PROKARYOTES
crossm Draft Genome Sequences of Bacillus cereus E41 and Bacillus anthracis F34 Isolated from Algerian Salt Lakes Mohamed Seghir Daas,a,b Albert Remus R. Rosana,c Jeella Z. Acedo,d Farida Nateche,e Salima Kebbouche-Gana,a John C. Vederas,d Rebecca J. Casec Valcore Laboratory, Department of Biology, University M’Hamed Bougara of Boumerdès, Boumerdès, Algeriaa; Food Technology Research Division, Institut National de la Recherche Agronomique d'Algérie, El Harrach, Algiers, Algeriab; Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canadac; Department of Chemistry, University of Alberta, Edmonton, Alberta, Canadad; Microbiology Group, Laboratory of Cellular and Molecular Biology, Faculty of Biological Sciences, USTHB, Bab Ezzouar, Algiers, Algeriae
ABSTRACT Two strains of Bacillus, B. cereus E41 and B. anthracis F34, were isolated from a salt lake in Aïn M’lila-Oum El Bouaghi, eastern Algeria, and Ain Baida-Ouargla, southern Algeria, respectively. Their genomes display genes for the production of several bioactive secondary metabolites, including polyhydroxyalkanoate, iron siderophores, lipopeptides, and bacteriocins.
B
acillus is a large and ubiquitous genus commonly isolated from soil and sediment habitats. Bacillus spp. are aerobic or facultative anaerobic Gram-positive rodshaped bacteria capable of forming spores, which allows them to persist and disperse in diverse habitats. Bacillus spp. also produce a variety of bioactive small molecules, and we report here the genome sequences of two isolates, which encode the production of polyhydroxyalkanoate, iron siderophores, lipopeptides, and bacteriocins. Genomic DNA was extracted from single-colony isolates using the DNeasy blood and tissue kit (Qiagen), according to the manufacturer’s protocol. Sequencing libraries from the genomic DNA extracts were prepared using the Nextera XT DNA library preparation kit (Illumina). Whole-genome sequencing was performed using the MiSeq reagent kit version 2 (2 ⫻ 250 cycles) and MiSeq sequencing technology (Illumina), generating 150-bp paired-end reads. De novo assembly of the reads into contiguous sequences (contigs) was done using the CLC Genomics Workbench version 7.5.2 (CLC bio, Aarhus, Denmark). All of the genomes sequenced exceeded 300⫻ coverage. The draft genomes of E41 and F34 yielded 29 and 66 contigs, respectively. The draft genomes were then annotated using RAST version 2.0 (1) or PGAP (http://www.ncbi .nlm.nih.gov/genome/annotation_prok). Species identities were determined by an average nucleotide identity (ANI) of ⬎97% using JSpecies version 1.2.1 (2) with previously sequenced genomes in the GenBank database. Secondary metabolites were predicted using antiSMASH version 4 (3). The potential to produce bacteriocins was detected using BAGEL3 (4). Genome annotation by the NCBI PGAP predicted 5,779 genes, including 5,492 coding sequences (CDSs), 12 rRNAs, and 98 tRNAs, in the genome of Bacillus cereus E41, and 6,265 genes, including 5,866 CDSs, 10 rRNAs, and 76 tRNAs, in the genome of Bacillus anthracis F34. Both Bacillus spp. have the complete gene cluster for polyhydroxyalkanoate biosynthesis that is used for the production of bioplastics. They are also predicted to produce the siderophore petrobactin (asbABCDEF) (5). In addition, they both contain the bacillibactin nonribosomal peptide synthetase (NRPS) operon dhbACEF and the corresponding iron-bacillibactin uptake cluster feuABCD-yuiI (6). Volume 5 Issue 20 e00383-17
Received 29 March 2017 Accepted 30 March 2017 Published 18 May 2017 Citation Daas MS, Rosana ARR, Acedo JZ, Nateche F, Kebbouche-Gana S, Vederas JC, Case RJ. 2017. Draft genome sequences of Bacillus cereus E41 and Bacillus anthracis F34 isolated from Algerian salt lakes. Genome Announc 5:e00383-17. https://doi.org/10.1128/ genomeA.00383-17. Copyright © 2017 Daas et al. This is an openaccess article distributed under the terms of the Creative Commons Attribution 4.0 International license. Address correspondence to Rebecca J. Case, [email protected]. M.S.D. and A.R.R.R. contributed equally to this work.
genomea.asm.org 1
Daas et al.
