Illumina MiSeq paired end sequencing; Antibiotic-induced Alternations in Gut Microflora are Associated with the Suppression of Immune-related Pathways in Grass Carp
The fish were unsystematically divided into three groups of 270 fish with triplicates. The corresponding fish dietary treatments were prepared using a basic feed (purchased from Tongwei Group, Chengdu, China) for the control group (CG) and the same but supplemented with enrofloxacin (EG) or florfenicol (FG) at a concentration of 10 mg/kg.The midgut tissues of 12 individual fish from each of the three treatment groups were snap-frozen and aseptically harvested in liquid nitrogen for their microbial analyses. The grass carp midguts were aseptically dissected and collected from the control, enrofloxacin, and florfenicol groups (respectively, n = 12 fish per tank). Total genomic DNA was isolated from the midgut samples with a DNeasy PowerSoil kit (Qiagen, Hilden, Germany) according its manufacturer's instructions. The V3–V4 hypervariable region was amplified by a universal pair of primers (343F-798R).Sequencing libraries were created by blending the amplicons and then assembling them on Illumina MiSeq platform PE300.