Core gastric microbiota linked to pathogenesis and preserved across age-stratified cohorts

The stomach harbors a complex microbial niche, yet the persistence and disease relevance of its core microbiota remain unclear. Using full-length 16S and ITS sequencing of 255 pediatric samples, this study identifies 11 core bacterial genera organized into two antagonistic communities, CST1A and CST1B. CST1A is enriched in non-ulcer controls, whereas CST1B is associated with gastroduodenal disease, with limited fungal involvement. Stratified analyses show that Helicobacter pylori infection depletes CST1A taxa. Functional profiling indicates that CST1A is linked to motility-related processes, while CST1B favors nucleotide and peptidoglycan biosynthesis. In vitro and in vivo experiments demonstrate that CST1A-derived Achromobacter spanius alleviates gastric mucosal injury by modulating inflammatory responses. Cross-cohort validation across eight datasets (n = 1,299) confirms the persistent relevance of the CST1A-CST1B structure across disease stages. Together, these findings define an early-life core gastric microbiota linked to disease risk and conserved across the lifespan.