Phylogeny of the defined murine microbiota: Altered Schaedler flora

The "altered Schaedler flora" (ASF) was developed for colonizing germfree r odents with a standardized microbiota, The purpose of this study was to ide ntify each of the eight ASF strains by 16S rRNA sequence analysis. Three st rains were previously identified as Lactobacillus acidophilus (strain ASP 3 60), Lactobacillus salivarius (strain ASF 361), and Bacteroides distasonis (strain ASF 519) based on phenotypic criteria. 16S rRNA analysis indicated that each of the strains differed from its presumptive identity. The 16S rR NA sequence of strain ASF 361 is essentially identical to the 16S rRNA sequ ences of the type strains of Lactobacillus murinis and Lactobacillus animal is (both isolated from mice), and all of these strains probably belong to a single species. Strain ASF 360 is a novel lactobacillus that clusters with L. acidophilus and Lactobacillus lactis. Strain ASF 519 falls into an unna med genus containing [Bacteroides] distasonis, [Bacteroides] merdae, [Bacte roides] forsythus, and CDC group DF-3. This unnamed genus is in the Cytopha ga-Flavobacterium-Bacteroides phylum and is most closely related to the gen us Porphyromonas. The spiral-shaped strain, strain ASF 457, is in the Flexi stipes phylum and exhibits sequence identity with rodent isolates of Robert son. The remaining four ASF strains, which are extremely oxygen-sensitive f usiform bacteria, group phylogenetically with the low-G+C-content gram-posi tive bacteria (Firmicutes, Bacillus-Clostridium group). ASF 356, ASF 492, a nd ASP 502 fall into Clostridium cluster XIV of Collins et al. Morphologica lly, ASF 492 resembles members of this cluster, Roseburia cecicola, and Eub acterium plexicaudatum. The 16S rRNA sequence of ASF 492 is identical to th at of E. plexicaudatum. Since the type strain and other viable original iso lates of E. plexicaudatum have been lost, strain ASF 492 is a candidate for a neotype strain. Strain ASF 500 branches deeply in the low-G+C-content gr am-positive phylogenetic tree but is not closely related to any organisms w hose 16S rRNA sequences are currently in the GenBank database. The 16S rRNA sequence information determined in the present study should allow rapid id entification of ASP strains and should permit detailed analysis of the inte ractions of ASF organisms during development of intestinal disease in mice that are coinfected with a variety of pathogenic microorganisms.