Mikrobiom & Darmflora: the pathway in the body

Mikrobiom & Darmflora is part of the pathway “Gut microbiome”. This page shows the whole pathway; the station of Mikrobiom & Darmflora is highlighted.

Where this laboratory value sits: List of taxa — matched against a database. The sequences are read and compared with a database. This yields a list of the groups found and how often they occur — depending on the section, down to genus, rarely to species. Source 1

In brief

The gut microbiome is the community of bacteria in the large intestine. They ferment dietary fibre, which human enzymes cannot break down, into short-chain fatty acids such as acetate, propionate and butyrate.

The pathway step by step

1. Stool sample → Bacterial DNA Cell lysis In the laboratory, the cell walls are broken open and the DNA is extracted. How well this works for tough cell walls already affects the result at this stage. Source 1
2. Bacterial DNA → 16S rRNA gene Polymerase (PCR) · Primer One gene occurs in all bacteria and yet differs between species: the 16S rRNA gene. A polymerase amplifies a section of it. Source 1
3. 16S rRNA gene → List of taxa Sequencing The sequences are read and compared with a database. This yields a list of the groups found and how often they occur — depending on the section, down to genus, rarely to species. Source 1
4. List of taxa → Shannon index Calculation The Shannon index combines two things in one number: how many groups are present and how evenly they are distributed. It describes a sample; it does not rate it. Source 2
5. List of taxa → Dysbiosis index Calculation A dysbiosis index compares the pattern of selected bacterial groups with that of a reference group and expresses the distance as a number. Which groups are included is set by each laboratory. Source 3
6. Dietary fibre → Short-chain fatty acids Bacterial enzymes Bacteria ferment the fibre without oxygen. This mainly produces three short-chain fatty acids: acetate, propionate and butyrate. Source 4, 5
7. Short-chain fatty acids → Butyrate Butyrate is formed mainly by bacteria of the genera Faecalibacterium and Roseburia, usually from two acetyl-CoA building blocks. Source 5
8. Short-chain fatty acids → Propionate Propionate arises by several routes, for example via succinate. It reaches the liver through the portal vein and serves there as a building block for new glucose. Source 5, 4
9. Short-chain fatty acids → Acetate Acetate is the most abundant of the three fatty acids. It enters the blood and is used in tissues as a fuel and as a building block. Source 4
10. Butyrate → Energy for colon cells β-oxidation · NAD⁺ The cells of the colon lining burn butyrate in their mitochondria; it is their main source of energy. The oxygen used in the process keeps the gut contents low in oxygen. Source 6
11. Propionate → FFAR2/3 receptors Acetate and propionate bind to the receptors FFAR2 and FFAR3 on gut cells, immune cells and nerve endings. Through them, information about what is fermented in the gut reaches the rest of the body. Source 7
12. Acetate → FFAR2/3 receptors Acetate and propionate bind to the receptors FFAR2 and FFAR3 on gut cells, immune cells and nerve endings. Through them, information about what is fermented in the gut reaches the rest of the body. Source 7

Cofactors in this pathway

• Coenzyme A — Butyrate is built from two acetyl-CoA units; the intermediates are bound to CoA Source 5
• Acetate — Taken up by a CoA transferase during the formation of butyrate Source 5
• Vitamin B12 — Cofactor of methylmalonyl-CoA mutase in the succinate route to propionate Source 8
• NAD⁺ — Accepts hydrogen when butyrate is broken down in the gut cells Source 6In the ORY catalogue as a laboratory value: NAD⁺ (Nicotinamidadenindinukleotid)

Sources

1. Johnson JS, Spakowicz DJ et al. Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis. Nat Commun 2019 · PubMed 31695033
2. Kers JG, Saccenti E. The Power of Microbiome Studies: Some Considerations on Which Alpha and Beta Metrics to Use and How to Report Results. Front Microbiol 2021 · PubMed 35310396
3. Casén C, Vebø HC et al. Deviations in human gut microbiota: a novel diagnostic test for determining dysbiosis in patients with IBS or IBD. Aliment Pharmacol Ther 2015 · PubMed 25973666
4. Koh A, De Vadder F et al. From Dietary Fiber to Host Physiology: Short-Chain Fatty Acids as Key Bacterial Metabolites. Cell 2016 · PubMed 27259147
5. Louis P, Flint HJ. Formation of propionate and butyrate by the human colonic microbiota. Environ Microbiol 2017 · PubMed 27928878
6. Donohoe DR, Garge N et al. The microbiome and butyrate regulate energy metabolism and autophagy in the mammalian colon. Cell Metab 2011 · PubMed 21531334
7. Kimura I, Ichimura A et al. Free Fatty Acid Receptors in Health and Disease. Physiol Rev 2020 · PubMed 31487233
8. Degnan PH, Taga ME, Goodman AL. Vitamin B12 as a modulator of gut microbial ecology. Cell Metab 2014 · PubMed 25440056

Whole pathway: Gut microbiome

Related pathways

• Gut bacteria — dietary fibre
• Fructose absorption — short-chain fatty acids
• Gut fermentation and breath gases — short-chain fatty acids
• Lactose digestion — short-chain fatty acids

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