SynCom inoculation suppresses B. goodwinii and G. quercinecans in oak seedlings and logs

SynComs were inoculated in oak seedlings and logs, in two independent trials. Seedlings and logs were challenged with the bacteria associated with acute oak decline, Brenneria goodwinii and Gibbsiella quercinecans. After 10 weeks of incubation in planta, swabs were collected from inoculation points, and stem pieces (chips) were collected for microbial back-isolation. Pathogen load (B. goodwinii and G. quercinecans) was analyzed in swabs and chip cultures via qPCR assays and 16S rRNA community profiling (read abundance).In this data set, .qmd files 1 and 2 correspond to the curation and pre-processing of 16S rRNA community profiling, and file 3 corresponds to the compiled analysis of qPCR and sequencing data. A directory containing the corresponding rendered files in html format is also provided (html_files). Input files to run the .qmd files are contained in directories general_inputs, phyloseq, supplementary_in_silico_pcr, swarm and taxonomy.Statistical analysis of 16S rRNA community profiling and qPCR data are provided in separate directories (stats_qpcr and stats_16S), which contain .qmd files, their corresponding rendered .html file and the inputs necessary to run the statistics code.A README.txt file with contents description and system requirements is also provided.