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Journal of Biotechnology journal homepage: www.elsevier.com/locate/jbiotec

Genome Announcement

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Complete genome sequence of Bacillus licheniformis BL-09, a probiotic strain isolated from naturally fermented congee

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Pengfei Gao, Guoqiang Yao, Weichen Bao, Jing Li, Heping Zhang, Wenyi Zhang ∗ Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, China

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Article history: Received 8 April 2015 Accepted 16 April 2015 Available online xxx

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Keywords: Bacillus licheniformis Genome Peptide biosynthesis

Bacillus licheniformis BL-09 is a probiotic strain isolated from naturally fermented congee in Inner Mongolia of China. The genome of this strain contains a 4.39 Mb circular chromosome with an average GC content of 45.9%. The analysis of the genome revealed two gene clusters that are related to the peptide biosynthesis. The available genetic information of these peptides makes it possible to construct an improved strain for the industrial production of antimicrobial agents. © 2015 Published by Elsevier B.V.

Bacillus licheniformis is a Gram-positive, spore-forming soil bacterium, which is applied in various aspects of biotechnology industry, such as manufacture of enzymes, antibiotics and 21 biochemicals (Nithya et al., 2013; Pedersen et al., 2012). Phyloge22 23Q3 netically, it is closely related to B. subtilis, the best-studied Bacillus member that undergoes two interesting developmental processes, 24 namely morphological differentiation into spores and physiologi25 cal differentiation into a genetically transformable state (Westers 26 et al., 2003). 27 B. licheniformis BL-09 (IMAUB1002) is a probiotic strain isolated 28 from naturally fermented congee in Inner Mongolia of China (Wang 29 et al., 2010). This strain displayed significant in vitro inhibitory 30 effects against Gram-positive (Listeria monocytogenes and Staphylo31 coccus aureus) and Gram-negative (Escherichia coli, Shigella flexneri 32 and Salmonella typhimurium) bacteria (Wang et al., 2010). It has 33 already been demonstrated that specific B. licheniformis strains are 34 capable of producing peptide antibiotics, including bacitracin, pro35 ticin, and lantibiotic (Rey et al., 2004). To determine the genetic 36 basis of the broad inhibitory effects of B. licheniformis BL-09 on 37 pathogenic bacteria, a whole-genome sequencing project was 38 therefore carried out. 39 Long-insert (3 kb) and short-insert (700 bp) libraries were 40 constructed according to the manufacturer’s instructions of the 41 Illumina Miseq system, which were sequenced in the manner 42 of paired end mode. The coverage of the generated reads was 43 19Q2 20

∗ Corresponding author at: Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, 306 Zhaowuda Street, Hohhot 010018, China. Tel.: +86 471 4316324; fax: +86 471 4305357. E-mail address: [email protected] (W. Zhang).

about 100-fold of the whole genome. The reads from clean data were first assembled using Newbler (version 2.8), yielding a number of contigs with different lengths. Thereafter, SSPACE (version 2.0) was used to combine contigs into scaffolds (Boetzer et al., 2011). Gaps between scaffolds were filled by sequencing the PCR products using Applied Biosystems 3730 DNA analyzer. Phred, Phrap, and Consed software packages (http://www.genome. washington.edu) were used for the final assembly. The analysis of the genome was performed as described previously (Zhang et al., 2015). The genome of B. licheniformis BL-09 contains a 4.39 Mb circular chromosome with an average GC content of 45.9%. There are 4188 coding sequences, 21 rRNAs and 72 tRNAs (Table 1). After annotation, a non-ribosomal peptide synthase operon coding for the pathway of lichenysin biosynthesis was revealed. The operon is highly similar to that of the type strain B. licheniformis ACTT 14580 (Rey et al., 2004), consisting of lichenysin synthetase A (SC10 B2orf00561), lichenysin synthetase B (SC10 B2orf00562) and lichenysin synthetase C (SC10 B2orf00564). As expected, one more peptide-related gene cluster of 13 genes, namely S8A family lantibiotic epidermin serine protease (SC10 B2orf00202), hypothetical protein BH0450 (SC10 B2orf00203), hypothetical protein BH0449 (SC10 B2orf00206), ABC transporter ATP-binding protein (SC10 B2orf00207), transcriptional regulator (SC10 B2orf00208), hypothetical protein BH0447 (SC10 B2orf00209), hypothetical protein BH0446 (SC10 B2orf00210), ABC transporter ATP-binding protein (SC10 B2orf00211), hypothetical protein (SC10 B2orf00212), lantibiotic mersacidin transporter system (SC10 B2orf00213), two lantibiotic mersacidin modifying enzymes (SC10 B2orf00215 and SC10 B2orf00217) and lantibiotic mersacidin (SC10 B2orf00218), was also detected. The availability of genetic information of these

http://dx.doi.org/10.1016/j.jbiotec.2015.04.010 0168-1656/© 2015 Published by Elsevier B.V.

