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Two probiotics of different ecological origin, Enterococcus faecium NCIMB 10415 and Bacillus cereus var. toyoi, were chosen as model organisms. Feed for sows during gestation/lactation and for piglets pre-/postweaning was supplemented with either of these probiotics. Furthermore, to evaluate the effect of different starting points of E. faecium NCIMB 10415 initiations the probiotic was administered to piglets from birth onwards or just postweaning. Here we report the impact of these variants on probiotic distribution in the gut, on the gut microbiota, on diarrhea and on performance. If fed to sows and piglets, both probiotic strains were detected immediately after the start of the supplementation in feces of sows and piglets. The vertical transfer of both probiotic strains with sow feces to piglets could be demonstrated already before suckling piglets had access to the supplemented diets. Both probiotics were recovered from all intestinal segments of piglets. The dominant autochthonous microbiota of young piglets as revealed by denaturing gradient gel electrophoresis was more similar within than between treatment groups (control vs. probiotic). Both probiotics reduced the incidence of postweaning diarrhea (p < 0.05). For the E. faecium probiotic the relative magnitude of this effect was largely independent of dietary probiotic concentration or starting time of supplementation. Significant overall influence on piglet performance was observed only with the B. cereus probiotic.