title: GSM5701926: 26791-D29_S58; Mus musculus; OTHER
library_construction_protocol: DNA was isolated from fecal samples using the DNeasy PowerSoil Kit (QIAGEN) Protocols 1 and 3: 15ng of DNA was used for an initial PCR amplification step of 25 cycles with specific bacterial 16S rRNA (V3-341F and V4-785R) hypervariable region oligos using Q5 High-Fidelity DNA polymerase (New England Biolabs, Whitby, Ontario, Canada). After purification with AxyPrep Mag PCR Clean-up kit (Axygen, Big Flats, NY, USA), a second PCR amplification step of 8 cycles was performed to incorporate specific index adaptors for multiplexing. This step was followed by a purification step using AxyPrep Mag PCR Clean-up kit (Axygen, Big Flats, NY, USA). The quality of the final libraries was examined with a DNA screentape D1000 on a TapeStation 2200 (Agilent Technologies, Santa Clara, CA, USA) and the quantification was performed with Quant-it HS (ThermoFisher Scientific, Canada) on a Victor3 plate reader fluorometer (PerkinElmer, Waltham, MA, USA). Protocol 2: DNA was quantified using QuantiFluor dye (Promega). Sequencing libraries were prepared using the Nextera Sample Preparation Kit (Illumina, San Diego, CA, USA) with 50 ng of purified DNA. Dual indices were added during library preparation. Libraries were validated using Agilent Bioanalyzer 2100 high sensitivity DNA chips (Agilent Technologies, Santa Clara, CA, USA) and were re-quantified with QuBit (ThermoFisher Scientific). Protocols 1 and 3: 16S rRNA gene V3-V4 region. Protocol 2: Whole-genome shotgun sequencing