Vitamins and Nutrition

Why What You Eat Isn't What You Absorb

A nutrition label tells you what went into your mouth. It says nothing about what crossed the gut wall. Between those two points sits a bacterial community that makes some vitamins itself, competes with you for others, and changes the chemical conditions determining how much of a mineral dissolves well enough to be absorbed. That's why two people eating identical amounts of calcium can end up with different amounts in their bones, and why supplementing a deficiency sometimes fails to correct it.

Absorption, manufacture and competition

Minerals depend on chemistry the bacteria control. When gut bacteria ferment fibre they produce acids that lower the pH of the large intestine, and minerals dissolve more readily in acidic conditions. A randomised trial found a specific prebiotic fibre increased magnesium absorption by more than 9 percentage points against placebo. A year-long trial in more than 100 children found a prebiotic fibre increased calcium absorption and left a measurable difference in bone mineral content.

Vitamins split into ones bacteria make and ones they take. Gut bacteria produce vitamin B12 in quantity, but almost all of it is made in the large intestine, past the point where the body absorbs it, so the production is largely wasted. Bacteria also produce folate, which creates a diagnostic quirk. An overgrowth of bacteria in the small intestine can push folate levels artificially high, and doctors use that as a clue.

Iron works differently again. A meta-analysis of 8 trials found probiotics and prebiotics raised haemoglobin in people with anaemia. In inflammatory bowel disease, up to 60% of people develop anaemia, and much of it isn't caused by low iron intake at all but by inflammation blocking iron release from stores.

The strongest single result concerns malnutrition. A food designed specifically to repair gut bacteria outperformed a higher-calorie standard treatment for severely malnourished children, despite providing less energy.

Not everything holds. The largest trial testing vitamin D supplementation on the gut community, in more than 800 people followed for five years, found no change in overall composition.

Source: Effects of oligofructose-enriched inulin on intestinal absorption of calcium and magnesium and bone turnover markers

Source: A microbiome-directed therapeutic food for children recovering from severe acute malnutrition

Source: Efficacy of probiotic, prebiotic, and synbiotic supplements in individuals with anemia

What this means for you

Suspected deficiency should be confirmed with a blood test rather than guessed at, since symptoms overlap heavily and taking supplements you don't need carries its own risks. In addition, the research above shows fermentation in the large intestine measurably increasing how much calcium and magnesium gets absorbed, a food designed around gut bacteria outperforming a higher-calorie one in malnutrition, and at least one large trial finding no effect at all. A varied, plant-rich diet supports the same gut bacteria this research ties to better mineral absorption. That's the same idea behind GutLab, everyday gut health starts with regularly feeding the microbiome a broad range of plant-rich ingredients.

Explore nutrition topics on this page

The panels on this page cover three different relationships between bacteria and nutrients.

Calcium, magnesium, zinc and iodine concern absorption, where fermentation changes the chemical conditions in the gut. Vitamin B12, folate and vitamin D concern manufacture and the limits of it.

Iron deficiency, anaemia and malnutrition concern what happens when absorption fails or inflammation interferes, and malnutrition is where the evidence is strongest.

Use the panels on this page to find the one relevant to you.