Complete genome sequence data of a broad-spectrum antipathogen, Bacillus amyloliquefaciens KCTC 18343P, isolated from Makgeolli, Korean traditional rice wine.

Bacillus amyloliquefaciens KCTC18343P(=MBE1283) isolated from Makgeolli, Korean traditional rice wine, strongly inhibits the growth of food and plant pathogens. A complete genome sequence of B. amyloliquefaciens KCTC18343P is presented in this report. The genome is 3,979,925 bp in size and harbors 3856 genes. The BioProject has been deposited at DDBJ/EMBL/GenBank. The GenBank accession numbers are PRJNA301202 for the BioProject, NZ_CP013727 for the chromosome, and NZ_CP013728 for the plasmid.

Data description

Bacillus amyloliquefaciens strains are reported to have antimicrobial activity exerted by the secondary metabolites, including bacillomycin D, fengycin, surfactin, subtilin, and subtilosin A [7,8]. The B. amyloliquefaciens strain KCTC18343P isolated from Makgeolli, Korean traditional rice wine, exhibited strong antimicrobial activity against the food and plant pathogens Aspergillus terreus, Aspergillus flavus, Staphylococcus aureus, Escherichia coli O157:H7, Bacillus cereus, Salmonella Typhimurium, and Listeria monocytogenes, which is consistent with previous reports [1,11]. We previously reported that B. amyloliquefaciens KCTC18343P is also antagonistic to the human pathogen Cryptococcus neoformans [11]. This strain has been deposited as KCTC18343P in the Korean Collection for Type Cultures (KCTC). The corresponding BioProject has been deposited at DDBJ/EMBL/GenBank. The GenBank accession number are PRJNA301202 for the BioProject, CP013727 for the chromosome, and NZ_CP013728 for the plasmid.

A total of 512,192,070 paired-end reads with an average read length of 5843 base pairs (bp) were obtained. The reads were assembled de novo into two contigs using a Hierarchical Genome Assembly Process (HGAP). The genome of strain KCTC18343P consisted of a single circular chromosome and one circular plasmid with a total length of 3,979,925 bp and 46.5% G + C content. In total, 3856 gene-coding regions, 27 rRNA operons, and 86 tRNAs were identified (Table 1). A genome-wide comparative analysis of two B. amyloliquefaciens strains, KCTC18343P and DSM7, revealed that the genome of KCTC18343P contains the gene clusters srf and dhb, which encode enzymes involved in biosynthesis of lipopeptide surfactin and bacillibactin, respectively [3,13]. Nine genes associated with macrolactin H, bacillaene, fengycin, difficidin, bacillibactin, bacilysin, mersacidin, surfectin, and butirosin A were identified by antiSMASH [2]. The gene cluster bacillibactin of B. amyloliquefacience KCTC18343P corresponded to that of B. subtilis 168 (similarity 100%). The gene cluster srf of B. amyloliquefaciens KCTC18343P was 82% similar to that of B. velezensis FZB42. The complete genome of B. amyloliquefaciens KCTC18343P showed the highest Average Nucleotide Identity (ANI) value of 99.41% with those of B. amyloliquefaciens Y14 (99.41%) and B. amyloliquefaciens JRS8 (99.27%; Table 2).

Table 1

Genomic features of six different Bacillus amyloliquefaciens strains.

	Length (bp)	G + C content (%)	Predicted ORFs	rRNA genes	tRNA genes	Reference
KCTC18343P	3,979,925	46.5	3725	27	86	–
DSM7	3,980,199	46.1	3870	30	94	[3]
CMW1	3,897,775	45.9	3762	64	5	[9]
MT45	3,897,521	46.1	3752	24	81	[13]
JRS8	4,090,896	46.3	4006	12	1	[1]
Y14	4,107,280	46.1	3623	33	100	[8]

Table 2

Average nucleotide identity values among six different Bacillus amyloliquefaciens strains.

	1	2	3	4	5	6
1. KCTC 18343P	100	94.13	93.90	95.04	99.27	99.41
2. DSM7	–	100	98.37	98.78	94.49	95.13
3. CMW1	–	–	100	61.18	56.00	62.14
4. MT45	–	–	–	100	57.70	95.12
5. JRS8	–	–	–	–	100	56.20
6. Y14	–	–	–	–	–	100

Plasmid pBABEL01 is a 13,003 bp circular molecule with a G + C content of 42.6% and harbors three components, replication initiator protein, double-strand origin, and single-strand origin [9], which are found in rolling-circle replication plasmids.

Bacillus amyloliquefaciens KCTC18343P has lower starch-degrading activity and lower resistance to high temperature than other B. amyloliquefaciens strains [11]. We compared the α-amylase amino acid sequences of B. amyloliquefaciens KCTC18343P and B. amyloliquefaciens KCTC13012 and found that the length and position of the active sites are notably different [4,6].

Bacillus amyloliquefaciens KCTC18343P exhibits powerful antimicrobial activity compared to previously reported strains.

Experimental design, materials, and methods

The genomic DNA of B. amyloliquefaciens KCTC18343P was prepared from cells in the exponential growth phase. Genomic DNA was extracted using a G-DEXTMIIc Genomic DNA Extraction Kit (iNtRON, Daejeon, Korea) according to the manufacturer's instructions.

The complete genome of B. amyloliquefaciens KCTC18343P was sequenced using the PacBio RSII (P6–C4) platform (Pacific Biosciences, Menlo Park, CA, USA). The reads were assembled de novo into two contigs (175-fold coverage) using a hierarchical genome assembly process. Prokka was used to predict and subsequently annotate open reading frames [10]. Annotations were computed using eggNOG-mapper based on eggNOG 4.5 orthology data [5]. Pairwise average nucleotide identity between KCTC18343P and other B. amyloliquefaciens strains in the database was determined using the EZBioCloud Web server [12]. On antiSMASH bacterial version 5.1.1(https://antismash.secondarymetabolites.org) was used to identify putative genes in the B. amyloliquefaciens KCTC18343P genome involved in the biological control of phytopathogens.

Specification Table

Subject	Genetics
Specific subject area	Genomics and Molecular Biology
Type of data	Table
How data were acquired	The complete genome sequence was determined using the Pac-Bio RSII(P6–C4).
Data format	Raw and Analyzed
Parameters for data collection	The reads of B. amyloliquefaciens genome by Pac-Bio were assembled de novo into two contigs using HGAP (Hierarchical Genome Assembly Process).
Description of data collection	Whole-genome sequencing followed by genome assembly
Data source location	B. amyloliquefaciens KCTC18343P was isolated from Korean rice wine produced in Kangwon-do, Republic of Korea.
Data accessibility	Data are available within this article, and the genome sequence of B. amyloliquefaciens KCTC18343P is available in GenBank under the accession number NZ_CP013727.
Related research article	Sim, H. S. and Kim, M. D., Antipathogenic activity of Bacillus amyloliquefaciens isolated from Korean traditional rice wine. Microbiol. Biotechnol. Lett. (2016), 44(1), 98–105.

Value of the Data• Bacillus amyloliquefaciens KCTC18343P isolated from Makgeolli (Korean rice wine) exhibits strong and broad antimicrobial activity against pathogens. • The data on genome sequence of strain KCTC18343P can be used to search and characterize biotechnology-relevant enzymes and gene clusters. • Gene clusters srf and dhb which contribute to broad antipathogenic activity were identified by whole-genome analysis.