Environmental and Rhizosphere Microbiome Drivers of Metabolic Profiles in Gastrodia elata: An Integrative Analysis of Soil, Metabolomics and Anti-Inflammatory Readouts

Background: Gastrodiae Rhizoma, the dried tuber ofGastrodia elataBl. (Orchidaceae), is a traditional Chinese medicinal (TCM) and edible plant. Its quality formation is closely associated with rhizosphere microorganisms; however, the specific underlying mechanisms remain unclear. Methods: Tubers and rhizosphere soils were collected from seven major production regions ofG. elata. Soil physicochemical properties were analyzed, and integrative analyses combining soil microbiome and untargeted metabolome profiling were conducted. The anti-inflammatory activity ofG. elataextracts was evaluated using a RAW264.7 macrophage model. Multivariate statistical approaches, including OPLS-DA and correlation network analysis, were used to decipher relationships among environmental factors, microbial communities, metabolic profiles, and bioactivities. Results: A total of 39,250 bacterial ASVs and 10,544 fungal ASVs were identified. The bacterial community, dominated byProteobacteriaandAcidobacteria, was strongly influenced by soil chemical factors, including pH and total nitrogen. The fungal community, primarily composed ofAscomycotaandBasidiomycota, exhibited marked sensitivity to altitudinal gradients. Correlation analysis revealed that key secondary metabolites, including flavonoids and phenolic acids, along with their anti-inflammatory activities, were significantly associated with rhizosphere microorganisms such asEdaphobaculum,Hypocrea, andPseudomonas. Conclusions: Our findings outline the pathways connecting environmental factors, the microbiome, and functional metabolites inG. elata, highlighting the importance of environmental–microbial interactions in determining metabolic outcomes. This work provides new insights into the ecological and molecular mechanisms behind the quality formation of this medicinal plant.