Fig. 1

Workflow and Read Processing. a Workflow of the pipeline for processing, annotation and analyses of metatranscriptome (RNA-seq). b Composition of sequence reads for twelve mouse metatranscriptome datasets and four additional microbiomes (see Methods). c Distribution of reads annotated through three complementary sequence similarity search tools: (1) BWA and (2) BLAT searches against a database of 2271 microbial genomes and (3) BLASTX searches against the protein non-redundant database. The mouse dataset represents a summary of all 12 datasets analysed in this study