We identified five different putative wav gene cluster types, which are responsible for the synthesis of the core oligosaccharide (OS) region of Vibrio cholerae lipopolysaccharide. Preliminary evidence that the genes encoded by this cluster are involved in core OS biosynthesis came from analysis of the recently released O1 El Tor V. cholerae genome sequence and sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis of O1 El Tor mutant strains defective in three genes (waaF, waaL, and wavB). Investigations of 38 different V. cholerae strains by Southern blotting, PCR, and sequencing analyses showed that the O1 El Tor wav gene cluster type is prevalent among clinical isolates of different serogroups associated with cholera and environmental O1 strains. In contrast, we found differences in the wav gene contents of 19 unrelated non-O1, non-O139 environmental and human isolates not associated with cholera. These strains contained four new wav gene cluster types that differ from each other in distinct gene loci, providing evidence for horizontal transfer of wav genes and for limited structural diversity of the core OS among V. cholerae isolates. Our results show genetic diversity in the core OS biosynthesis gene cluster and predominance of the type 1 wav gene locus in strains associated with clinical cholera, suggesting that a specific core OS structure could contribute to V. cholerae virulence.Vibrio cholerae is a genetically diverse species that persists in aquatic ecosystems and is often associated with plankton and other aquatic organisms (13). V. cholerae is classified on the basis of biochemical tests and DNA homology studies and is further subdivided into serogroups based on the antigenicity of surface polysaccharides (20). Today more than 193 serogroups are known (72). The ability to cause pandemic cholera is mainly restricted to the nonencapsulated serogroup O1, which is further subdivided mainly into two serotypes (Inaba and Ogawa) and biotypes (classical and El Tor). However, during 1992 and 1993, cholera-like outbreaks in Asia were caused by strains of serogroup O139. Molecular and epidemiological analyses, as well as phage typing, revealed that O139 strains are highly related to the O1 El Tor strains. Hence, it is assumed that the epidemic O139 strains were derived from O1 El Tor strains (for a review see reference 20), differing specifically in the genes encoding for the synthesis of a novel type of cell surface polysaccharide (71). In particular, it was found that the genes encoding the O1 antigen had been replaced by a capsule gene locus carrying the genes involved in the synthesis and transport of the O139 antigen and the O139 capsule (reviewed in reference 64). It was also determined that the structures of the O139 antigen and the O139 capsule were identical (36, 38).There is good evidence that pandemic V. cholerae O1 strains have become adapted to the human intestine by acquisition of virulence factors. Two known factors are cholera toxin (CT), encoded by the filamentous phage CTX⌽, and ...