An ancient ecospecies of Helicobacter pylori

Elise Tourrette, Roberto C. Torres, Sarah L. Svensson, Takashi Matsumoto, Muhammad Miftahussurur, Kartika Afrida Fauzia, Ricky Indra Alfaray, Ratha-Korn Vilaichone, Vo Phuoc Tuan, Difei Wang, Abbas Yadegar, Lisa M. Olsson, Zhemin Zhou, Yoshio Yamaoka (), Kaisa Thorell () and Daniel Falush ()
Additional contact information
Elise Tourrette: Chinese Academy of Sciences
Roberto C. Torres: Chinese Academy of Sciences
Sarah L. Svensson: Chinese Academy of Sciences
Takashi Matsumoto: Oita University Faculty of Medicine
Muhammad Miftahussurur: Universitas Airlangga
Kartika Afrida Fauzia: Oita University Faculty of Medicine
Ricky Indra Alfaray: Oita University Faculty of Medicine
Ratha-Korn Vilaichone: Thammasat University
Vo Phuoc Tuan: Oita University Faculty of Medicine
Difei Wang: Frederick National Lab for Cancer Research
Abbas Yadegar: Shahid Beheshti University of Medical Sciences
Lisa M. Olsson: University of Gothenburg
Zhemin Zhou: Soochow University
Yoshio Yamaoka: Oita University Faculty of Medicine
Kaisa Thorell: University of Gothenburg
Daniel Falush: Chinese Academy of Sciences

Nature, 2024, vol. 635, issue 8037, 178-185

Abstract: Abstract Helicobacter pylori disturbs the stomach lining during long-term colonization of its human host, with sequelae including ulcers and gastric cancer1,2. Numerous H. pylori virulence factors have been identified, showing extensive geographic variation1. Here we identify a ‘Hardy’ ecospecies of H. pylori that shares the ancestry of ‘Ubiquitous’ H. pylori from the same region in most of the genome but has nearly fixed single-nucleotide polymorphism differences in 100 genes, many of which encode outer membrane proteins and host interaction factors. Most Hardy strains have a second urease, which uses iron as a cofactor rather than nickel3, and two additional copies of the vacuolating cytotoxin VacA. Hardy strains currently have a limited distribution, including in Indigenous populations in Siberia and the Americas and in lineages that have jumped from humans to other mammals. Analysis of polymorphism data implies that Hardy and Ubiquitous coexisted in the stomachs of modern humans since before we left Africa and that both were dispersed around the world by our migrations. Our results also show that highly distinct adaptive strategies can arise and be maintained stably within bacterial populations, even in the presence of continuous genetic exchange between strains.

Date: 2024
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DOI: 10.1038/s41586-024-07991-z

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