Reciprocal subtractive libraries were prepared for two strains of Flavobacterium psychrophilum, one virulent and the other avirulent in a trout challenge model. Unique clones were sequenced and their distribution assessed among 34 strains. The analysis showed that F. psychrophilum is composed of two genetic lineages, possibly reflecting host specificity.Flavobacterium psychrophilum is the causative agent of bacterial coldwater disease and rainbow trout fry syndrome, both of which affect salmonid fish and impact commercial aquaculture and resource enhancement hatcheries worldwide (12,19,21). Coho salmon (Oncorhynchus kisutch [Walbaum]) and rainbow trout (O. mykiss) are particularly susceptible, although F. psychrophilum also infects other fish species (21). F. psychrophilum strains vary greatly in the ability to establish disease (virulence). For example, one well-studied strain (ATCC 49418 [4,6]) is unable to cause significant mortality (9) while strain CSF 259-93 causes high mortality (16) in a trout challenge model. There are no commercial vaccines available for bacterial coldwater disease, although several research groups have active programs in this area (11,14,20). From these studies we know that not all strains elicit an antibody response that is effective against other strains and consequently there may be considerable genetic variation between strains.The goals of this project were (i) to examine genetic differences between two strains of F. psychrophilum and ATCC 49418 [16]) and (ii) to assess the extent and distribution of genetic variation between other strains relative to geographical source and host species. Strains for the latter assessment were chosen based on availability at the time of this study. All strains were stored at Ϫ80°C and were cultured at 16 to 17°C in tryptone yeast extract salts medium (TYES; 0.4% tryptone, 0.04% yeast extract, 0.05% calcium chloride, 0.05% magnesium sulfate, pH 7.2). Genomic DNA (gDNA) was extracted using the DNeasy tissue kit (QIAGEN, Valencia, CA).We prepared reciprocal suppression subtractive hybridization libraries for the two strains by using the PCR-Select Bacterial Genomic Subtraction Kit (Clontech, Palo Alto, CA) according to the manufacturer's protocol, except that tester and driver gDNAs were restriction enzyme digested with RsaI (supplied with the kit) and DraI (New England Biolabs, Inc,, Beverly, MA) and the hybridization step was at 59°C. Resulting DNA fragments were cloned in pCR2.1 (Invitrogen, Carlsbad, CA), and 576 randomly chosen recombinant clones were used to make a microarray as previously described (8, 10). gDNA (0.5 g) was nick translated for 2 h in the presence of biotindATP (BioNick Labeling System; Invitrogen) and hybridized to the microarray (data not shown). Microarray slides were processed, imaged, and analyzed as described previously (23). Using stringent selection criteria, where the median probe intensity was Ն95% of the maximum pixel intensity in one strain and Յ5% of the maximum pixel intensity in the other strain, we identified...