Catalog of operational taxonomic units and unified amplicon sequencing data for the microbiomes of medicinal plant roots

China has a rich history of cultivating medicinal plants, whose root microbial communities closely interact with the medicinal plants, thereby influencing their growth, health, and medicinal properties. Currently, researchers widely use 16S rRNA gene amplicon sequencing to study these root microbial communities. However, publicly available sequence datasets often lack essential sample information or contain errors, impeding the reuse of the datasets in the future. In this study, we aimed to create a united, reliable, and readily usable source of 16S rRNA gene sequences for medicinal plant root microbiomes. We compiled a catalog of 1392 microbiome samples for 58 medicinal plants from 58 studies, and manually provided essential sample information based on the experimental setup described in the associated papers. We then processed the sequences using a custom pipeline, generating a united catalog of operational taxonomic units (OTUs) and conducting taxonomic classification. We also predicted the ecological functions of the communities for each sample. Finally, we used this dataset, to compare the rhizosphere bacterial communities of Pseudostellaria heterophylla from Fujian and Guizhou Provinces, revealing significant differences in the community composition of the same plant from different geographic locations. By providing a comprehensive and united catalog of amplicon sequences and OTUs for medicinal plant root bacterial communities, this study offers an invaluable resource for future comparative studies and data mining.