RNA-Seq of gut content of Salmo trutta fario
The DNA samples were processed and analyzed with the ZymoBIOMICS Targeted Sequencing Service (Zymo Research, Irvine, CA, USA). The DNA samples were prepared for targeted sequencing with the Quick-16S NGS Library Prep Kit (Zymo Research, Irvine, CA, USA).  The primer sets used in this study was Quick-16S Primer Set V3-V4 (Zymo Research, Irvine, CA, USA). The sequencing library was prepared using an innovative library preparation process in which PCR reactions were performed in real-time PCR machines to control cycles and therefore limit PCR chimera formation. The final PCR products were quantified with qPCR fluorescence readings and pooled together based on equal molarity. The final pooled library was cleaned up with the Select-a-Size DNA Clean & Concentrator (Zymo Research, Irvine, CA, USA), then quantified with TapeStation (Agilent Technologies, Santa Clara, CA) and Qubit (Thermo Fisher Scientific, Waltham, WA).