16S RNA-Seq: Adult caecal digesta
Nextera XT DNA Library Preparation Kit and IDT Unique Dual Indexes were used to prepare DNA libraries (1 ng input). Genomic DNA was fragmented with the Nextera XT fragmentation enzyme, and unique dual indexes were added to each sample. The libraries were subsequently amplified through 12 cycles of PCR. Following amplification, the libraries were purified with AMPure magnetic beads and eluted in Qiagen EB buffer. Finally, the quantification of libraries was performed using the Qubit 4 fluorometer and the Qubit dsDNA HS Assay Kit. Libraries sequencing was performed on an Illumina HiSeq 4 000 platform, 2  150 bp, and paired reads were generated.