Total RNA was extracted using the RNeasy PowerFecal Pro Kit. The RNA quality was evaluated using the TapeStation, and the quantity was determined with the Qubit RNA BR Kit.The ribosomal RNAs were depleted from total RNA samples. The remained RNAs were fragmented into around 250~300 bp and then reverse-transcribed into double-stranded cDNAs which subsequently went through end repair, A tailing and adapter ligation. After fragments size selection and PCR amplification, the metatranscriptome library was ready for library QC and sequencing.