How does foodborne illness effect the digestion?

Slows or prevents. Two types of illness: intoxication- a preformed toxin affects your gut. Infection- organism in food actually infects lining of gut. Both result in temporary disruption of ability to digest food and absorb nutrients. Most 1st world illness is short lived and mild. Some can be severe. Persistent symptoms, elderly, recent antibiotics, severe abd pain or blood in stool should prompt eval.
Commonest. There are many forms of foodborne illness but the commonest is traveler's diarrhea which generally causes diarrhea and nausea. Appetite is impaired during acute illness and, with it, digestion.