Aims This study aimed to determine whether host-adapted lactobacilli exhibit superior survival during intestinal transit relative to nomadic and free-living organisms, and to characterize the impact of probiotic lactobacilli on autochthonous lactobacilli. Methods and Results Mixed cultures of Lactobacillus casei K9-1 and Lactobacillus fermentum K9-2, or reutericyclin producing Lactobacillus reuteri and its isogenic mutant were fed to piglets as freeze-dried culture, or as part of fermented feed. Lactobacilli in digesta and faecal samples were quantified by strain-specific quantitative PCR (qPCR), high-resolution-melting curve qPCR, and high-throughput sequencing of 16S rRNA gene sequence tags. The abundance of the host adapted L. reuteri in digesta and faeces was higher (P < 0 center dot 05) when compared to L. casei or L. fermentum. Feed fermentation or chemical acidification of feed reduced (P < 0 center dot 05) cell counts of Lactobacillus salivarius in colonic digesta. The reutericyclin producing L. reuteri TMW1.656 transiently reduced (P < 0 center dot 05) the faecal abundance of lactobacilli. However, the overall impact of probiotic intervention on autochthonous lactobacilli was minor. Conclusions The vertebrate host-adapted L. reuteri survives better during intestinal transit of piglets compared to L. casei and L. fermentum. Significance and Impact of the Study Ecology and lifestyle of Lactobacillus strains may be suitable criteria for selection of probiotic strains for use in swine production.