1. Astra Research Center Boston, 128 Sidney Street, Cambridge, Massachusetts 02139-4239, USA
2. Genome Therapeutics Corporation, 100 Beaver Street, Waltham, Massachusetts 02453-8443, USA
3. Department of Medical Microbiology & Immunology and Canadian Bacterial Diseases Network, University of Alberta , Edmonton T6G 2H7, Canada

Correspondence to: Richard A. Alm¹ Correspondence and requests for materials should be addressed to R.A.A. (e-mail: Email: richard.alm@arcb.us.astra.com). The annotated genome sequence and further information are available in the H. pylori database (http://www.astra-boston.com/hpylori or http://www.genomecorp.com/hpylori ) and will appear in GenBank under accession number AE001439.

Helicobacter pylori, one of the most common bacterial pathogens of humans, colonizes the gastric mucosa, where it appears to persist throughout the host's life unless the patient is treated. Colonization induces chronic gastric inflammation which can progress to a variety of diseases, ranging in severity from superficial gastritis and peptic ulcer to gastric cancer and mucosal-associated lymphoma¹. Strain-specific genetic diversity has been proposed to be involved in the organism's ability to cause different diseases or even be beneficial to the infected host²,³ and to participate in the lifelong chronicity of infection⁴. Here we compare the complete genomic sequences of two unrelated H. pylori isolates. This is, to our knowledge, the first such genomic comparison. H. pylori was believed to exhibit a large degree of genomic and allelic diversity, but we find that the overall genomic organization, gene order and predicted proteomes (sets of proteins encoded by the genomes) of the two strains are quite similar. Between 6 to 7% of the genes are specific to each strain, with almost half of these genes being clustered in a single hypervariable region.