The present invention relates to use of a fermented soy extract as a prebiotic composition to protect beneficial bacteria in the gastrointestinal tract of an animal. Particularly, the fermented soy extract of the invention exhibits the prebiotic activity even under an antibiotic treatment. Also disclosed is combined use of an antibiotic and the fermented soy extract of the invention, which has advantages over administration of the antibiotic alone, such as decreasing the effective dose of the antibiotic and/or reducing side effects resulting from the antibiotic treatment.
