Muscovy duck ileum microflora
Host genomic DNA was isolated from each ileum sample using a QIAamp DNA Stool Mini Kit (Qiagen, Valencia, CA) according to the manufacturers instructions. High quality DNA was sequenced by next-generation sequencing .The V4-V5 region of the bacterial 16S rRNA gene was amplified using the barcode-fusion forward primer 515F (5-GTGCCAGCMGCCGCGGTAA-3) and the reverse primer 907R (5- CCGTCAATTCMTTTRAGTTT -3).  After PCR, the 2% (w/v) agarose gel was used to separate and qualify the amplicons, and then purified by a GeneJET Gel Extraction Kit (Thermo Scientific) according to the manufacturers instructions. An Illumina TruSeq DNA PCR-Free Library Preparation Kit (Illumina) was applied for sequencing library generation. A Qubit 2.0 Fluorometer (Thermo Scientific) and an Agilent Bioanalyzer 2100 system were used to evaluate the quality of the generated library. The qualified library was sequenced commercially by Mingke Biotechnology (Hangzhou) on an Illumina NovaSeq platform, generating 250 bp paired-end read.