Complete Genome Sequence of Bacillus velezensis YJ11-1-4, a Strain with Broad-Spectrum Antimicrobial Activity, Isolated from Traditional Korean Fermented Soybean Paste.

Bacillus velezensis YJ11-1-4 is a strain that exhibits broad-spectrum antimicrobial activity against various pathogens. It was isolated from doenjang, a traditional Korean fermented soybean paste. The genome comprises a single circular chromosome of 4,006,637 bp with 46.42% G+C content without plasmids.

GENOME ANNOUNCEMENT

Bacillus velezensis was first proposed by Ruiz-García et al. (1) as a surfactant-producing bacterium and was subsequently validated in a later heterotypic synonym of B. amyloliquefaciens based on DNA-DNA hybridization (2). Recently, Dunlap et al. (3) suggested that Bacillus methylotrophicus, Bacillus amyloliquefaciens subsp. plantarum, and “Bacillus oryzicola,” reported as plant pathogen antagonists, should be reclassified as a heterotypic synonym of B. velezensis based on phylogenomic analysis using core genomes. Because diverse foodborne pathogens have been detected from doenjang samples, the use of a starter culture with a broad-spectrum antimicrobial activity is important for food safety during fermentation. Therefore, Bacillus velezensis YJ11-1-4 (Korean Agricultural Culture Collection [KACC] 18396) which has revealed good antimicrobial activities against various foodborne pathogens, including Bacillus cereus, Escherichia coli, Listeria monocytogenes, Staphylococcus aureus, and Aspergillus flavus subsp. Flavus, was isolated from homemade doenjang, and its complete genome was sequenced.

The whole genome of B. velezensis YJ11-1-4 was sequenced using a Pacific Biosciences RS II platform with a 20-kb SMRTbell template library at Macrogen (Seoul, Republic of Korea). It generated a total of 969,934,944 bp (about 198-fold coverage) with 112,837 reads. The sequencing reads were assembled using the Hierarchical Genome Assembly Process version 2.0 (HGAP2.0). The assembled genome of strain YJ11-1-4 comprises a single circular chromosome of 4,006,637 bp with a 46.42% G+C content without plasmids. The complete genome sequence was annotated using the NCBI Prokaryotic Genomes Automatic Annotation Pipeline (PGAAP) (http://www.ncbi.nlm.nih.gov/genomes/static/Pipeline.html). The tRNA and rRNA genes were detected using tRNAscan-SE (4) and RNAmmer version 1.2 (5) software, respectively. Strain YJ11-1-4 contains 3,586 predicted protein-coding sequences. The chromosome harbors 86 tRNA genes for 20 amino acids and 9 rRNA operons.

Genomic analysis reveals that the genome contains two complete antibiotic biosynthesis operons of bacilysin (targeting a wide range of bacteria and the yeast Candida albicans) encoded by bacABCDE (AAV30_01545 to AAV30_01565) (6) and amylocyclicin (targeting mostly Gram-positive bacteria) encoded by acnABCDEF (AAV30_04380 to AAV30_04405) (7). Strain YJ11-1-4 harbors many operons encoding nonribosomal synthesized antimicrobial peptides, including fengycin (targeting fungi) encoded by fenEDCBA (AAV30_10135 to AAV30_10160), bacillomycin D (targeting yeast) encoded by bmyDABC (AAV30_10275 to AAV30_10290), surfactin (targeting virus) encoded by srfABCD (AAV30_17390 to AAV30_17405), and an LCI gene (targeting some Gram-negative bacteria) (AAV30_17550) (6). Several biosynthesis clusters of antibacterial polyketides, such as bacillaene (AAV30_10840 to AAV30_10905), macrolactin (AAV30_12135 to AAV30_12175), and difficidin (AAV30_07950 to AAV30_08020), were also found in the genome. In conclusion, genomic analysis suggests that B. velezensis YJ11-1-4 can be used as a biocontrol agent of various foodborne pathogens in doenjang.

Accession number(s).

The genome information for B. velezensis YJ11-1-4 was deposited in NCBI under GenBank accession number CP011347.