Mgieasy universal dna library prep set

Microbial DNA extraction from stool samples was performed using the MGISP-960 Automated Sample Preparation System (MGI Tech Co., Ltd., Wuhan, China) and MagPure Stool DNA LQ Kit (Angen Biotech Co., Ltd., Guangzhou, China). MGIEasy Universal DNA Library Prep Set (MGI Tech Co., Ltd., Wuhan, China) was used for DNA library preparation according to the manufacturer’s instructions, and the following sequencing was done with the DNBSEQ-G400RS sequencing platform using DNBSEQ-G400RS High-throughput Sequencing Set (PE 150) (MGI Tech Co., Ltd., Wuhan, China), providing 150 bp paired-end sequencing reads. Quantity and quality of DNA were evaluated using the Qubit 2.0 fluorometer (ThermoFisher Scientific, Waltham, MA, USA) and Agilent 2100 Bioanalyzer system (Agilent Technologies, Santa Clara, CA, USA), respectively.

In total, 40 E. coli strains were subjected to whole genome sequencing (WGS). WGS was outsourced to Bioengineering Lab. Co., Ltd. (Kanagawa, Japan). First, the DNA was fragmented using an ultrasonicator (Covaris Inc, MA, USA) to a fragment length of 400 bp. The library preparation was conducted according to the manual using a MGIEasy Universal DNA Library PrepSet (MGI Tech Co., Ltd, Shenzhen, China). The concentration of the prepared library was measured using the Qubit 30 Fluorometer (Promega Co., WI, USA) and the Qubit dsDNA HS assay kit (Promega). The quality of the prepared library was confirmed using Fragment Analyzer and a dsDNA 915 Reagent Kit (Advanced Analytical Technologies, NY, USA). Circular DNA was prepared according to the manual using the created library and the MGIEasy Circularization Kit (MGI Tech Co.). A DNBSEQ G400RS high-throughput sequencing kit (MGI Tech) was used to prepare DNA nanoballs (DNBs) according to the manual. Sequencing analysis of the prepared DNBs was performed using DNBSEQ G400 under the condition of 2 × 150 bp.