Metatranscriptomic sequencing of Mus musculus cecal microbiome
Total RNA was first depleted of bacterial ribosomal and host reads using the MICROBExpress kit (Invitrogen) and the NEBNext rRNA depletion kit for mouse/rat/human (New England BioLabs). Enriched RNA was then prepared into sequencing libraries with the NEBNext Ultra II Directional RNA Library Prep Kit (New England BioLabs) according to the manufacturers instructions