Please cite this article in press as: Gao, P., et al., Complete genome sequence of Bacillus licheniformis BL-09, a probiotic strain isolated from naturally fermented congee. J. Biotechnol. (2015), http://dx.doi.org/10.1016/j.jbiotec.2015.04.010

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2 Table 1 General genome features of Bacillus licheniformis BL-09. Attributes

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Genome size (bp) GC content (%) rRNAs tRNA s Total predicted CDSs

4.39 Mb 45.9% 21 72 4188

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peptides makes it possible to construct an improved industrial strain for the production of antimicrobial agents.

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Nucleotide sequence accession number

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Genome information for the chromosome B. licheniformis BL09 is available in the GenBank database with accession number CP010524. The strain has been deposited at the China General Microbiological Culture Collection Center (CGMCC No. 5686).

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This research was supported by the National Natural Science Foundation of China (Grant No. 31101315 and 31201396), Hi-Tech Research and Development Program of China (863 Planning, Grant No. 2011AA100902), International S&T Cooperation Program of

China (ISTCP, Grant No. 2014DFR31150), and the China Agriculture Research System (Grant No. CARS-37). References Boetzer, M., Henkel, C.V., Jansen, H.J., Butler, D., Pirovano, W., 2011. Scaffolding preassembled contigs using SSPACE. Bioinformatics 27, 578–579. Nithya, V., Murthy, P.S., Halami, P.M., 2013. Development and application of active films for food packaging using antibacterial peptide of Bacillus licheniformis Me1. J. Appl. Microbiol. 115, 475–483. Pedersen, M.B., Yu, S., Plumstead, P., Dalsgaard, S., 2012. Comparison of four feed proteases for improvement of nutritive value of poultry feather meal. J. Anim. Sci. 90 (Suppl. 4), 350–352. Rey, M.W., Ramaiya, P., Nelson, B.A., Brody-Karpin, S.D., Zaretsky, E.J., Tang, M., Lopez de Leon, A., Xiang, H., Gusti, V., Clausen, I.G., Olsen, P.B., Rasmussen, M.D., Andersen, J.T., Jorgensen, P.L., Larsen, T.S., Sorokin, A., Bolotin, A., Lapidus, A., Galleron, N., Ehrlich, S.D., Berka, R.M., 2004. Complete genome sequence of the industrial bacterium Bacillus licheniformis and comparisons with closely related Bacillus species. Genome Biol. 5, R77. Wang, Y.Y., Zhang, H.P., Zhang, L., Liu, W.J., Zhang, Y., Zhang, X.C., Sun, T.S., 2010. In vitro assessment of probiotic properties of Bacillus isolated from naturally fermented congee from Inner Mongolia of China. World J. Microbiol. Biotechnol. 26, 1369–1377. Westers, H., Dorenbos, R., van Dijl, J.M., Kabel, J., Flanagan, T., Devine, K.M., Jude, F., Seror, S.J., Beekman, A.C., Darmon, E., Eschevins, C., de Jong, A., Bron, S., Kuipers, O.P., Albertini, A.M., Antelmann, H., Hecker, M., Zamboni, N., Sauer, U., Bruand, C., Ehrlich, D.S., Alonso, J.C., Salas, M., Quax, W.J., 2003. Genome engineering reveals large dispensable regions in Bacillus subtilis. Mol. Biol. Evol. 20, 2076–2090. Zhang, W.Y., Sun, Z.H., Menghe, B.L.G., Zhang, H.P., 2015. Short communication: single molecule, real-time sequencing technology revealed species- and strainspecific methylation patterns of 2 Lactobacillus strains. J. Dairy Sci., http://dx. doi.org/10.3168/jds. 2014-9272.

Please cite this article in press as: Gao, P., et al., Complete genome sequence of Bacillus licheniformis BL-09, a probiotic strain isolated from naturally fermented congee. J. Biotechnol. (2015), http://dx.doi.org/10.1016/j.jbiotec.2015.04.010

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Complete genome sequence of Bacillus licheniformis BL-09, a probiotic strain isolated from naturally fermented congee.

Bacillus licheniformis BL-09 is a probiotic strain isolated from naturally fermented congee in Inner Mongolia of China. The genome of this strain cont...
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