Analysis scripts and processed data for: Plant spatial compartmentalization buffers bacteriome structure and function under antibiotic stress

Reproducible analysis package containing R scripts, processed 16S rRNA gene amplicon data, metadata, functional annotation database, and environment specifications for a study investigating lettuce (Lactuca sativa) associated bacterial community responses to sulfamethoxazole and trimethoprim across bulk soil, rhizosphere, and endosphere compartments. Raw sequencing data are deposited in the NCBI Sequence Read Archive under BioProject PRJNA1302662. The companion research article is published in Scientific Reports (doi:10.1038/s41598-026-46797-z).