The Helicobacter pylori Genome Project : insights into H. pylori population structure from analysis of a worldwide collection of complete genomes

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

Exploring Microbial Rhizosphere Communities in Asymptomatic and Symptomatic Apple Trees Using Amplicon Sequencing and Shotgun Metagenomics

The rhizosphere is a dynamic and highly interactive habitat where diverse microbial communities are established, and it plays crucial roles in plant health and disease dynamics. In this study, microbial communities and functional profiles in the rhizosphere of both asymptomatic and symptomatic apple trees were investigated through amplicon sequencing and shotgun metagenomics. The research was conducted at a location in the municipality of Cuauhtemoc, Chihuahua State, Mexico, and a total of 22 samples were collected, comprising 12 for amplicon sequencing and 10 for shotgun metagenomic sequencing. Symptomatic trees were identified based on reddish branches and internal necrosis in the trunk and root, while asymptomatic trees exhibited a healthy physiology. The findings showed that the dominant bacterial phyla included Proteobacteria, Actinobacteria, and Bacteroidetes, with prevalent genera such as Streptomyces, Pseudomonas, and Rhodanobacter. The fungal communities featured Ascomycota, Mortierellomycota, and Basidiomycota, which were dominated by Fusarium, Penicillium, and Mortierella. In the fungal communities, Mortierellomycota, notably abundant in asymptomatic trees, holds potential as a biocontrol agent, as seen in other studies on the suppression of Fusarium wilt disease. The application of shotgun metagenomic sequencing revealed significant differences in alpha and beta diversities in bacterial communities, suggesting a health-dependent change in species composition and abundance. Functional profile analysis highlighted enzymatic activities associated with lipid synthesis/degradation, amino acid biosynthesis, carbohydrate metabolism, and nucleotide synthesis, which have been documented to participate in symbiotic relationships between plants. These insights not only contribute to understanding the dynamics of rhizosphere microbial activity but also provide valuable perspectives on the potential application of microbial communities for tree health and implications for the management of apple orchards

The Helicobacter pylori Genome Project: insights into H. pylori population structure from analysis of a worldwide collection of complete genomes

