Abstract
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.
| Original language | English |
|---|---|
| Article number | 8184 |
| Journal | Nature Communications |
| Volume | 14 |
| Issue number | 1 |
| DOIs | |
| State | Published - 11 Dec 2023 |
| Externally published | Yes |
Bibliographical note
Publisher Copyright:© 2023, The Author(s).
ASJC Scopus subject areas
- General Chemistry
- General Biochemistry, Genetics and Molecular Biology
- General Physics and Astronomy
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In: Nature Communications, Vol. 14, No. 1, 8184, 11.12.2023.
Research output: Contribution to journal › Article › peer-review
TY - JOUR
T1 - The Helicobacter pylori Genome Project
T2 - insights into H. pylori population structure from analysis of a worldwide collection of complete genomes
AU - Thorell, Kaisa
AU - Muñoz-Ramírez, Zilia Y.
AU - Wang, Difei
AU - Sandoval-Motta, Santiago
AU - Boscolo Agostini, Rajiv
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AU - Bentolila, Federico
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AU - Pelosof, Adriane
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AU - Dias-Neto, Emmanuel
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AU - Goodman, Karen J.
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AU - Riquelme, Arnoldo
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AU - Parra-Sepúlveda, Cristian
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AU - Taylor, Philip R.
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AU - Pazos, Alvaro
AU - Bravo, Luis E.
AU - Wilson, Keith T.
AU - Fox, James G.
AU - Ramírez-Mayorga, Vanessa
AU - Molina-Castro, Silvia
AU - Durán-Bermúdez, Sundry
AU - Campos-Núñez, Christian
AU - Chaves-Cervantes, Manuel
AU - Tshibangu-Kabamba, Evariste
AU - Tumba, Ghislain Disashi
AU - Tshimpi-Wola, Antoine
AU - de Jesus Ngoma-Kisoko, Patrick
AU - Ngoyi, Dieudonné Mumba
AU - Cruz, Modesto
AU - Hosking, Celso
AU - Abreu, José Jiménez
AU - Varon, Christine
AU - Benejat, Lucie
AU - Secka, Ousman
AU - Link, Alexander
AU - Malfertheiner, Peter
AU - Adinortey, Michael Buenor
AU - Bockarie, Ansumana Sandy
AU - Adinortey, Cynthia Ayefoumi
AU - Ofori, Eric Gyamerah
AU - Sgouras, Dionyssios N.
AU - Martinez-Gonzalez, Beatriz
AU - Michopoulos, Spyridon
AU - Georgopoulos, Sotirios
AU - Hernandez, Elisa
AU - Tacatic, Braulio Volga
AU - Aguilar, Mynor
AU - Dominguez, Ricardo L.
AU - Morgan, Douglas R.
AU - Harðardóttir, Hjördís
AU - Gunnarsdóttir, Anna Ingibjörg
AU - Guðjónsson, Hallgrímur
AU - Jónasson, Jón Gunnlaugur
AU - Björnsson, Einar S.
AU - Ballal, Mamatha
AU - Shetty, Vignesh
AU - Miftahussurur, Muhammad
AU - Sugihartono, Titong
AU - Alfaray, Ricky Indra
AU - Waskito, Langgeng Agung
AU - Fauzia, Kartika Afrida
AU - Syam, Ari Fahrial
AU - Maulahela, Hasan
AU - Malekzadeh, Reza
AU - Sotoudeh, Masoud
AU - Peretz, Avi
AU - Azrad, Maya
AU - On, Avi
AU - De Re, Valli
AU - Zanussi, Stefania
AU - Cannizzaro, Renato
AU - Canzonieri, Vincenzo
AU - Shimura, Takaya
AU - Tokunaga, Kengo
AU - Osaki, Takako
AU - Kamiya, Shigeru
AU - Jadallah, Khaled
AU - Matalka, Ismail
AU - Igissinov, Nurbek
AU - Moldobaeva, Mariia Satarovna
AU - Rakhat, Attokurova
AU - Choi, Il Ju
AU - Kim, Jae Gyu
AU - Kim, Nayoung
AU - Song, Minkyo
AU - Leja, Mārcis
AU - Vangravs, Reinis
AU - Šķenders, Ģirts
AU - Rudzīte, Dace
AU - Rūdule, Aiga
AU - Vanags, Aigars
AU - Kikuste, Ilze
AU - Kupcinskas, Juozas
AU - Skieceviciene, Jurgita
AU - Jonaitis, Laimas
AU - Kiudelis, Gediminas
AU - Jonaitis, Paulius
AU - Kiudelis, Vytautas
AU - Varkalaite, Greta
AU - Vadivelu, Jamuna
AU - Loke, Mun Fai
AU - Vellasamy, Kumutha Malar
AU - Herrera-Goepfert, Roberto
AU - Alonso-Larraga, Juan Octavio
AU - Yee, Than Than
AU - Htet, Kyaw
AU - Matsuhisa, Takeshi
AU - Shrestha, Pradeep Krishna
AU - Ansari, Shamshul
AU - Abiodun, Olumide
AU - Jemilohun, Christopher
AU - Akande, Kolawole Oluseyi
AU - Olu-Abiodun, Oluwatosin
AU - Magaji, Francis Ajang
AU - Omotoso, Ayodele
AU - Osuagwu, Chukwuemeka Chukwunwendu
AU - Okonkwo, Uchenna
AU - Owoseni, Opeyemi O.
AU - Castaneda, Carlos
AU - Castillo, Miluska
AU - Velapatino, Billie
AU - Gilman, Robert H.
