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Interactions › Metabolites

What gut microbes eat and make

Most gut microbes live off each other. Some break down what you eat and what your body makes; others live on what those leave behind. Here’s the gut food web, with the microbes we hold at each step.

From genome analysis, lab tests and records: what microbes can do, not what they’re doing in you.

A group of microbes A metabolite Tap a group’s name to fold or open it; tap anything to follow it.
What reaches themBreakersWhat they leaveCross-feedersWhat’s left for you▾ Fibers and sugars · 30InulinFructooligosaccharides (FOS)FructanPectinXylanXylooligosaccharides (XOS)CelluloseHemicelluloseArabinogalactanArabinanGalactanStarchResistant starchGlycogenRaffinoseStachyoseSucroseLactoseMaltoseCellobioseTrehaloseMelibioseGlucoseFructoseGalactoseMannoseXyloseArabinoseRiboseRhamnose▾ From you · 6Gut mucusSialic acidFucoseN-acetylglucosamineN-acetylgalactosamineBile acids (from your liver)▾ Protein · 22ProteinTryptophanTyrosineHistidineGlutamateGlutamineArginineLeucineIsoleucineValinePhenylalanineCysteineMethionineLysineProlineSerineThreonineGlycineAlanineAspartateAsparagineOrnithine▾ Other food compounds · 1Choline▾ Left by fermentation · 7AcetateLactateSuccinateFormateHydrogenCarbon dioxideEthanol▾ Freed bile acids · 2Cholic acidChenodeoxycholic acid▾ Short-chain fatty acids · 5ButyratePropionateValerateIsobutyrateIsovalerate▾ Gases · 2MethaneHydrogen sulfide▾ Vitamins · 9Thiamine (B1)Riboflavin (B2)Niacin (B3)Pantothenate (B5)Vitamin B6Biotin (B7)Folate (B9)Vitamin B12Vitamin K2▾ Signals and others · 5IndoleGABAHistamineTyramineTMA▾ Reshaped bile acids · 3Deoxycholic acidLithocholic acidOxo- and epi- bile acidsFiber and sugar breakers495 speciesMucus foragers14 speciesProtein fermenters54 speciesBile acid freers67 speciesTMA makers9 speciesButyrate makers118 speciesPropionate makers132 speciesHydrogen users27 speciesBile acid reshapers26 speciesVitamin makers37 species
Tap a group or a metabolite to follow it
Every metabolite

A to Z, by group

Fibers and sugars

From you

Protein

Other food compounds

Left by fermentation

Freed bile acids

Short-chain fatty acids

Gases

Vitamins

Signals and others

  • GABA 22 can make · 6 can eat
  • Histamine 1 can make · 2 can eat
  • Indole 89 can make · 5 can eat
  • TMA 12 can make · 0 can eat
  • Tyramine 6 can make · 1 can eat

Reshaped bile acids

Groups of microbes

Who does what

  • Fiber and sugar breakers 495 species Break down fiber and starch our own enzymes can’t, and ferment the sugars. All 495 species →
  • Mucus foragers 14 species Live on the mucus your gut lining keeps making. All 14 species →
  • Protein fermenters 54 species Ferment protein and amino acids that reach the colon. All 54 species →
  • Bile acid freers 67 species Unhook bile acids from the amino acids the liver attaches to them. All 67 species →
  • TMA makers 9 species Make TMA from choline and carnitine. All 9 species →
  • Butyrate makers 118 species Turn acetate, lactate and sugars into butyrate. All 118 species →
  • Propionate makers 132 species Turn succinate or lactate into propionate. All 132 species →
  • Hydrogen users 27 species Use hydrogen, formate and carbon dioxide, making methane, hydrogen sulfide or acetate.
  • Bile acid reshapers 26 species Reshape freed bile acids; a few make secondary bile acids. All 26 species →
  • Vitamin makers 37 species Make B vitamins and vitamin K2. All 37 species →
Its limits

What the food web can’t tell you

  • Can, not does. A microbe that can make butyrate may not be making it in a gut today; what reaches it and who it lives with decide.
  • Groups overlap. Many species do several of these, so they sit in more than one group.
  • Common compounds don’t make neighbors. Acetate and hydrogen are made and used by most gut microbes; sharing them alone doesn’t mean two species interact.
  • Nothing here says a group or a compound is good or bad for you.