SynCom inoculation suppresses <i>B. goodwinii</i> and <i>G. quercinecans</i> 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, <i>Brenneria goodwinii </i>and <i>Gibbsiella quercinecans</i>. 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 (<i>B. goodwinii </i>and <i>G. quercinecans</i>) 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.