<b><i>Helicobacter pylori</i></b><b> Bacteriophage Exhibit Unique Epidemiology Pattern, Genomic Features, Distinct Phage Defense Systems from Bacterial Stomach, and Carry Clinical Implications</b>
Creators: name: Alfaray, Ricky Indra
name: Saruuljavkhlan, Batsaikhan
name: Fauzia, Kartika Afrida
name: Torres, Roberto C
name: Tourrette, Elise
name: Vale, Filipa F
name: Thorell, Kaisa
name: JATI, AFIF PRANAYA
name: Matsumoto, Takashi
name: Akada, Junko
name: Kryukov, Kirill
name: Dewayani, Astri
name: Mimuro, Hitomi
name: Kiga, Kotaro
name: Miftahussurur, Muhammad
name: Falush, Daniel
name: Graham, David Y.
name: Yamaoka, Yoshio
Publisher: name: figshare
Year: 2025
Subjects: classificationCode: 320203
subject: Clinical microbiology
classificationCode: 310704
subject: Microbial genetics
classificationCode: 320209
subject: Gastroenterology and hepatology

description: This dataset includes the following supplementary materials and analysis information:<b>Supplemental Data</b>Main Supplementary Information Tables and Figures<br>This file contains supplementary tables and figures referenced in the main manuscript. It covers key aspects of the study, including epidemiological data, phage-defense system analyses, genomic characteristics of H. pylori, and clinical implications. The supplementary materials provide additional context, detailed results, and visual representations that support and enhance the findings presented in the main manuscript.Supplementary Data 1. Global Metadata and Clustering Results of H. pylori Phage Identification<br>This dataset provides comprehensive global metadata and clustering analysis results related to the identification of H. pylori phages. It highlights their distribution, genetic diversity, and classification. Additionally, the dataset includes species identification and lifestyle predictions of the phages, offering valuable insights into their ecological roles and potential impact on H. pylori populations.<br>Supplementary Data 2. Helicobacter pylori phage genome annotation<br>This dataset presents annotated genomic features of H. pylori phages generated using RAST and Prokka. It includes detailed information on gene functions, structural components, and other genomic elements essential for understanding phage biology, genetic architecture, and potential roles in H. pylori pathogenesis.<br>Supplementary Data 3. Metadata of Phage Defense System from Stomach Bacteria<br>This dataset provides detailed metadata on phage defense systems identified from 2,170 H. pylori genomes and 1,515 genomes of other stomach bacteria. It highlights various defense mechanisms against viral infections, emphasizing differences in phage defense strategies between H. pylori and other gastric bacterial species. The data offer valuable insights into the adaptive immune responses and survival strategies employed by stomach bacteria in hostile environments.<br>Supplementary Data 4. Helicobacter pylori Whole Genome Sequence (WGS) Global Metadata and their Quality Investigation based on QUAST<br>This dataset contains comprehensive global metadata of H. pylori whole-genome sequencing (WGS) samples, including detailed quality evaluations performed with QUAST to assess genomic accuracy, completeness, and assembly statistics. The data cover raw WGS samples prior to filtering, ultimately refining the dataset to 2,170 high-quality H. pylori genomes for further analysis. This resource supports robust genomic investigations by ensuring reliable and well-characterized sequence data.<br>Supplementary Data 5. Helicobacter pylori Sequence Global Metadata Information<br>This dataset provides global sequence metadata for H. pylori, including information on strain accession number and source.<br>Supplementary Data 6. Global Metadata of Helicobacter pylori Antimicrobial Susceptibility Information<br>This dataset contains detailed metadata on antimicrobial susceptibility profiles of H. pylori strains, supporting the investigation of antimicrobial resistance patterns in H. pylori containing phage. It includes clinical data from hundreds of cases across multiple countries, enabling a comprehensive analysis of phage impact towards H. pylori antimicrobial resistance phenotype.<br>Supplementary Data 7. Metadata of Clinical Patient Disease Profile with or without infection of Helicobacter pylori<br>This dataset includes clinical metadata of patients, encompassing diagnostic information and pathological disease profiles associated with H. pylori infection status. It facilitates the investigation of how phage presence may influence H. pylori pathogenicity, contributing to a deeper understanding of host-pathogen dynamics.<br>Supplementary Data 8. Stomach Bacterial Genome Metadata<br>This dataset comprises genome metadata from 1,515 diverse stomach bacterial species, offering a broad context for studying phage defense systems in gastric microbiota.<b>Analysis Information</b>This section includes the R script used for bootstrapping and performing significance analysis. Since each bootstrap run can yield slightly different results, we have provided the specific bootstrap dataset used during our analysis.<b>Sequence Files of Phage</b>All phage sequences identified by PHASTER from the WGS data of H. pylori are provided. The names of the FASTA files correspond to the actual strain names of the H. pylori WGS data. Additional information about each strain can be found in the main supplementary file.<i>Note:</i> Additional files containing further details on phage element sequences or annotations are available upon request. Please contact the corresponding author for access to these files or for any other data availability inquiries.<b>Contact for Further Information</b>For any additional details, please reach out to the corresponding author, Prof. Yoshio Yamaoka, MD, PhD, Faculty of Medicine, Oita University, Japan, via email at yyamaoka@oita-u.ac.jp.Thank you.