Cross-Regional Reanalysis of 16S rDNA Amplicon Sequence Data Reveals Core Taxa and Regional Modular Dynamics in the Panax ginseng Rhizosphere Bacterial Community

The rhizosphere microbiome plays a crucial role in the development, health, and therapeutic properties of Panax ginseng. Therefore, we evaluated the spatial trends in bacterial communities using a comprehensive meta-analysis of 359 sequenced rhizosphere samples from seven NCBI Sequence Read Archive BioProjects. The SILVA reference database was used to compare the Chinese and Korean sequencing datasets, focusing on quality filtering, denoising, amplicon sequence variants, and taxonomy assignment. The bacterial community structure was characterized, and differentially abundant taxa were identified using the Kruskal-Wallis test with false discovery rate correction. Co-occurrence network analysis illustrated region-specific microbial relationships and community organization, whereas functional profiles were projected to assess potential metabolic differences. Despite regional and technical variations, 37 bacterial species consistently emerged as conserved core microbiome members. Regional analyses revealed distinct bacterial drivers, such as Ligilactobacillus, Romboutsia, Nitrospira, and Bradyrhizobium in the Korean samples and Sphingoaurantiacus and Holophaga in the Chinese samples. Functional predictions showed that plant-associated defense mechanisms, nutrient mobilization, and carbon cycling varied geographically. Network studies demonstrated that community structures differed across regions. Overall, these findings indicate that although a conserved core community exists, regional differences significantly influence the composition, functional potential, and ecological relationships of the P. ginseng rhizosphere.