The concentration of the antibiotic is diluted by food in the stomach, versus taking it “straight up”–this avoids irritation. Think of it like using bleach in your washing machine: diluting it into the washer water, then washing the clothes is a lot less destructive than merely *pouring* the bleach directly onto the clothing.
Also, taking it with food means a steady release of the antibiotic into your system, rather than a quick, concentrated dose. Nowadays, we have time release capsules that dissolve in stomach acid at a slow rate to do the same thing, but depending on the medicine, eating with it is more effective.
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