AU - Krzyżek, Paweł
AU - Gościniak, Grażyna
AU - Pawełka, Dorota
AU - Korona-Glowniak, Izabela
AU - Cichoz-Lach, Halina
AU - Oleastro, Monica
AU - Figueiredo, Ceu
AU - Machado, Jose C.
AU - Ferreira, Rui M.
AU - Bordin, Dmitry S.
AU - Livzan, Maria A.
AU - Tsukanov, Vladislav V.
AU - Tan, Patrick
AU - Yeoh, Khay Guan
AU - Zhu, Feng
AU - Ally, Reid
AU - Haas, Rainer
AU - Montes, Milagrosa
AU - Fernández-Reyes, María
AU - Tamayo, Esther
AU - Lizasoain, Jacobo
AU - Bujanda, Luis
AU - Lario, Sergio
AU - Ramírez-Lázaro, María José
AU - Calvet, Xavier
AU - Brunet-Mas, Eduard
AU - Domper-Arnal, María José
AU - García-Mateo, Sandra
AU - Abad-Baroja, Daniel
AU - Delgado-Guillena, Pedro
AU - Moreira, Leticia
AU - Botargues, Josep
AU - Pérez-Martínez, Isabel
AU - Barreiro-Alonso, Eva
AU - Flores, Virginia
AU - Gisbert, Javier P.
AU - Muro, Edurne Amorena
AU - Linares, Pedro
AU - Martin, Vicente
AU - Alcoba, Laura
AU - Fleitas-Kanonnikoff, Tania
AU - Altayeb, Hisham N.
AU - Engstrand, Lars
AU - Enroth, Helena
AU - Keller, Peter M.
AU - Wagner, Karoline
AU - Pohl, Daniel
AU - Lee, Yi Chia
AU - Liou, Jyh Ming
AU - Wu, Ming Shiang
AU - Kocazeybek, Bekir
AU - Sarıbas, Suat
AU - Tasçı, İhsan
AU - Demiryas, Süleyman
AU - Kepil, Nuray
AU - Quiel, Luis
AU - Villagra, Miguel
AU - Norton, Morgan
AU - Johnson, Deborah
AU - Huang, Robert J.
AU - Hwang, Joo Ha
AU - Szymczak, Wendy
AU - Rajagopalan, Saranathan
AU - Asare, Emmanuel
AU - Jacobs, William R.
AU - In, Haejin
AU - Bollag, Roni
AU - Lopez, Aileen
AU - Kruse, Edward J.
AU - White, Joseph
AU - Graham, David Y.
AU - Lane, Charlotte
AU - Gao, Yang
AU - Fields, Patricia I.
AU - Gold, Benjamin D.
AU - Cruz-Correa, Marcia
AU - González-Pons, María
AU - Rodriguez, Luz M.
AU - Tuan, Vo Phuoc
AU - Dung, Ho Dang Quy
AU - Binh, Tran Thanh
AU - Trang, Tran Thi Huyen
AU - Van Khien, Vu
AU - Chen, Xiongfong
AU - Raley, Castle
AU - Kessing, Bailey
AU - Zhao, Yongmei
AU - Tran, Bao
AU - Gutiérrez-Escobar, Andrés J.
AU - Wan, Yunhu
AU - Hicks, Belynda
AU - Zhu, Bin
AU - Yu, Kai
AU - Zhu, Bin
AU - Yeager, Meredith
AU - Hutchinson, Amy
AU - Teshome, Kedest
AU - Jones, Kristie
AU - Luo, Wen
AU - Jehanne, Quentin
AU - Katsura, Yukako
AU - Gonzalez-Hormazabal, Patricio
AU - Didelot, Xavier
AU - Sheppard, Sam
AU - Tarazona-Santos, Eduardo
AU - Mariño-Ramírez, Leonardo
AU - Loh, John T.
AU - Backert, Steffen
AU - Naumann, Michael
AU - Abnet, Christian C.
AU - Smet, Annemieke
AU - Berg, Douglas E.
AU - Chiner-Oms, Álvaro
AU - Comas, Iñaki
AU - Martínez-Martínez, Francisco José
AU - Zamudio, Roxana
AU - Lehours, Philippe
AU - Megraud, Francis
AU - Yahara, Koji
AU - Blaser, Martin J.
AU - Vincze, Tamas
AU - Morgan, Richard D.
AU - Roberts, Richard J.
AU - Chanock, Stephen J.
AU - Dekker, John P.
AU - Torres, Javier
AU - Cover, Timothy L.
AU - Noureen, Mehwish
AU - Fischer, Wolfgang
AU - Vale, Filipa F.
AU - Cherry, Joshua L.
AU - Osada, Naoki
AU - Fukuyo, Masaki
AU - Arita, Masanori
AU - Yamaoka, Yoshio
AU - Kobayashi, Ichizo
AU - Uchiyama, Ikuo
AU - Falush, Daniel
AU - Camargo, M. Constanza
AU - Rabkin, Charles S.
N1 - Publisher Copyright: © 2023, The Author(s).
PY - 2023/12/11
Y1 - 2023/12/11
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=85179650185&partnerID=8YFLogxK
U2 - 10.1038/s41467-023-43562-y
DO - 10.1038/s41467-023-43562-y
M3 - Article
C2 - 38081806
AN - SCOPUS:85179650185
SN - 2041-1723
VL - 14
JO - Nature Communications
JF - Nature Communications
IS - 1
M1 - 8184
ER -