“…Several “hspUral” genomes also showed an association with hpSahul in the chromosome painting (Supplementary Fig. 2 ), which may indicate a relationship between this group and the recently suggested hpRyukyu 15 . Fig.…”
Section: Resultsmentioning
confidence: 52%
“…The intimate association between humans and H. pylori started at the beginning of our species and represents a unique story of co-evolution between kingdoms that has fascinated researchers and the public and contributed to understanding human migration dynamics 14 , 17 . However, the challenge is to understand the consequences of this thousands-of-years of co-evolution for human health, and on the whole-genome level, bacterial population structure has mostly been studied in the setting of specific geographical areas 8 , 10 , 13 – 15 , 18 – 20 . Ongoing analyses by the Hp GP Research Network are comparing between strains from patients with different gastric diseases in order to identify genetic and epigenetic bacterial features that determine human pathogenicity.…”
Helicobacter pylori, a dominant member of the gastric microbiota, shares co-evolutionary history with humans. This has led to the development of genetically distinct H. pylori subpopulations associated with the geographic origin of the host and with differential gastric disease risk. Here, we provide insights into H. pylori population structure as a part of the Helicobacter pylori Genome Project (HpGP), a multi-disciplinary initiative aimed at elucidating H. pylori pathogenesis and identifying new therapeutic targets. We collected 1011 well-characterized clinical strains from 50 countries and generated high-quality genome sequences. We analysed core genome diversity and population structure of the HpGP dataset and 255 worldwide reference genomes to outline the ancestral contribution to Eurasian, African, and American populations. We found evidence of substantial contribution of population hpNorthAsia and subpopulation hspUral in Northern European H. pylori. The genomes of H. pylori isolated from northern and southern Indigenous Americans differed in that bacteria isolated in northern Indigenous communities were more similar to North Asian H. pylori while the southern had higher relatedness to hpEastAsia. Notably, we also found a highly clonal yet geographically dispersed North American subpopulation, which is negative for the cag pathogenicity island, and present in 7% of sequenced US genomes. We expect the HpGP dataset and the corresponding strains to become a major asset for H. pylori genomics.
“…Several “hspUral” genomes also showed an association with hpSahul in the chromosome painting (Supplementary Fig. 2 ), which may indicate a relationship between this group and the recently suggested hpRyukyu 15 . Fig.…”
Section: Resultsmentioning
confidence: 52%
“…The intimate association between humans and H. pylori started at the beginning of our species and represents a unique story of co-evolution between kingdoms that has fascinated researchers and the public and contributed to understanding human migration dynamics 14 , 17 . However, the challenge is to understand the consequences of this thousands-of-years of co-evolution for human health, and on the whole-genome level, bacterial population structure has mostly been studied in the setting of specific geographical areas 8 , 10 , 13 – 15 , 18 – 20 . Ongoing analyses by the Hp GP Research Network are comparing between strains from patients with different gastric diseases in order to identify genetic and epigenetic bacterial features that determine human pathogenicity.…”
Helicobacter pylori, a dominant member of the gastric microbiota, shares co-evolutionary history with humans. This has led to the development of genetically distinct H. pylori subpopulations associated with the geographic origin of the host and with differential gastric disease risk. Here, we provide insights into H. pylori population structure as a part of the Helicobacter pylori Genome Project (HpGP), a multi-disciplinary initiative aimed at elucidating H. pylori pathogenesis and identifying new therapeutic targets. We collected 1011 well-characterized clinical strains from 50 countries and generated high-quality genome sequences. We analysed core genome diversity and population structure of the HpGP dataset and 255 worldwide reference genomes to outline the ancestral contribution to Eurasian, African, and American populations. We found evidence of substantial contribution of population hpNorthAsia and subpopulation hspUral in Northern European H. pylori. The genomes of H. pylori isolated from northern and southern Indigenous Americans differed in that bacteria isolated in northern Indigenous communities were more similar to North Asian H. pylori while the southern had higher relatedness to hpEastAsia. Notably, we also found a highly clonal yet geographically dispersed North American subpopulation, which is negative for the cag pathogenicity island, and present in 7% of sequenced US genomes. We expect the HpGP dataset and the corresponding strains to become a major asset for H. pylori genomics.
“…Second, there is geographic variation in disease prevalence, pathogen subtype, and infection rate of pathogens between Hondo and Ryukyu ( Hayashi et al 1990 ; Fukiyama et al 2000 ; Aoki et al 2008 ; Takeuchi et al 2014 ). For example, strains of Helicobacter pylori , which are associated with the development of gastric cancer, differ between Hondo and Ryukyu; the strains specific to Ryukyu are less virulent ( Suzuki et al 2022 ). Another example is a notably higher prevalence of Human T lymphotropic virus type 1 (HTLV-1) infection in Ryukyu than in Hondo, which can result in a range of clinical manifestations ( Morikawa et al 1988 ; Watanabe 2011 ; Iwanaga 2020 ).…”
Natural selection signatures across Japanese subpopulations are under-explored. Here we conducted genome-wide selection scans with 622,926 single nucleotide polymorphisms for 20,366 Japanese individuals, who were recruited from the main-islands of Japanese Archipelago (Hondo) and the Ryukyu Archipelago (Ryukyu), representing two major Japanese subpopulations. The integrated haplotype score (iHS) analysis identified several signals in one or both subpopulations. We found a novel candidate locus at IKZF2, especially in Ryukyu. Significant signals were observed in the major histocompatibility complex region in both subpopulations. The lead variants differed and demonstrated substantial allele frequency differences between Hondo and Ryukyu. The lead variant in Hondo tags HLA-A*33:03-C*14:03-B*44:03-DRB1*13:02-DQB1*06:04-DPB1*04:01, a haplotype specific to Japanese and Korean. While in Ryukyu, the lead variant tags DRB1*15:01-DQB1*06:02, which had been recognized as a genetic risk factor for narcolepsy. In contrast, it is reported to confer protective effects against type 1 diabetes and human T lymphotropic virus type 1-associated myelopathy/tropical spastic paraparesis. The FastSMC analysis identified 8 loci potentially affected by selection within the past 20–150 generations, including 2 novel candidate loci. The analysis also showed differences in selection patterns of ALDH2 between Hondo and Ryukyu, a gene recognized to be specifically targeted by selection in East Asian. In summary, our study provided insights into the selection signatures within the Japanese and nominated potential sources of selection pressure.
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