SAMN41052931
External Id
Fudan University Shanghai Cancer Center
INSDC center name
2024-04-23T00:00:00Z
INSDC first public
2024-04-23T05:01:41.930Z
INSDC last update
live
INSDC status
Microbe, viral or environmental
NCBI submission model
Microbe.1.0
NCBI submission package
ERS19292430
SRA accession
2021-03-01
collection_date
Background: This study aimed to explore and compare the differences in the genomics and pathogenicity of Helicobacter pylori (H. pylori) strains derived from the gastric cancer (GC) and gastritis (GI) in the Chinese population. Methods: We sequenced 12 H. pylori from GC and GI patients in china by whole genome sequencing. 20 H. pylori sequencing data from other regions of the world were obtained from the public platform as reference genes. Then, the evolutionary tree was drawn based on multi-omics, and the differences of virulence factors (VF) and gene function were analyzed Results: In GC stains, the 1544-1640 coding genes, with a total length of 1,549,790-1,605,249 bp, were predicted. In GI stains, the 1552-1668 coding genes, with a total length of 1,552,426-1,665,981 bp, were identified. In addition, the average length of coding genes in GC and GI strain, was approximately 1594 (90.91%) and 1589 genes (90.81%), respectively. We found that the VFs predicted by the two cohort strains had high consistency, but their cagA status was significantly different. Additionally, the clustering results indicated that there were significant differences in core Single Nucleotide Polymorphism (SNP) between GC and GI strains, but no significant differences in homologous proteins and gene island prediction between the two strains. Subsequently, the results of pan-genomic and Average Nucleotide Identity (ANI) analyses suggested that GC, GI and other reference H. pylori strains had high homology consistency. Furthermore, the gene function annotation results suggested that the H. pylori strains of GC and GI also had high similarity in gene function, and their specific gene functions were mainly concentrated in the process of metabolism, transcription and repair. Conclusions: GC and GI patient-derived H. pylori have some differences in VF and SNP, but they also have high homologous consistency at other level of the genome in Chinese population.
description
China
geo_loc_name
Homo sapiens
host
gastric cancer patients
isolate
gastric mucosa
isolation_source
Helicobacter pylori
http://purl.obolibrary.org/obo/NCBITaxon_210
organism
bacterial culture
sample_type
GC-01
strain
Microbe sample from Helicobacter pylori
title