0) using the “no – Open Read Frameorfs” (no-ORFs) option and the MgRast metagenomics analysis server this website (version 3.2 Argonne National Laboratory. Argonne, IL http://​metagenomics.​anl.​gov)

[20]. Different maximum e-value cutoffs, minimum percentage identity cutoffs and minimum alignment length cutoffs were used for different questions (see individual list in Results section). For overall phylogenetic designation at phylum level – default parameters were 80% similarity over 100 bases at 1e-5. CloVR-Metagenomics was used with a BLAST-based protocol to perform taxonomic and functional annotations as well as statistical analysis with Metastats and R. CloVR pipeline for metagenomes was used with the following SOPs: 1) UCLUST first clusters

redundant sequences that show 99% nucleotide identity and removes artificial 454 replicate reads. 2) Representative DNA sequences are searched against the NCBI COG database using BLASTX. 3) Representative DNA sequences are searched against the NCBI RefSeq database of finished prokaryotic genomes using BLASTN. 4) Metastats and CloVR-implemented R selleck scripts are applied for additional statistical and graphical evaluations of the pipeline results. Functional annotation was examined using the COGs database [21]. A full description of the CloVR-Metagenomics SOP is available online at http://​clovr.​org. Salmonella detection pipeline In order to create a pipeline for detecting the presence of Salmonella, the IMG contig and genes databases were split into two databases: one that represented all Salmonella contigs and genes present in the IMG and the second that represented the remainder of the database (minus all Salmonella). A BLAST approach with extremely relaxed parameters was used to gather hits to Salmonella from both of the databases. A bit score with at least 50% the size of the average length of each

shotgun data set and a variable id percentage (in this case 40, 50,..100) was used to create plots of hits to Salmonella and the bit score of these hits. Data Deposition PRKD3 All metagenomes are available in Mg Rast; accession numbers; 4488526.3 (Bottom Leaves), 4488531.3 (Stems), 4488530.3 (leaves), 4488529.3 (Tomato Fruits), 4488528.3 (Roots), 4488527.3 (Flowers) and SRA at NCBI Genbank (SRA Accession number SRA061333). Submissions conform to the “Minimum Information Standards” [22] recommended by the Genomic Standards Consortium. Results and Discussion Figure 1 shows ten diverse phyla from bacterial, eukaryotic, and viral domains observed across all the sampled tomato plant organs in the shotgun metagenomic data using M5NR for annotation (Mg Rast version 3.2) with a maximum e-value of 1e-5 and minimum identity of 80%, over 150 bases. A total of 92,695 16S rRNA gene sequences were used to examine bacterial taxonomy and 194,260 18S rRNA gene sequences were used to describe eukaryotes (primarily fungal) associated with diverse tomato organs.