Brucella is a Gram-negative bacterium that causes a worldwide-distributed zoonosis. The genus includes smooth (S) and rough (R) species that differ in the presence or absence, respectively, of the O-polysaccharide of lipopolysaccharide. In S brucellae, the O-polysaccharide is a critical diagnostic antigen and a virulence determinant. However, S brucellae spontaneously dissociate into R forms, a problem in antigen and S vaccine production. Spontaneous R mutants of Brucella abortus, Brucella melitensis, and Brucella suis carried the chromosomal scar corresponding to genomic island 2 (GI-2) excision, an event causing the loss of the wboA and wboB O-polysaccharide genes, and the predicted excised circular intermediate was identified in B. abortus, B. melitensis, and B. suis cultures. Moreover, disruption of a putative phage integrase gene in B. abortus GI-2 caused a reduction in O-polysaccharide loss rates under conditions promoting S-R dissociation. However, spontaneous R mutants not carrying the GI-2 scar were also detected. These results demonstrate that the phage integrase-related GI-2 excision is a cause of S-R brucella dissociation and that other undescribed mechanisms must also be involved. In the R Brucella species, previous works have shown that Brucella ovis but not Brucella canis lacks GI-2, and a chromosomal scar identical to those in R mutants was observed. These results suggest that the phage integrase-promoted GI-2 excision played a role in B. ovis speciation and are consistent with other evidence, suggesting that this species and B. canis have emerged as two independent lineages.Brucellosis is one of the most important bacterial zoonotic diseases. This infection is caused by the members of the genus Brucella, a group of Gram-negative, intracellular facultative microorganisms (13). Brucella abortus, Brucella melitensis, Brucella suis, Brucella neotomae, Brucella ceti, and Brucella pinnipedialis are denominated smooth (S) brucellae because their colonies have glossy, bluish surfaces that contrast with the rough (R), granular aspect of the Brucella canis and Brucella ovis colonies. Moreover, S brucellae had a marked tendency to yield mixtures of S and R colonies, a phenomenon known as Brucella S-R dissociation (4). These colony phenotypes respectively relate to the presence or absence of the O-polysaccharide of lipopolysaccharide (LPS) (1, 14), and since this structure is a major diagnostic antigen and virulence factor, S-R dissociation has drawn considerable attention (1, 4, 14, 21). Indeed, S-R dissociation is a problem in the production of diagnostic antigens and vaccines (3). Although first observed over 70 years ago, the genetic bases of Brucella S-R dissociation have not been elucidated as of yet.Up to now, 10 Brucella O-polysaccharide genes (putatively coding for enzymes furnishing sugar precursors, glycosyltransferases, and the O-chain transport system) have been identified, and the corresponding mutants show the R phenotype (1, 9). These genes are located in two major genetic regions, wbo and w...