effects of host genetics and environmental conditions on fecal microbiota composition of pigs since microbiota may influence the physiology of its host including body weight increase growth rate or feed intake in this study we determined the microbiota composition in high or low residual feed intake hrfi and lrfi pig lines of different age andor subjected to sanitary stress by sequencing the v3v4 variable region of 16s rrna genes allisonella megasphaera mitsuokella acidaminococcus all belonging to firmicutesclass negativicutes lactobacillus faecalibacterium catenibacterium butyrivibrio erysipelotrichaceae holdemania olsenella and collinsella were more abundant in hrfi pigs on the other hand 26 genera including bacteroides clostridium sensu stricto oscillibacter paludibacter elusimicrobium bilophila pyramidobacter and tm7 genera and clostridium xi and clostridium xiva clusters were more abundant in lrfi than hrfi pigs adaptation of microbiota to new diet after weaning was slower in lrfi than in hrfi pigs sanitary stress was of relatively minor influence on pig microbiota composition in both tested lines although abundance of helicobacter increased in lrfi pigs subjected to stress selection for residual feed intake thus resulted in a selection of fecal microbiota of different composition however we cannot conclude whether residual feed intake was directly affected by different microbiota composition or whether the residual feed intake and microbiota composition are two independent consequences of yet unknown genetic traits differentially selected in the pigs of the two lines