Illumina HiSeq 2500 paired end sequencing
Faecal pellets from a wild type mouse (WTdm1_4) were collected before Streptomycin treatment. DNA was isolated using QIAamp DNA Stool Mini Kits (Qiagen), and DNA concentration and purity was monitored on 1% agarose gels. The V4 16S rRNA gene region was PCR amplified using primers V4-515F and V4-806R with barcodes by Novogene (Hong Kong). PCR reaction was carried out with Phusion� High Fidelity PCR Master Mix (New England Biolabs).
Sequencing libraries were generated using TruSeq� DNA PCR-Free sample preparation kit (Illumina, USA) following the manufacturer�s recommendations, and index codes were added. The library was then sequenced on an IlluminaHiSeq2500 platform and 250 bp paired-end reads were generated (Novogene, Hong Kong).