design: For the microbial RNA extraction, we followed an in-house developed protocol described in Bozzi et al. 2021. The RNA was quantified using a Qubit RNA HS Assay Kit and a Qubit 3.0 Fluorometer (Invitrogen), following the manufacturers instructions. The RNA extracts were shipped to Novogene (Cambridge, UK) for preparation of metatranscriptome strand-specific libraries, pooling, and sequencing on the Illumina NovaSeq 6000 platform to obtain 12 Gb of PE 150 bp data per sample.