Hydrogen sulfide and methane: the other gases in the gut

Healthy state

When bacteria ferment carbohydrates, hydrogen is produced. It is the raw material for two other groups of microbes. Methane-producing archaea, in humans mainly Methanobrevibacter smithii, turn hydrogen and carbon dioxide into methane. Archaea are not bacteria but a separate group of single-celled organisms. Sulfur-using bacteria such as Desulfovibrio or Bilophila wadsworthia produce hydrogen sulfide, the gas that smells of rotten eggs.

At first, this is normal. 30 to 50 percent of healthy adults breathe out measurable methane. Because methane producers and sulfur users consume hydrogen, they influence how much of it shows up on a breath test Breath test After drinking a sugar solution, hydrogen and methane in the breath are measured several times. This can reveal sugar intolerances and signs of bacterial overgrowth. More in the chapter “Gut tests: what they show and what they do not”.

Hydrogen sulfide belongs to normal gut life too. There is plenty of it in the large intestine, but most is bound. In small amounts, the cells of the gut lining can detoxify it and even use it for energy. In large amounts it blocks their cellular respiration.

The sulfur comes from sulfur-containing amino acids in protein, from sulfate and sulfite in foods, and from taurine attached to bile acids Bile acids Substances made by the liver that make fat digestible. About 95 percent are reabsorbed in the last part of the small intestine; gut bacteria transform the rest. More in the chapter “Bile acids: when bile causes diarrhoea”. When five men ate between 0 and 600 grams of meat a day for ten days, the sulfide content of their stool rose more than tenfold with the amount of meat. In people who ate only animal foods for five days, Bilophila wadsworthia increased. In mice, milk fat promoted exactly this bacterium via taurine-bound bile acids.

Methane has been measured in breath tests for years; from 10 ppm a test counts as methane-positive. The US guideline then speaks of intestinal methanogen overgrowth IMO (intestinal methanogen overgrowth) Too many methane-producing archaea in the gut, shown by methane of 10 ppm or more on a breath test. Often goes along with constipation. , IMO for short, instead of SIBO Small intestinal bacterial overgrowth (SIBO) Too many bacteria in the small intestine, where normally few live. Bloating and diarrhoea are typical; it is usually diagnosed with a breath test. More in the chapter “When the small intestine is too densely colonised”, because archaea are not bacteria and can also live in the large intestine. For some years there has also been a three-gas breath test for home use, sold in the US as trio-smart, that measures hydrogen sulfide too. The research group behind it calls raised values “intestinal sulfide overproduction”, ISO for short.

Disrupted state: causes and effects

Methane and constipation are linked. In a meta-analysis Meta-analysis An analysis that combines the results of several studies. It is only as good as the studies it includes. of nine studies with 1277 people, those with methane on the breath had about 3.5 times higher odds of constipation. In an experiment in dogs, methane fed directly into the small intestine slowed transit by an average of 59 percent. Whether methane causes constipation in humans, or whether a slow gut simply gives archaea more time to grow, is not yet proven. Probably both are true.

Hydrogen sulfide is linked to diarrhoea. In an analysis of 3004 home tests in the US, higher levels went along with more diarrhoea, urgency and abdominal pain. In small-bowel samples, higher levels came with more sulfide-producing bacteria, and in rats such bacteria made stool looser. This fits together, but it comes almost entirely from a single research group in Los Angeles that co-developed the test. Several authors hold shares in the manufacturing company or work there.

What a three-gas test cannot do: it does not show where in the gut the gas is produced. It has no independently set cut-off; in studies by the same group, sometimes 1.5 and sometimes 2 ppm counted as abnormal. The 2022 European breath-test guideline does not address hydrogen sulfide at all and states that even for hydrogen and methane the criteria for SIBO are neither confirmed nor uniformly accepted. An abnormal result is therefore a clue, not a diagnosis.

Experts also warn of overdiagnosis. A 2025 review concludes that SIBO and IMO are diagnosed too often, especially with the lactulose test, and advises using antibiotics very cautiously. Methane producers are part of the normal gut flora Microbiome, gut microbiota The community of all microbes in the gut, mainly bacteria, plus viruses, fungi and archaea. Most live in the colon. More in the chapter “Building microbial diversity” in many healthy people.

In forums, a “low-sulfur diet” is popular for hydrogen sulfide: no garlic, no onions, no cabbage, no eggs, little meat, often with molybdenum or bismuth added. We found no study of this diet in SIBO. It cuts out precisely many vegetables that the gut flora lives on and is hard to keep balanced. The opposite lever is more plausible: less red meat and saturated fat, and enough fibre.

Bismuth binds hydrogen sulfide. In 10 healthy people, bismuth subsalicylate taken for a few days cut its release in stool by more than 95 percent. This shows that bismuth binds the gas, not that it treats SIBO. With long-term use bismuth can build up in the body; case reports describe confusion, muscle jerks and unsteady gait after months to years of daily use. The salicylate it contains is related to aspirin.