Diversity Analysis and Functional Prediction of Endophytic Bacteria in Different Tissues of Duchesnea indica Based on Illumina High-Throughput Sequencing

• • A total of 1,914,360 raw sequences were obtained from four tissues, with Proteobacteria dominating at the phylum level; this baseline confirms that endophytic bacterial load is sufficient for robust functional prediction and that Proteobacteria-centric consortia are the primary target for downstream metabolic engineering. • • Stem tissue exhibited the highest endophytic bacterial richness, while root tissue showed the highest diversity; this tissue-specific partitioning implies that stems may serve as a reservoir for culturable strains, whereas roots harbor a more heterogeneous community potentially adapted to soil-derived stress, guiding tissue selection for isolation campaigns. • • Sphingomonas was identified as the key biomarker distinguishing intergroup differences and showed a significant positive correlation with Pseudomonas; both genera were major contributors to the N10-formyltetrahydrofolate biosynthesis pathway, suggesting a conserved one-carbon metabolism module that could be exploited to enhance host nucleic acid synthesis and methylation capacity. • • Leaf, fruit, and stem communities exhibited high similarity but were significantly distinct from root communities; this structural segregation indicates that aerial tissues share a core endophytic microbiome, which may simplify bioprospecting for secondary metabolite-producing strains and reduce the need for tissue-specific isolation protocols.