genome-seq of E. fergusonii
Previously cultured isolate was streaked onto Luria-Bertani (LB) agar and incubated at 37C for 12 hours. A single colony was selected and inoculated into 10 mL of LB broth for DNA extraction. Genomic DNA was extracted using the QIAprep Spin Miniprep Kit (QIAGEN, Germany). The extracted DNA was detected by NanoDrop One UV-Vis spectrophotometer (Thermo Fisher Scientific, USA) for DNA purity, then Qubit 3.0 Fluorometer (Invitrogen, USA) was used to quantify DNA accurately. Since the sample was qualified, size-select long DNA fragments using the BluePippin system (Sage Science, USA). Libraries were prepared with a ligation sequencing kit (SQK-LSK109 kit, Oxford Nanopore Technologies [ONT]). Sequencing was performed using a GridION sequencer (ONT) using a FLO-MIN106D R9.4 flow cell (ONT).