The nucleotide variations in the gyrB sequences of the type strains of Stenotrophomonas spp. follow
the same pattern as that observed for the genes of the strains for which the genome sequences have been determined. The greatest variation was observed in the 3′ region of the gene, corresponding to gyrB Region 2 (Fig. 1). In the Stenotrophomonas genus, the gyrB Region 1, comprising 915 nucleotides, corresponds to 37% of the complete gene and included 306 variable nucleotide positions (33% of the sequence). The gyrB Region 2, comprising 705–711 nucleotides, corresponds to 29% of the gene and included 377 variable nucleotide positions (53% of the sequence). The amplified gyrB Regions 1 and 2 of the Stenotrophomonas strains investigated were of the same nucleotide lengths, respectively, with the exception of the gyrB Tanespimycin in vitro Region 2 sequence of S. koreensis CCUG 53887T, which contained a gap of six nucleotides. The gyrB sequence similarity between the type strains of the 12 Stenotrophomonas spp. was as low as 82.0% for Region
1 and 71.1% for Region 2 (Fig. 2b, c and Table S2). The levels of sequence similarities, with few exceptions, were lower in the gyrB Region 2. The gyrB Region 1 and Region 2 of most of the Stenotrophomonas species type strains were < 92.8% and 92.3%, respectively, similar to that of the PLX3397 datasheet type strains of any other species (Table S2). The exception to these findings were the type strains of S. maltophilia and S. pavanii, for which the sequence similarities of the two gyrB regions were 95.4% and 93.7%, respectively. The type strains of the S. acidaminiphila CCUG
46887T and S. nitritireducens CCUG 46888T exhibited gyrB Region 1 and Region 2 similarities of 92.8% and 92.3%, respectively. The genomic DNA similarity between the type strains of these two species (65.7%) and 99.4% 16S rRNA gene sequence similarity do indicate a close phylogenetic relationship between these species (Assih et al., 2002). S. daejeonensis gyrB Region 1 and Region 2 were 92.4% and 92.0% similar, respectively, to those of its closest relative, the S. acidaminiphila type strain. Thalidomide Those two species exhibited 97.9% 16S rRNA gene sequence similarity and lower levels of genomic DNA similarity (34%) (Lee et al., 2011). For all other Stenotrophomonas spp., the sequences of both gyrB regions were < 91% similar to any other species. Also included in this study was the type strain of ‘Pseudomonas’ pictorum, CCUG 3368T, which has been shown previously to be closely related to Stenotrophomonas spp. (Van den Mooter & Swings, 1990; Anzai et al., 2000). Both gyrB regions of ‘P’. pictorum were observed to be < 90% similar to those of any Stenotrophomonas spp. type strain; this level of gyrB sequence difference is in same range as that observed between other Stenotrophomonas spp.