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Fermented foods contain various beneficial microorganisms. Lactic acid bacteria (LAB) including Lactobacillus, Bifidobacterium, and Pediococcus are most popular microorganisms in fermented foods. Theses bacteria exist in gastrointestinal (GI) tract and affect digestion system maintaining microorganism balance. In this study, we investigated the effect of LAB culture extracts on the nematode Caenorhabditis elegans focusing on host animals’ digestion system. In order to verify whether the small molecules or metabolites produced by LAB are beneficial for host animals’ digestion system, the extracellular extract was administered into C. elegans together with their food bacteria, E. coli. As a result, extracellular non-protein part of extracts significantly reduced the indigestion of foods in intestine and improved the defecation. Enhanced digestion and defecation increased the body growth of adult animals and improved the survival ratio of middle-aged adults. We have also found that LAB extracts inhibited the growth of E. coli when the extract was added to the culture of E. coli. These results demonstrate that LAB extracts have a great potential as health beneficial supplements by improving digestion and killing harmful bacteria in GI tract.