Figure 1

Flow diagram of the bioinformatics analysis pipeline. The rRNA/tRNA reads were removed from the unique Illumina reads using SortMeRNA software followed by BLASTN alignment to NCBI and SILVA ribosomal databases. The mRNA reads are assigned to the prokaryote genomes of NCBI using MegaBLAST followed by BLASTN, followed by classification according to alignment bit scores using a minimum bit score of 148 and 110 for prediction of phylogenetic origin at genus and family level, respectively. The genome assigned reads were classified into protein encoding or non-coding reads, followed by COG and KEGG functional annotation and metabolic mapping. Additional functional assignment was performed for evaluation purposes by assigning 10% of randomly selected unassigned reads (bit score ≤74) to the NCBI protein database followed by MetaHIT and SI metagenome databases using BLASTX (see methods for details).