HpGP Research Network: Judith Romero-Gallo, Uma Krishna, Richard M Peek Jr, M Blanca Piazuelo, Naïma Raaf, Federico Bentolila, Hafeza Aftab, Junko Akada, Takashi Matsumoto, Freddy Haesebrouck, Rony P Colanzi, Thais F Bartelli, Diana Noronha Nunes, Adriane Pelosof, Claudia Zitron Sztokfisz, Emmanuel Dias-Neto, Paulo Pimentel Assumpção, Ivan Tishkov, Laure Brigitte Kouitcheu Mabeku, Karen J Goodman, Janis Geary, Taylor J Cromarty, Nancy L Price, Douglas Quilty, Alejandro H Corvalan, Carolina A Serrano, Robinson Gonzalez, Arnoldo Riquelme, Apolinaria García-Cancino, Cristian Parra-Sepúlveda, Giuliano Bernal, Francisco Castillo, Alisa M Goldstein, Nan Hu, Philip R Taylor, Maria Mercedes Bravo, Alvaro Pazos, Luis E Bravo, Keith T Wilson, James G Fox, Vanessa Ramírez-Mayorga, Silvia Molina-Castro, Sundry Durán-Bermúdez, Christian Campos-Núñez, Manuel Chaves-Cervantes, Evariste Tshibangu-Kabamba, Ghislain Disashi Tumba, Antoine Tshimpi-Wola, Patrick de Jesus Ngoma-Kisoko, Dieudonné Mumba Ngoyi, Modesto Cruz, Celso Hosking, José Jiménez Abreu, Christine Varon, Lucie Benejat, Ousman Secka, Alexander Link, Peter Malfertheiner, Michael Buenor Adinortey, Ansumana Sandy Bockarie, Cynthia Ayefoumi Adinortey, Eric Gyamerah Ofori, Dionyssios N Sgouras, Beatriz Martinez-Gonzalez, Spyridon Michopoulos, Sotirios Georgopoulos, Elisa Hernandez, Braulio Volga Tacatic, Mynor Aguilar, Ricardo L Dominguez, Douglas R Morgan, Hjördís Harðardóttir, Anna Ingibjörg Gunnarsdóttir, Hallgrímur Guðjónsson, Jón Gunnlaugur Jónasson, Einar S Björnsson, Mamatha Ballal, Vignesh Shetty, Muhammad Miftahussurur, Titong Sugihartono, Ricky Indra Alfaray, Langgeng Agung Waskito, Kartika Afrida Fauzia, Ari Fahrial Syam, Hasan Maulahela, Reza Malekzadeh, Masoud Sotoudeh, Avi Peretz, Maya Azrad, Avi On, Valli De Re, Stefania Zanussi, Renato Cannizzaro, Vincenzo Canzonieri, Takaya Shimura, Kengo Tokunaga, Takako Osaki, Shigeru Kamiya, Khaled Jadallah, Ismail Matalka, Nurbek Igissinov, Mariia Satarovna Moldobaeva, Attokurova Rakhat, Il Ju Choi, Jae Gyu Kim, Nayoung Kim, Minkyo Song, Mārcis Leja, Reinis Vangravs, Ģirts Šķenders, Dace Rudzīte, Aiga Rūdule, Aigars Vanags, Ilze Kikuste, Juozas Kupcinskas, Jurgita Skieceviciene, Laimas Jonaitis, Gediminas Kiudelis, Paulius Jonaitis, Vytautas Kiudelis, Greta Varkalaite, Jamuna Vadivelu, Mun Fai Loke, Kumutha Malar Vellasamy, Roberto Herrera-Goepfert, Juan Octavio Alonso-Larraga, Than Than Yee, Kyaw Htet, Takeshi Matsuhisa, Pradeep Krishna Shrestha, Shamshul Ansari, Olumide Abiodun, Christopher Jemilohun, Kolawole Oluseyi Akande, Oluwatosin Olu-Abiodun, Francis Ajang Magaji, Ayodele Omotoso, Chukwuemeka Chukwunwendu Osuagwu, Uchenna Okonkwo, Opeyemi O Owoseni, Carlos Castaneda, Miluska Castillo, Billie Velapatino, Robert H Gilman, Paweł Krzyżek, Grażyna Gościniak, Dorota Pawełka, Izabela Korona-Glowniak, Halina Cichoz-Lach, Monica Oleastro, Ceu Figueiredo, Jose C Machado, Rui M Ferreira, Dmitry S Bordin, Maria A Livzan, Vladislav V Tsukanov, Patrick Tan, Khay Guan Yeoh, Feng Zhu, Reid Ally, Rainer Haas, Milagrosa Montes, María Fernández-Reyes, Esther Tamayo, Jacobo Lizasoain, Luis Bujanda, Sergio Lario, María José Ramírez-Lázaro, Xavier Calvet, Eduard Brunet-Mas, María José Domper-Arnal, Sandra García-Mateo, Daniel Abad-Baroja, Pedro Delgado-Guillena, Leticia Moreira, Josep Botargues, Isabel Pérez-Martínez, Eva Barreiro-Alonso, Virginia Flores, Javier P Gisbert, Edurne Amorena Muro, Pedro Linares, Vicente Martin, Laura Alcoba, Tania Fleitas-Kanonnikoff, Hisham N Altayeb, Lars Engstrand, Helena Enroth, Peter M Keller, Karoline Wagner, Daniel Pohl, Yi-Chia Lee, Jyh-Ming Liou, Ming-Shiang Wu, Bekir Kocazeybek, Suat Sarıbas, İhsan Tasçı, Süleyman Demiryas, Nuray Kepil, Luis Quiel, Miguel Villagra, Morgan Norton, Deborah Johnson, Robert J Huang, Joo Ha Hwang, Wendy Szymczak, Saranathan Rajagopalan, Emmanuel Asare, William R Jacobs Jr, Haejin In, Roni Bollag, Aileen Lopez, Edward J Kruse, Joseph White, David Y Graham, Charlotte Lane, Yang Gao, Patricia I Fields, Benjamin D Gold, Marcia Cruz-Correa, María González-Pons, Luz M Rodriguez, Vo Phuoc Tuan, Ho Dang Quy Dung, Tran Thanh Binh, Tran Thi Huyen Trang, Vu Van Khien, Xiongfong Chen, Castle Raley, Bailey Kessing, Yongmei Zhao, Bao Tran, Andrés J Gutiérrez-Escobar, Yunhu Wan, Belynda Hicks, Bin Zhu, Kai Yu, Bin Zhu, Meredith Yeager, Amy Hutchinson, Kedest Teshome, Kristie Jones, Wen Luo, Quentin Jehanne, Yukako Katsura, Patricio Gonzalez-Hormazabal, Xavier Didelot, Sam Sheppard, Eduardo Tarazona-Santos, Leonardo Mariño-Ramírez, John T Loh, Steffen Backert, Michael Naumann, Christian C Abnet, Annemieke Smet, Douglas E Berg, Álvaro Chiner-Oms, Iñaki Comas, Francisco José Martínez-Martínez, Roxana Zamudio, Philippe Lehours, Francis Megraud, Koji Yahara, Martin J Blaser, Tamas Vincze, Richard D Morgan, Richard J Roberts, Stephen J Chanock, John P Dekker, Javier