Aims: To investigate which specific bacterial species that were stimulated or inhibited in the proximal colon of pigs when a fructan-rich diet was compared with a diet that contained resistant carbohydrates. The study focussed especially on Bifidobacterial species by using a noncultureable approach. Methods and Results: Terminal restriction fragment length polymorphism (T-RFLP) was used to describe differences in the total colonic microbiota as well as in the populations of Bifidobacterium spp. in pigs fed with a fructan-rich diet and a diet containing resistant carbohydrates. The fructan-rich diet has previously been shown to prevent swine dysentery caused by Brachyspira hyodysenteriae. The T-RFLP profiling, 16S rRNA gene cloning and in situ hybridization showed that the pigs fed with the fructan-rich diet had a higher proportion of Bifidobacterium thermacidophilum subsp. porcinum and Megasphaera elsdenii. Conclusions: These findings suggested that the bacterial fructan fermentation occurring in the porcine colon might be cross-feeding of lactate produced by B. thermacidophilum and used by M. elsdenii. Significance and Impact of the Study: B. thermacidophilum and M. elsdenii may be the course of the inhibition of the pathogenic bacteria Brach. hyodysenteriae in colon of pigs when they are fed fructan-rich diets.