The colon: salvage absorption, gut bacteria, gas and stool
- Concept
- Exam priority: medium
The colon dries the stool, its bacteria ferment fibre into fuel and gas, and bile pigments turned brown by bacteria give stool its colour.
Also called: Short-chain fatty acids, Flatus, Stool colour
See it in 3D: Cecum · Ascending colon · Transverse colon · Sigmoid colon
What it is
The colon reclaims most of the water and salt that reach it and houses the densest bacterial community in the body. Bacteria ferment undigested carbohydrate into short-chain fatty acids and gas, make vitamin K and transform bile acids and bilirubin. What is left, plus dead bacteria and shed cells, is the stool.
Key facts
- The proximal colon (cecum, ascending) does most of the absorbing; the distal colon and rectum mainly store and propel.
- Colonic bacteria number around 10¹¹ per gram of content, mostly strict anaerobes; they also deconjugate bile acids and turn primary into secondary bile acids.
- Bacterial urease and amino acid breakdown release ammonia, which enters portal blood; a failing liver cannot clear it (hepatic encephalopathy).
- Lactulose is fermented to acids that lower colonic pH, trapping ammonia as NH₄⁺; rifaximin lowers the bacterial load that makes ammonia.
- Gas comes from swallowed air (N₂, O₂), bacterial fermentation (H₂, CO₂ and, in some people, CH₄) and diffusion from blood; most colonic gas is absorbed, a smaller part is passed as flatus.
- Odour comes from bacterial products such as indole, skatole, thiols and hydrogen sulfide, not from the main gases, which are odourless.
How it works, step by step
- Ileal effluent, still liquid, enters the cecum through the ileocecal valve.
- Colonocytes absorb Na⁺ through apical channels and exchangers; Cl⁻ follows and water follows osmotically through tight epithelium.
- Bacteria ferment fibre and resistant starch into SCFAs; colonocytes absorb SCFAs with Na⁺ and burn butyrate for energy.
- Fermentation also releases H₂ and CO₂; some bacteria use H₂ to make methane or sulfide.
- Bilirubin glucuronide from bile is deconjugated and reduced to urobilinogen; part is reabsorbed and leaves in urine, the rest oxidizes to brown stercobilin.
- Slow mixing movements in the proximal colon extend contact time, so the stool becomes semisolid by the transverse colon.
Approximate values (healthy adult on a mixed diet)
| Parameter | Value | Note |
|---|---|---|
| Fluid entering the colon | ≈ 1–1.5 L/day | |
| Water lost in stool | ≈ 100–200 mL/day | |
| Maximum colonic absorption | several L/day | beyond it, diarrhea |
| Stool water content | ≈ 75% | solids ≈ 25% |
| Bacteria in stool solids | ≈ one third or more of dry weight | |
| Flatus passed | ≈ 0.5–1.5 L/day | rises with fermentable sugars |
Approximate values for a healthy adult at rest; each laboratory sets its own ranges.
Stool colour and what it tells you
| Colour | Cause | Typical setting |
|---|---|---|
| Brown | Stercobilin from bilirubin | Normal |
| Pale, clay-coloured | No bile pigment reaches the gut | Biliary obstruction, cholestasis |
| Black, tarry | Blood digested to hematin | Upper GI bleeding (melena); also iron or bismuth |
| Bright red | Fresh blood | Lower GI bleeding, hemorrhoids |
| Green | Biliverdin not yet reduced | Fast transit, diarrhea |
| Greasy, pale, floating | Unabsorbed fat (steatorrhea) | Pancreatic insufficiency, celiac disease |
Clinical notes
- Lactose intolerance: lactose reaches the colon, is fermented to gas and acids and draws water in, causing bloating, flatus and osmotic diarrhea.
- Secretory or high-volume diarrhea removes K⁺ and HCO₃⁻, producing hypokalemia and a normal-anion-gap acidosis.
- Simethicone does not reduce gas production; it lowers surface tension so small bubbles merge and pass more easily.
- Neonates have a sterile gut at birth and low vitamin K stores, one reason newborns receive vitamin K.
Test yourself
Think of the answer, then tap the question to see it.
Why does prolonged diarrhea cause a normal-anion-gap metabolic acidosis and hypokalemia?
Colonic and intestinal fluid is rich in HCO₃⁻ and K⁺; losing it removes base (Cl⁻ is retained, so the gap stays normal) and potassium.
What is the main energy source of colonocytes, and where does it come from?
Butyrate, a short-chain fatty acid made when colonic bacteria ferment dietary fibre and resistant starch.
Why does stool become pale or clay-coloured in complete bile duct obstruction?
No bilirubin reaches the gut, so bacteria cannot make urobilinogen and stercobilin, the pigments that make stool brown; urine urobilinogen also falls.
What is the physiological basis of the hydrogen breath test for lactose intolerance?
Undigested lactose reaches colonic bacteria, which ferment it to H₂; H₂ is absorbed into blood and exhaled, so breath H₂ rises after a lactose load.
How does lactulose lower blood ammonia in hepatic encephalopathy?
Bacteria ferment it to acids that lower colonic pH, so NH₃ is trapped as NH₄⁺ and lost in stool; it also speeds transit and shifts the flora away from ammonia producers.
Connections
See it in 3D4
The structures of Durgical's 3D anatomy where it happens.
In Biochemistry3
In Pharmacology3
Educational physiology content; not a diagnostic or treatment guide and no substitute for a health professional's advice. Values are approximate references. No doses are given.
Sources: Gas | Flatulence | Burp | MedlinePlus (MedlinePlus, US National Library of Medicine, 2025); Lactose intolerance: MedlinePlus Medical Encyclopedia (MedlinePlus, US National Library of Medicine, 2025); Stools - pale or clay-colored: MedlinePlus Medical Encyclopedia (MedlinePlus, US National Library of Medicine, 2025); Irritable Bowel Syndrome (StatPearls (NCBI Bookshelf), 2025).
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Representative model, for educational purposes only.