Torres, Timothy L Cover, Mehwish Noureen, Wolfgang Fischer, Filipa F Vale, Joshua L Cherry, Naoki Osada, Masaki Fukuyo, Masanori Arita, Yoshio Yamaoka, Ichizo Kobayashi, Ikuo Uchiyama.HpGP Research Network: Instituto Nacional de Saúde Dr. Ricardo Jorge, Lisboa, Portugal (Mónica Oleastro)Helicobacter pylori, a dominant member of the gastric microbiota, shares coevolutionary 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 highquality 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.Funding: This work was supported in part by the intramural research programs of the US National Library of Medicine, the US National Institute on Minority Health and Health Disparities, and the US National Institute of Allergy and Infectious Diseases. The members of the bioinformatics group received support from the Swedish Society for Medical Research (K.T.), Assar Gabrielsson Foundation (K.T.), and Magnus Bergvall Foundation (K.T.). The collaborating centers for sample collection received grant support from the US NIH (P01CA116087, R01CA077955, R01DK058587 and P30DK058404 to R.M.P.; P01CA028842 and R01CA190612 to K.T.W.; P01CA028842, R01CA190612, K07CA125588, R03CA167773 and P30CA068485 to D.R.M.; K08CA252635 to R.J.H., K22CA226395 to M.G.-P.; and U54GM133807 to M.C.-C.), the German Federal Ministry of Education and Research (BMBF-0315905D, ERA-NET PathoGenoMics to P.M.), the French Association pour la Recherche Contre le Cancer (8412 to F.M.), the French Institut National du Cancer (07/3D1616/IABC-23-12/NC-NG and 2014-152 to F.M.), the Canceropole Grand Sud-Ouest (2010-08-canceropole GSO-Universite Bordeaux 2 to F.M.), the Japanese National Institutes of Health (DK62813 to Y.Y.), the Japanese Ministry of Education, Culture, Sports, Science, and Technology (18KK0266, 19H03473, 21H00346 and 22H02871 to Y.Y.), the National Fund for Innovation and Development of Science and Technology from the Ministry of Higher Education Science and Technology of the Dominican Republic (2012-2013-2A1-65 and 2015-3A1-182 to M.C.), the National Cancer Center of South Korea (2210630, I.J.C.), ArcticNet (RES0010178 to K.J.G.), the Network of Centres of Excellence of Canada, the Canadian Institutes for Health Research (MOP115031 to K.J.G.), Alberta Innovates Health Solutions (201201159 to K.J.G.), the University of Malaya-Ministry of Higher Education (UM.C/625/1/HIR/MOHE/CHAN-02 to J.V.), the Ministry of Science and Technology of Vietnam, the Kyrgyz State Medical Academy, the Italian Ministry of Health for Institutional Research, the Chilean National Fund for Health Research and Development (FONIS A19/0188, FONDECYT 1230504 and ANID-FONDAP 152220002 to A.R.; CONICYT-FONDAP 15130011 and FONDECYT 1231773 to A.H.C.), the Chilean Cancer Prevention and Control Center, the Horizon 2020 Programme of European Union (825832, “CeLac and European consortium for a personalized medicine approach to Gastric Cancer,” LEGACy, to T.F.-K. and A.R.), the Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP; 2014/26847-0, 2018/14267-2, 2018/02972-3 to E.D.-N.), the Departamento de Ciência e Tecnologia (DECIT), Ministry of Health, Brazil (PRONON, SIPAR 2500.035-167/2015-23 to E.D.-N.), the Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq, 314344/2020-9 to E.T.-S.), the Universidad de Costa Rica (742-B9-310 and 742-90912-19 to V.R.-M.), LABGIPAT (S.D.-B.), the Hospital Clínica Bíblica (C.C.-N.), the Greek Ministry of Culture and Education (InfeNeutra Project, NSRF 2007-2013, MIS450598, D.N.S.), the National Strategic Reference Framework Operational Program “Competitiveness, Entrepreneurship and Innovation” (NSRF 2014-2020, MIS5002486, D.N.S.), the Hellenic Helicobacter pylori Study Group (2012-2016, B.M.-G.), the Hellenic Society of Gastroenterology (National Multicenter Laboratory Surveillance Studies, 2018-2019, B.M.-G.), the Ministry of Science and Technology, Executive Yuan, Taiwan (109-2314-B-002-096; MOST 111-2314-B-002-012; MOST 109-2314-B-002-090-MY3 to J.-M.L. and M.-S.W.), the National Research Foundation of Singapore, the Singapore Ministry of Health’s National Medical Research Council (Open Fund-Large Collaborative Grant, MOH-OFLCG18May-0003), the University of Puerto Rico Comprehensive Cancer Center, the Fondo Nacional de Desarrollo Científico y Tecnológico (196-2015-FONDECYT to C.C.), Universidad Científica del Sur, and Instituto Nacional de Enfermedades Neoplasicas (INEN, Peru). The computations and data storage required for the analyses presented were enabled by resources in projects snic-2021/22-229 and snic-2021/23-234 provided by the National Academic Infrastructure for Supercomputing in Sweden (NAISS) and the Swedish National Infrastructure for Computing (SNIC) at the UPPMAX HPC, partially funded by the Swedish Research Council through grant agreements 2022-06725, and 2018-05973.info:eu-repo/semantics/publishedVersio