Segmented filamentous bacteria (SFB) are nonpathogenic bacteria that are commonly found attached to the intestinal walls of many animals. Until now, these bacteria have not been cultured in vitro. Recently, a 16s rRNA sequence analysis revealed that SFB isolated from mice represent a distinct subline within the Cfostridium subphylum of the gram-positive bacteria. Since SFB isolated from mice, rats, and chickens are known to be host specific, we investigated the phylogenetic relationships among SFB obtained from these three hosts.Total DNAs from the intestinal floras of chickens and rats were used as templates for PCR amplification of 16s rRNA genes. PCR products were cloned and screened by a dot blot hybridization procedure to identify homologous sequences that cross-reacted with mouse SFB-specific oligonucleotide probes. A phylogenetic analysis of these 16s ribosomal DNA sequences revealed that SFB isolated from these three hosts form a natural group, which is peripherally related to the genus Cfostridiurn sensu strict0 (group I Cfostridiurn). The SFB obtained from chickens, rats, and mice had closely related, albeit different, 16s rRNA gene sequences. The observed levels of 16s rRNA sequence divergence, ca. 1.5 to 3%, together with host specificity, suggest that SFB isolated from mice, rats, and chickens represent different species and that coevolution of the SFB and their hosts occurred. "Candidatus Arthromitus" is proposed as the provisional generic name for this group of organisms.The small intestines of many animals (e.g., mice, rats, pigs, and other mammals, as well as chickens, amphibians, and insects) are inhabited by segmented filamentous bacteria (SFB), which are also referred to as long segmented filamentous organisms (reviewed in reference 10). These bacteria cannot be cultured in vitro and do not have official taxonomic names. Until recently, SFB could be recognized only on the basis of their morphology and their ecological niches. In intestines, these gram-positive, endospore-forming organisms are attached via holdfasts to the epithelial walls. In rodents, colonization by SFB is restricted to the ileum (4). In birds, SFB are also found in the ceca (9). No pathologic effects of SFB have been found, even in immunodeficient animals. SFB found in different animal species are morphologically very similar. However, attempts to transfer bacteria from one host species to another have revealed that SFB found in mice, rats, and chickens exhibit host specificity (1, 13, 21). It is not known if SFB that inhabit different hosts are taxonomically closely related or whether they belong to different species.In a recent study, the 16s rRNA-encoding gene sequence of SFB obtained from mice was determined (19). This study was greatly facilitated by the use of a monoculture of these organisms in formerly germfree mice (12). A comparative 16s rRNA * Corresponding author. Mailing address: Central Animal Laboratory, University of Nijmegen, P.O. Box 9101, NL-6500 HB Nijmegen, 'The Netherlands. analysis revealed that th...