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Chlamydiae are obligate intracellular pathogens which cause infections associated with a broad range of diseases in both livestock and humans. Epidemiologically persistently clinically inapparent infected animals are of particular importance. As a result of persistent infection these animals become a reservoir of pathogens for other animals, shedding these potential zoonotic pathogens. It is therefore of utmost importance to definitive diagnose infection on a species-specific level and to decrease the chlamydial load of these animals. The aim of this study was to examine the gut as a habitat of Chlamydiae utilizing conventional as well as modern molecular tools for determination of possible latent chlamydial infection. Cell cultures were used for cultivation of Chlamydiae from faeces or mucosal samples from swine. Species-specific polymerase chain reactions (PCR) were applied on samples from ileum, colon and faeces. To confirm active infection, immunhistochemistry (IHC) and fluorescence-in-situ-hybridisation (FISH) procedures were carried out with samples from the small and large intestines. In the course of the FISH examinations, a hierarchic oligonucleotide probe set was applied for the first time on tissue to demonstrate intestinal chlamydial infection. Reason of systematic examination was to performe a study comparing the efficacy of feeding with a probiotic strain of Enterococcus faecium NCIMB 10415 on the rate of natural infection of Chlamydiae in gut of swine. To determine this, we performed a study comparing two groups of animals, one that was fed with Enterococcus faecium (probiotic group) and one that did not receive probiotics (control group). Initially the carrier status of sows (n = 22) was determined in both feeding groups, then the piglets of Chlamydia-positive sows were examined systematically for carry-over infections and potential differences between these two groups. Therefore 4 piglets from each of five Chlamydia- positive sows (n=20 piglets) from either the control or probiotic group were examined for the frequency of Chlamydia at ages of 14, 21, 35 and 56 days post partum. In the examined population of conventional sows a high rate of latent Chlamydia suis infection could be determined. A clear difference in infection rate in the comparison of both groups could be detected. 85% (17/20) of the piglets from the control group were found to be Chlamydiae-positive by PCR, whereas Chlamydiae were found in only 60% (12/20) of piglets from the probiotic group. These results were confirmed by a higher infection rate of ileal and colon tissues by FISH and immuno¬histology. In addition to the reduced frequency of Chlamydiae-positive piglets in the probiotic group, the time point of infection was also delayed. Cell cultivation was not found to be a reliable diagnostic method for determining latent chlamydial infection of pig gut. The elabaated species-specific nested-PCR with detection limit of <1 IFU/ml was the most sensitive technique. The comparison of techniques for in- situ detection of Chlamydiae showed that IHC and FISH could be considered equivalent with regard to identification frequency. The advantage of FISH in comparison to IHC was the possibility to acquire a species-specific diagnosis using the developed hierarchic probe set.