To process data I used the SAMSA2 metatranscriptome analysis pipeline.
Documentation based on SAMSA2 tutorial: https://github.com/transcript/samsa2.
The statitiscal analyses presented here were all performed using R.
The present results are based on microbial annotations against the SEED Subsystems hierarchical database (scripts starting with "ss") and the NCBI’s RefSeq bacterial genomes (scripts starting with "fb") and eukaryotic genomes (scripts starting with "fu") databases.