Objective To analyze the diversity and functional potential of endophytic bacterial communities in different tissues of Duchesnea indica and explore their potential relationship with the medicinal activity of the host plant. Methods Endophytic bacteria from the root, stem, leaf and fruit tissues of D. indica were studied. DNA fragments of the microbial communities were subjected to paired-end sequencing using Illumina high-throughput technology. Sequences were processed using DADA2 and Vsearch, followed by bioinformatics analysis and functional potential prediction. Results High-throughput sequencing of the endophytic bacterial genomes yielded a total of 1 914 360 raw sequences. At the phylum level, Proteobacteria was the dominant group. Among different tissues, the stem exhibited the highest richness of endophytic bacteria, while the root showed the highest diversity. Sphingomonas was identified as a key biomarker distinguishing intergroup differences and showed a significant positive correlation with Pseudomonas. Both bacterial genuses were major contributors to the N₁₀-formyltetrahydrofolate biosynthesis pathway. Conclusion The endophytic bacterial communities in the leaf, fruit and stem tissues of D. indica exhibited high similarity but were significantly distinct from those in the root. Pseudomonas and Sphingomonas may play synergistic roles in the synthesis of secondary metabolites or in enhancing host stress resistance.

Duchesnea indica(Andr.) Focke  /  endophytic bacteria  /  high-throughput sequencing  /  diversity  /  community structure