Takara minibest bacteria genomic dna extraction kit ver 3

E. coli DH5α and E. coli BL21 (DE3) were provided by Tiangen Biochemical Technology Co., Ltd. (Beijing, China). Lactobacillus sakei LS was isolated from a kind of fermented fish product [10 (link)]. TaKaRa MiniBEST Bacteria Genomic DNA Extraction Kit Ver.3.0, DNA Ligation Kit Ver.2.1, PrimeSTAR^® Max DNA Polymerase, enzymes (SacI and XhoI) and DNA markers for molecular cloning were obtained from Takara Bio Inc. (Dalian, China). Copper chloride (CuCl₂), isopropyl-β-D-thiogalactopyranoside (IPTG), histamine, and tyramine were purchased from Aladdin Company (Shanghai, China). Nickel-chelating nitrilotriacetic acid (Ni-NTA) agarose gel was purchased from Shanghai Yuanye Biotechnology Co., Ltd. (Shanghai, China). Various kits (SanPrep Column Plasmid Mini-Preps Kit, SanPrep Column DNA Gel Extraction Kit, SanPrep Column PCR Product Purification Kit), 2,2 -azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) were purchased from Sigma (Shanghai, China). Kanamycin was purchased from Shenggong Bioengineering Co., Ltd. (Shanghai, China). A protein marker was purchased from Biyuntian Biotechnology Co., Ltd. (Shanghai, China). LB medium was purchased from Qingdao Haibo Biotechnology Co., Ltd. (Qingdao, China). All other chemicals and reagents were analytical grade. Fish, tofu, and grape juice were purchased from the local market (Dalian, China).

The genomes of the isolates were extracted using the TaKaRa MiniBEST Bacteria Genomic DNA Extraction Kit Ver.3.0 (TAKARA, Dalian, China) according to manufacturer’s instructions. Genome sequencing was carried out by the Shanghai Majorbio company. DNA libraries harboring 400 bp DNA fragments were prepared using the NEXTflex^TMRapid DNA-Seq following manufacturer’s instructions and pair-end sequenced (2 × 150 bp) on the HiSeq × 10 system (Illumina, San Diego, CA, United States). The quality of the sequence criteria was Q20 ≥ 90%, the depth of sequencing was 100-fold of the genome coverage. The original image data is transferred into sequence data via base calling, which is defined as raw reads and saved as FASTQ file. Quality information by Fastp software V0.20.1² was applied for quality trimming, by which the low-quality data was removed to form clean data. The assembly of the clean reads was performed using SOAPdenovo2³. The sequence reads for 64 isolates are deposited and publicly available under the bioproject accession number PRJEB41790. Publicly available genome sequences of 20 clinical isolates were referred to compare the evolutionary relationship (Supplementary Table 2).