Diversity Analysis and Functional Prediction of Endophytic Bacteria in Different Tissues of Duchesnea indica Based on Illumina High-Throughput Sequencing
Endophytic bacterial communities associated with the medicinal plant Duchesnea indica were profiled across root, stem, leaf, and fruit tissues using Illumina paired-end high-throughput sequencing. A total of 1,914,360 raw sequences were generated and processed via DADA2 and Vsearch pipelines. At the phylum level, Proteobacteria dominated all tissues. Tissue-specific variation was pronounced: the stem harbored the highest richness, whereas the root exhibited the highest diversity. Sphingomonas was identified as a key biomarker discriminating intergroup differences and displayed a significant positive correlation with Pseudomonas. Both genera were principal contributors to the N10-formyltetrahydrofolate biosynthesis pathway. Leaf, fruit, and stem communities clustered with high similarity, while root communities were distinctly separated. Functional prediction indicated that Pseudomonas and Sphingomonas may act synergistically in secondary metabolite synthesis or host stress resistance. These findings establish a microbiological basis for the pharmacological activity of D. indica and suggest that endophytic community modulation could enhance the accumulation of bioactive flavonoids, triterpenoids, and polyphenols, offering a novel avenue for the sustainable development of traditional Chinese medicine resources.