16S rRNA V3-V4 amplicon sequencing data from caecal microbiota of control and genistein-supplemented finishing pigs

Paired-end Illumina NovaSeq 6000 (2 x 250 bp) sequencing of the bacterial 16S rRNA gene V3-V4 region was carried out on caecal content samples from 165-day-old Duroc x Landrace x Yorkshire finishing pigs. Animals received either a control diet or the same diet supplemented with 160 mg kg-1 genistein for 8 weeks. Raw reads are provided to facilitate comparative studies on microbiota composition, functional prediction and host-microbe interactions in swine.