Gut fermentation and breath gases: the pathway in the body

This page shows the biochemical pathway behind the laboratory value Hydrogen H₂ and methane CH₄ in exhaled air: which stations follow one another, which enzymes carry out each step and which cofactors they use. Every statement has a source. The page describes general textbook knowledge and says nothing about any individual person.

In brief

Hydrogen (H₂) and methane (CH₄) are gases formed not by the human body but by microorganisms in the gut. They arise when bacteria break down undigested sugars without oxygen, and reach the exhaled air via the blood and lungs.

The pathway step by step

1. Starch and sugars → Simple sugars Amylase, lactase Pancreatic amylase breaks down starch. Enzymes on the brush border of the small intestine, including lactase, split the double sugars into simple sugars. Source 1
2. Simple sugars → Uptake into blood SGLT1, GLUT5 Transport proteins such as SGLT1 and GLUT5 move the simple sugars across the gut wall into the blood. Whatever is not absorbed here travels on. Source 1
3. Undigested sugars → Bacterial fermentation · Gut bacteria Bacteria break down the sugars without oxygen. This happens mainly in the colon; when more bacteria live in the small intestine, fermentation already starts there. Source 5, 4
4. Bacterial fermentation → Short-chain fatty acids Most fermentation ends in short-chain fatty acids. The gut lining absorbs them; butyrate serves as fuel for the gut cells themselves. Source 2
5. Bacterial fermentation → Hydrogen H₂ Hydrogenases Fermentation leaves spare electrons. Enzymes called hydrogenases release them as hydrogen gas – human cells themselves make no H₂. Source 3, 6
6. Hydrogen H₂ → Methane CH₄ Methyl-CoM reductase · Archaea, CO₂ Methane-producing archaea, such as Methanobrevibacter smithii, consume the hydrogen and combine it with CO₂ to form methane. Other bacteria use H₂ to make acetate or sulphide. Source 3, 6
7. Hydrogen H₂ → Gases in blood Part of both gases passes through the gut wall into the blood. The rest leaves the body as intestinal gas. Source 5
8. Methane CH₄ → Gases in blood Part of both gases passes through the gut wall into the blood. The rest leaves the body as intestinal gas. Source 5
9. Gases in blood → Exhaled air In the lungs, the gases pass into the exhaled air. The breath test measures H₂ and CH₄ at regular intervals after a defined portion of sugar. Source 4

Cofactors in this pathway

• Nickel — Metal in coenzyme F430 of methyl-CoM reductase, which archaea use to form methane Source 7
• Iron — Metal in the hydrogenases that bacteria use to release electrons as H₂ Source 6
• NAD⁺ — Electron carrier of fermentation; bacteria release part of the electrons from NADH as H₂ Source 6
• Sodium — Drives the SGLT1 transporter, which carries glucose and galactose into the gut cell Source 1In the ORY catalogue as a laboratory value: Natrium (intrazellulär)
• Calcium — Bound ion of alpha-amylase, which breaks down starch in the small intestine Source 8In the ORY catalogue as a laboratory value: Calcium (intrazellulär)
• Chloride — Bound ion near the active site of alpha-amylase Source 8

Sources

1. Drozdowski LA, Thomson AB. Intestinal sugar transport. World J Gastroenterol 2006 · PubMed 16586532
2. den Besten G, van Eunen K, Groen AK et al. The role of short-chain fatty acids in the interplay between diet, gut microbiota, and host energy metabolism. J Lipid Res 2013 · PubMed 23821742
3. Smith NW, Shorten PR, Altermann EH et al. Hydrogen cross-feeders of the human gastrointestinal tract. Gut Microbes 2019 · PubMed 30563420
4. Rezaie A, Buresi M, Lembo A et al. Hydrogen and Methane-Based Breath Testing in Gastrointestinal Disorders: The North American Consensus. Am J Gastroenterol 2017 · PubMed 28323273
5. Di Stefano M, Mengoli C, Bergonzi M et al. Hydrogen breath test and intestinal gas production. Eur Rev Med Pharmacol Sci 2013 · PubMed 24443066
6. Carbonero F, Benefiel AC, Gaskins HR. Contributions of the microbial hydrogen economy to colonic homeostasis. Nat Rev Gastroenterol Hepatol 2012 · PubMed 22585131
7. Thauer RK. Methyl (Alkyl)-Coenzyme M Reductases: Nickel F-430-Containing Enzymes Involved in Anaerobic Methane Formation and in Anaerobic Oxidation of Methane or of Short Chain Alkanes. Biochemistry 2019 · PubMed 30951290
8. Brayer GD, Luo Y, Withers SG. The structure of human pancreatic alpha-amylase at 1.8 A resolution and comparisons with related enzymes. Protein Sci 1995 · PubMed 8528071

Related pathways

• Fructose absorption — short-chain fatty acids
• Lactose digestion — short-chain fatty acids
• Gut microbiome — short-chain fatty acids
• Magnesium — Natrium (intrazellulär), Calcium (intrazellulär)
• Pancreatic elastase — Natrium (intrazellulär), Calcium (intrazellulär)

As of 2026-09-16. Draft written by Claude to schema v2; sources checked in PubMed; expert review pending
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