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To understand the recently proposed tripartite model suggesting three ancestral origins for the Japanese population and address the enigma of the high incidence of gastric cancer in Northeast Hondo (Hondo is mainland Japan), we conducted a fine-scale population structure analysis using a large Japanese <jats:italic>H. pylori<\/jats:italic> dataset, including 438 strains from 9 regions based on whole-genome sequences. As a result of fineSTRUCTURE analysis, it was found that <jats:italic>H. pylori<\/jats:italic> in Northeast Hondo is genetically distinct from hspEAsia subgroup 7 (sg7), which is widely distributed elsewhere in Hondo. We named this new subgroup hspEAsia-sg8 (Northeast Hondo). Ancestry analysis using ChromoPainter revealed that, while a large proportion of the genomes of hspEAsia-sg8 strains were painted by donors from their own population, the ancestry components of hspEAsia-sg7 showed a high proportion of Chinese and Korean components, suggesting that they were formed through admixture with continental hspEAsia subgroups. These results align with human genome studies, which indicate an original ancestry component in Northeast Hondo and a higher proportion of East Asian components in West Hondo, supporting the tripartite model. This also suggests novel potential for biogeographic ancestry inference in forensic science, as the <jats:italic>H. pylori<\/jats:italic> genome can distinguish Hondo populations. Furthermore, fixation index analysis comparing the genome of hspEAsia-sg8 with other Japanese hspEAsia subgroups revealed a high number of nonsynonymous mutations in <jats:italic>hp0378<\/jats:italic> (<jats:italic>ccsBA<\/jats:italic>) and <jats:italic>hp0377<\/jats:italic> (<jats:italic>dsbC<\/jats:italic>\/<jats:italic>ccmG<\/jats:italic>). Because these genes are involved in cytochrome c maturation and disulphide bond formation, the detected mutations may affect bacterial survival, growth or pathogenicity. This study supports the tripartite model for the formation of modern Japanese people and suggests that the strain of <jats:italic>H. pylori<\/jats:italic> prevalent in the Northeast Hondo region may contribute to the high incidence of gastric cancer there.<\/jats:p>","DOI":"10.1099\/mgen.0.001419","type":"journal-article","created":{"date-parts":[[2025,6,10]],"date-time":"2025-06-10T16:16:17Z","timestamp":1749572177000},"source":"Crossref","is-referenced-by-count":2,"title":["Fine-scale population structure of Japanese Helicobacter pylori provides new anthropological and epidemiological insights"],"prefix":"10.1099","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0136-9793","authenticated-orcid":false,"given":"Kohei","family":"Tomonari","sequence":"first","affiliation":[{"name":"Criminal Investigation Laboratory, Oita Prefectural Police, Oita, Oita, Japan"},{"name":"Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu, Oita, 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