In this contribution compositional shifts of intestinal bacterial communities in response to different nutritional factors (enzymes, probiotics, rare earth elements) are reported, as determined with nucleic acid based methods, i.e. 16S RNA probes, denaturing gradient gel electrophoresis, Real-time PCR, Multiplex PCR. These techniques enabled the detection of a promotion of jejunal L. reuteri activity by xylanase as well as a reduction of the E. faecalis/E. faecium ratio and frequency of potentially pathogenic E. coli in piglets by probiotic supplementation. While the probotic altered the faecal microbiota of sows, an influence of REE on species composition in faeces of weaned piglets was not detectable by DGGE.