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Background The influence of external environmental factors on secondary metabolites of medicinal plants has always been studied. However, little is known about the relationships between endophytes and host metabolites, especially the relationship differences between different plant species. Thus, we used high-throughput sequencing methods to compare endophyte diversity from roots of two closely related species,  Gentiana officinalis  and  G. siphonantha , from the same production area, and analyze the association with four secondary metabolites (Gentiopicroside, Loganic acid, Swertiamarine and Sweroside). Results The fungal and bacteria communities’ richness and diversity of  G. siphonantha  was higher than  G. officinalis . Ascomycota and Proteobacteria were dominant fungal and bacterial phylum of the two closely related species. At the genus level,  Tetracladium  and  Cadophora  were dominant fungal genus in  G. officinalis  and  G. siphonantha  samples, respectively. While  Pseudomonas  was dominant bacterial genus in two closely related species, with relative abundances were 8.29 and 8.05%, respectively. Spearman analysis showed that the content of loganic acid was significantly positively correlated with endophytic fungi, the content of gentiopicroside, swertiamarine and sweroside were significantly positively correlated with endophytic bacteria in the two related species .  PICRUSt and FUNGuild predictive analysis indicated that metabolism and saprotroph was primary function of endophytic bacteria and fungi in the two related species .  Conclusion Our results will expand the knowledge on relationships of plant-microbe interactions and offer pivotal information to reveal the role of endophytes in the production of  Gentiana  plant and its important secondary metabolite.

Analysis of endophyte diversity of two Gentiana plants species and the association with secondary metabolite