Meyer et al. 2023. Cell Host & Microbe. Conspecific versus heterospecific transmission shapes host specialization of the phyllosphere microbiome. https://doi.org/10.1016/j.chom.2023.11.002

These are the data from Meyer et al. 2023. Cell Host & Microbe. Conspecific versus heterospecific transmission of bacteria between plants shapes host specialization of the phyllosphere microbiome. Please cite the paper when using these data. Article DOI: https://doi.org/10.1016/j.chom.2023.11.002There are four main experiments designed to test the effects of microbiome transmission between the same host species (conspecific) vs between different host species (heterospecific). These are 1) the main passaging experiment, in which microbiomes were passaged for 6 experimental month-long passages, 2) the specialization assay (aka follow-up 2) where microbiomes were competed using community coalescence, 3) the generalism common garden experiment (aka follow-up 1), where microbiomes were inoculated onto novel host plants, and 4) RNAseq of the specialization experiment, to test whether host specialization of microbiomes influences differential gene expression in the leaf tissue of the recipient host species.Included are raw genetic sequences of the V5-V7 region of the bacterial 16S rRNA gene derived from experimental leaf surfaces of tomato, Solanum pimpinellifolium, pepper, bean, canola, sorghum, and corn plants.Included in this archive are:Raw sequence data (RawFASTQ_PassagingFollow1.zip, RawFASTQ_PassagingFollow2.zip)Reproducible R script (MeyerEtAl2023.R)R objects corresponding to script MeyerEtAl2023.R (.RDS)Data for generating certain plots (PermanovaRValues_Passaging_edit_noT.txt)Sample metadata (SampleInfoPassagingAndFollowup1_edit.txt, MetaDataPassagingFollow2, RNAseqMetaData) corresponding to MeyerEtAl2023.RPhylogenetic Tree file for sample ASVs (PhyloTreePassaging.tre)Plant health and fitness data (FruitFlowerTimeSeriesFollow2.txt, PassagingFollow2TomatoData)ddPCR (microbial abundance) data (R_CFU_HarvestvInoculum.csv)R script for rarefication function (Rarefy_mean.R) and read tree function (read.newick.R)RNAseq concatanated gene counts (Raw RNAseq fastq files available at NCBI BioProject database, Project ID: PRJNA1012508)Individual ASV tables for differential ASV abundance analysis in MeyerEtAl2023.R (data-to-send.zip)