wadsworthia and Proteus mirabilis. They use different metabolic pathways. Finding them alone does not prove H₂S-SIBO; a breath test cannot identify these bacteria individually.
Do rifaximin or bismuth help with H₂S-SIBO?
Rifaximin is used for SIBO. Bismuth subsalicylate is discussed internationally as a possible H₂S binder. However, sufficiently validated, standardized protocols for specifically treating H₂S overproduction—including combining the two agents—are lacking. Treatment should not be undertaken without medical supervision and requires individual assessment.
Does a low-sulfur diet help with H₂S-SIBO?
A temporary reduction in dietary sulfur is discussed as an additional strategy. Its effectiveness specifically for H₂S-SIBO has not been sufficiently established. Restrictions should be time-limited, assessed individually and preferably supervised by a nutrition professional.
SIBO Academy® Newsletter
Get the latest updates from the world of SIBO delivered to your inbox for free.
Scientific References
Cryan, J. F., O’Riordan, K. J., Cowan, C. S. M., Sandhu, K. V., Bastiaanssen, T. F. S., Boehme, M., Codagnone, M. G., Cussotto, S., Fulling, C., Golubeva, A. V., Guzzetta, K. E., Jaggar, M., Long-Smith, C. M., Lyte, M., Martin, J. A., Molinero-Perez, A., Moloney, G., Morelli, E., Morillas, E., . . . Dinan, T. G. (2019). The microbiota-gut-brain axis. Physiological Reviews, 99(4), 1877–2013. DOI: 10.1152/physrev.00018.2018
Damianos, J. A., Matar, A., & Halawi, H. (2025). Gas-tly interpretations: A case-based approach to the nuances of SIBO breath testing. Current Gastroenterology Reports, 27, Article 30. DOI: 10.1007/s11894-025-00977-5
Hammer, H. F., Fox, M. R., Keller, J., Salvatore, S., Basilisco, G., Hammer, J., Lopetuso, L., Benninga, M., Borrelli, O., Dumitrascu, D., Hauser, B., Herszenyi, L., Nakov, R., Pohl, D., Thapar, N., Sonyi, M., & European H2-CH4-breath test group. (2022). European guideline on indications, performance, and clinical impact of hydrogen and methane breath tests in adult and pediatric patients: European Association for Gastroenterology, Endoscopy and Nutrition, European Society of Neurogastroenterology and Motility, and European Society for Paediatric Gastroenterology Hepatology and Nutrition consensus. United European Gastroenterology Journal, 10(1), 15–40. DOI: 10.1002/ueg2.12133
Kashyap, P., Moayyedi, P., Quigley, E. M. M., Simren, M., & Vanner, S. (2024). Critical appraisal of the SIBO hypothesis and breath testing: A clinical practice update endorsed by the European Society of Neurogastroenterology and Motility (ESNM) and the American Neurogastroenterology and Motility Society (ANMS). Neurogastroenterology & Motility, 36(6), Article e14817. DOI: 10.1111/nmo.14817
Lacy, B. E., Pimentel, M., Brenner, D. M., Chey, W. D., Keefer, L. A., Long, M. D., & Moshiree, B. (2021). ACG clinical guideline: Management of irritable bowel syndrome. The American Journal of Gastroenterology, 116(1), 17–44. DOI: 10.14309/ajg.0000000000001036
Peck, S. C., Denger, K., Burrichter, A., Irwin, S. M., Balskus, E. P., & Schleheck, D. (2019). A glycyl radical enzyme enables hydrogen sulfide production by the human intestinal bacterium Bilophila wadsworthia. Proceedings of the National Academy of Sciences, 116(8), 3171–3176. DOI: 10.1073/pnas.1815661116
Pimentel, M., Saad, R. J., Long, M. D., & Rao, S. S. C. (2020). ACG clinical guideline: Small intestinal bacterial overgrowth. The American Journal of Gastroenterology, 115(2), 165–178. DOI: 10.14309/ajg.0000000000000501
Singh, S. B., & Lin, H. C. (2015). Hydrogen sulfide in physiology and diseases of the digestive tract. Microorganisms, 3(4), 866–889. DOI: 10.3390/microorganisms3040866
Suarez, F. L., Furne, J. K., Springfield, J., & Levitt, M. D. (1998). Bismuth subsalicylate markedly decreases hydrogen sulfide release in the human colon. Gastroenterology, 114(5), 923–929. DOI: 10.1016/S0016-5085(98)70311-7
Villanueva-Millan, M. J., Leite, G., Mathur, R., Rezaie, A., Moreno Fajardo, C., de Freitas Germano, J., Morales, W., Sanchez, M., Rivera, I., Parodi, G., Weitsman, S., Rashid, M., Hosseini, A., Brimberry, D., Barlow, G. M., & Pimentel, M. (2025). Hydrogen sulfide and methane on breath test correlate with human small intestinal hydrogen sulfide producers and methanogens. Digestive Diseases and Sciences, 70(11), 3846–3856. DOI: 10.1007/s10620-025-09156-y
