A novel taxon selection method, aimed at minimizing recombination, clarifies the discovery of a new sub‐population of Helicobacter pylori from Australia

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• The infection rate can be as high as 90% in developing countries, though it is usually less than 30% in developed countries

• general prevalence of H. pylori in Australia has been reported as ranging from 15% to 30%

• the prevalence among Aboriginal Australians can reach as high as 76%

• Helicobacter pylori is believed to be transmitted between close family members via oral–oral, gastric–oral or faecal–oral routes, usually during childhood and usually from mother to children

• the sequence heterogeneity within H. pylori is very high (Tay et al., 2009), likely due to the lack of a proof-reading function in DNA polymerase I (Garcia-Ortiz et al., 2011) together with a very high recombination rate that facilitates the exchange of genes between genetically different isolates

• To date, H. pylori has been classified into 7 distinct populations that are associated with particular geographic areas: hpAfrica2, hpAfrica1, hpNEAfrica, hpEurope, hpAsia2, hpEastAsia and hpSahul

• hpSahul is named after the ancient Sahul continent, that is mainland Australia, Tasmania and New Guinea, which were joined from 100 kya (100,000 years ago) to relatively recent times, some 31,000–37,000 years ago

• hpSahul is only carried by Aboriginal Australians and is thought to have been split from the East Asia H. pylori population (Moodley et al., 2009) when Aboriginal Australians first migrated to Australia 65,000 years ago

• originally obtained during the Windsor et al. (2005) study, with MLST sequences reported in Moodley et al. (2009), were fully sequenced in this study.

• Genes present in 100% of the strains constituted the core genome, which consisted of 898 genes. Gene-by-gene alignments of single-copy orthologous core genes were performed using MAFFT version 7.271 (Katoh & Standley, 2013) with options –maxiterate = 1,000 and -localpair. The SNPs were extracted using SNP sites (Page et al., 2016).