RNA-Seq of con2: pig ileum
Briefly, the ileal mucus was scraped and the bacterial genomic DNA was extracted with a DNA Stool Mini-Kit (QIAGEN, Hilden, Germany). The DNA concentration was estimated on a NanoDrop spectrophotometer (Thermo Scientific). The 16S rRNA gene was amplied by PCR with specific primers. The DNA libraries were constructed on the amplicons with the SMRT Bell technology on a PacBio RS II sequencer (Pacific Biosciences, Menlo Park, CA, USA) 19. The raw reads were processed using Lima software (version 1.11.0) to obtain circular consensus sequence (CCS) reads. Further sample sorting, trimming, clustering of OTUs were conducted with the USEARCH software 20.