Connections among biochemical pathways should help buffer organisms against environmental stress and affect the pace and trajectory of genome evolution. To explore these ideas, we studied consequences of inactivating the gene for polyphosphate kinase 1 (ppk1) in strains of Helicobacter pylori, a genetically diverse gastric pathogen. The PPK1 enzyme catalyzes synthesis of inorganic polyphosphate (poly P), a reservoir of high-energy phosphate bonds with multiple roles. Prior analyses in less-fastidious microbes had implicated poly P in stress resistance, motility, and virulence. In our studies, ppk1 inactivation caused the expected near-complete absence of poly P (>250-fold decrease) but had phenotypic effects that differed markedly among unrelated strains: (i) poor initial growth on standard brain heart infusion agar (five of six strains tested); (ii) weakened colonization of mice (4 of 5 strains); (iii) reduced growth on Ham's F-12 agar, a nutritionally limiting medium (8 of 11 strains); (iv) heightened susceptibility to metronidazole (6 of 17 strains); and (v) decreased motility in soft agar (1 of 13 strains). Complementation tests confirmed that the lack of growth of one ⌬ppk1 strain on F-12 agar and the inability to colonize mice of another were each due to ppk1 inactivation. Thus, the importance of ppk1 to H. pylori differed among strains and the phenotypes monitored. We suggest that quantitative interactions, as seen here, are common among genes that affect metabolic pathways and that H. pylori's high genetic diversity makes it well suited for studies of such interactions, their underlying mechanisms, and their evolutionary consequences.Many biochemical pathways are connected, in that a given metabolite can be generated and/or consumed by any of several enzymes, and the flux along one pathway can be influenced by genetic, culture-related, or environmental factors that affect traffic along complementary or competing pathways (30, 38). The resulting complex networks of interaction constitute a major focus of the new discipline of systems biology (see, e.g., reference 24); may underlie many of the epistasis (gene-gene interaction), penetrance, and quantitative-trait phenomena that are of major importance in medical, agricultural, and evolutionary genetics (13, 31); and are likely to affect the specificity and vigor of infection and virulence of pathogens. Metabolic networks exhibit intriguing formal similarities to phenomena such as food webs in natural ecosystems, patterns of human interaction, and the routing of electricity in power grids (43).It is with this perspective that we have been studying how inactivation of the ppk1 gene, which encodes polyphosphate kinase, affects Helicobacter pylori