Segmented filamentous bacteria (SFB) have been observed in the small intestine of many animals, in humans and in the intestinal content of trouts affected by diarrhea. Some papers report the nonpathogenic nature of these microorganisms, while other reports associate the occurrence of illness with the presence of SFB. Since SFB cannot be cultured in vitro, they do not have an official taxonomic name: only the provisional status Candidatus and the genus name Arthromitus. Molecular methods have facilitated studies on culture-independent microorganisms. Most of them are based on direct DNA extraction from samples and a subsequent study of 16S rRNA genes. Two couples of primers were designed for C. arthromitus detection by nested-PCR on DNA extracted from the gut of trouts. Another method was set up to detect Candidatus Arthromitus using a specific probe labeled with digoxigenin. The probe was tested on amplification products and DNA samples using DNA blotting techniques. Both nested-PCR and DNA blotting showed specificity.
