An ancient ecospecies of Helicobacter pylori

Helicobacter pylori disturbs the stomach lining during long-term colonization of its human host, with sequelae including ulcers and gastric cancer<sup>1,2</sup>. Numerous H. pylori virulence factors have been identified, showing extensive geographic variation<sup>1</sup>. 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 nickel<sup>3</sup>, 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.

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Journal
Nature
Published
2024-10-16
DOI
https://doi.org/10.1038/s41586-024-07991-z
Citations
28
Primary Topic
Helicobacter pylori-related gastroenterology studies
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article
Field-Weighted Citation Impact
15.46

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article

An ancient ecospecies of Helicobacter pylori

Mohammad Reza Zali, Elise Tourrette, Lars Agréus, Ricky Indra Alfaray et al.
28 citations
Nature
Helicobacter pylori-related gastroenterology studies
15.46
article

An ancient ecospecies of Helicobacter pylori

Mohammad Reza Zali, Elise Tourrette, Lars Agréus, Ricky Indra Alfaray, Hasan Maulahela, Vũ Văn Khiên, Batsaikhan Saruuljavkhlan, Kammal Kumar Pawa, Ghislain Disashi Tumba, Rabi Prakash Sharma, Langgeng Agung Waskito, Saeid Latifi‐Navid, Hò Thị Dung, Yoshio Yamaoka, Pradeep Krishna Shrestha, Thein Myint, Lisa Olsson, Difei Wang, Titong Sugihartono, Kazunari Murakami, Shaho Negahdar Panirani, M. D. Lamawansa, Abbas Yadegar, Celso Hosking, Patrick de Jesus Ngoma-Kisoko, Varocha Mahachai, Jukka Ronkainen, Antoine Tshimpi-Wola, Anna Andréasson, Fukunori Kinjo, Thawee Ratanachu‐ek, Kaisa Thorell, Muhammad Miftahussurur, Ratha‐Korn Vilaichone, Evariste Tshibangu‐Kabamba, Vo Phuoc Tuan, Nasrin Mirzaei, Jeewantha Rathnayake, J Abreu, Than Than Yee, Phawinee Subsomwong, Takeshi Matsuhisa, Dou Narith, Dieudonné Mumba Ngoyi, Kyaw Ko Ko Htet, Pertti Aro, Hideo Terao, Yudith Annisa Ayu Rezkitha, Than Than Aye, Roberto C. Torres, Kartika Afrida Fauzia, Tadashi Shimoyama, Daniel Falush, Hafeza Aftab, New Ni, Sarah L. Svensson, Modesto Cruz, Emilio Rudbeck, Zhemin Zhou, Trần Thanh Bình, Hamid Asadzadeh Aghdaei, Pascal Tshiamala Kashala, Lars Engstrand, Nagisa Kinjo, Trần Thị Huyền Trang, D. Theertha Prasad, Ari Fahrial Syam, Lotay Tshering, Takashi Matsumoto
article en
28 citations

Abstract

Helicobacter pylori disturbs the stomach lining during long-term colonization of its human host, with sequelae including ulcers and gastric cancer<sup>1,2</sup>. Numerous H. pylori virulence factors have been identified, showing extensive geographic variation<sup>1</sup>. 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 nickel<sup>3</sup>, 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.

NatureVol. 635(8037)
Thammasat University (TH), University of Peradeniya (LK), Hirosaki University (JP), Universidad Autónoma de Santo Domingo (DO), Stockholm University (SE), University of Surabaya (ID), Baylor College of Medicine (US), Oita University (JP), Chinese Academy of Sciences (CN), Universitas Airlangga (ID), East Yangon General Hospital (MM), Cho Ray Hospital (VN), Bangkok Hospital (TH), University of Mbuji Mayi (CD), University of Medicine Mandalay (MM), Kinshasa General Hospital (CD), Karolinska Institutet (SE), University of Indonesia (ID), University of Kinshasa (CD), Soochow University (CN), Centre for Bhutan Studies and GNH Research (BT), Rajavithi Hospital (TH), Tribhuvan University Teaching Hospital (NP), Shanghai Institute of Applied Physics (CN), National Institute of Biomedical Research (CD), Kensei Hospital (JP), Khanh Hoa General Hospital (VN), University of Medicine 2 Yangon (MM), University Of Medicine 1 Yangon (MM), 108 Military Central Hospital (VN), Urasoe General Hospital, Shahid Beheshti University of Medical Sciences (IR), University of Mohaghegh Ardabili (IR), Nippon Medical School (JP), University of Gothenburg (SE), Dhaka Medical College and Hospital (BD), University of Oulu (FI)
U.S. Department of Health and Human Services, Wellcome Trust, Ministry of Education, Culture, Sports, Science and Technology, National Natural Science Foundation of China, Svenska Sällskapet för Medicinsk Forskning, Vetenskapsrådet, Göteborgs Universitet, Thammasat University, Shahid Beheshti University of Medical Sciences, Magnus Bergvalls Stiftelse, Thailand Science Research and Innovation, National Institutes of Health, Japan Society for the Promotion of Science, Research Institute for Gastroenterology and Liver Diseases, Uppsala Multidisciplinary Center for Advanced Computational Science, National Cancer Institute
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Helicobacter pylori-related gastroenterology studies
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