The B. cereus E41 genome contains a complete gene cluster for the lantibiotic thusin (thsA1TM1A2A2=M2FE) (7). Furthermore, the genome contains biosynthetic gene clusters for surfactin, polyoxypeptin, as well as sugar compounds, such as S-glycan and exopolysaccharides. Accession number(s). The whole-genome shotgun projects have been deposited in DDBJ/ENA/GenBank for B. cereus E41 (MTAT00000000) and B. anthracis F34 (MTAU00000000). ACKNOWLEDGMENTS We gratefully acknowledge the help of Georgina McIntyre from the Applied Genomic Core, University of Alberta for assisting in library preparation and wholegenome sequencing. We thank Fabini D. Orata for assistance in bioinformatics analysis. This work was performed under the auspices of the Natural Sciences and Engineering Research Council of Canada to R.J.C. and J.C.V. This work, including the efforts of A.R.R.R. and J.Z.A., was funded by Alberta Innovates–Technology Futures and Alberta Innovates–Health Solutions, respectively. M.S.D. is funded by Agence Universitaire de la Francophonie, France. M.S.D., F.N. and S.K.-G. were supported by the National Fund for Scientific Research of Algeria.
REFERENCES 1. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O. 2008. The RAST server: rapid annotations using subsystems technology. BMC Genomics 9:75. https://doi.org/10.1186/1471-2164-9-75. 2. Richter M, Rosselló-Móra R. 2009. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 106: 19126 –19131. https://doi.org/10.1073/pnas.0906412106. 3. Weber T, Blin K, Duddela S, Krug D, Kim HU, Bruccoleri R, Lee SY, Fischbach MA, Müller R, Wohlleben W, Breitling R, Takano E, Medema MH. 2015. antiSMASH 3.0 —a comprehensive resource for the genome mining of biosynthetic gene clusters. Nucleic Acids Res 43:W237–W243. https:// doi.org/10.1093/nar/gkv437. 4. van Heel AJ, de Jong A, Montalbán-López M, Kok J, Kuipers OP. 2013. BAGEL3: automated identification of genes encoding bacteriocins and (non-)bactericidal posttranslationally modified peptides. Nucleic Acids Res 41:W448 –W453. https://doi.org/10.1093/nar/gkt391.
Volume 5 Issue 20 e00383-17
5. Read TD, Peterson SN, Tourasse N, Baillie LW, Paulsen IT, Nelson KE, Tettelin H, Fouts DE, Eisen JA, Gill SR, Holtzapple EK, Okstad OA, Helgason E, Rilstone J, Wu M, Kolonay JF, Beanan MJ, Dodson RJ, Brinkac LM, Gwinn M, DeBoy RT, Madpu R, Daugherty SC, Durkin AS, Haft DH, Nelson WC, Peterson JD, Pop M, Khouri HM, Radune D, Benton JL, Mahamoud Y, Jiang L, Hance IR, Weidman JF, Berry KJ, Plaut RD, Wolf AM, Watkins KL, Nierman WC. 2003. The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria. Nature 423:81– 86. https://doi.org/10 .1038/nature01586. 6. Hotta K, Kim CY, Fox DT, Koppisch AT. 2010. Siderophore-mediated iron acquisition in Bacillus anthracis and related strains. Microbiology 156: 1918 –1925. https://doi.org/10.1099/mic.0.039404-0. 7. Xin B, Zheng J, Liu H, Li J, Ruan L, Peng D, Sajid M, Sun M. 2016. Thusin, a novel two-component lantibiotic with potent antimicrobial activity against several Gram-positive pathogens. Front Microbiol 7:1115. https:// doi.org/10.3389/fmicb.2016.01115.
genomea.asm.org 2
crossm Draft Genome Sequences of Bacillus cereus E41 and Bacillus anthracis F34 Isolated from Algerian Salt Lakes Mohamed Seghir Daas,a,b Albert Remus R. Rosana,c Jeella Z. Acedo,d Farida Nateche,e Salima Kebbouche-Gana,a John C. Vederas,d Rebecca J. Casec Valcore Laboratory, Department of Biology, University M’Hamed Bougara of Boumerdès, Boumerdès, Algeriaa; Food Technology Research Division, Institut National de la Recherche Agronomique d'Algérie, El Harrach, Algiers, Algeriab; Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canadac; Department of Chemistry, University of Alberta, Edmonton, Alberta, Canadad; Microbiology Group, Laboratory of Cellular and Molecular Biology, Faculty of Biological Sciences, USTHB, Bab Ezzouar, Algiers, Algeriae
ABSTRACT Two strains of Bacillus, B. cereus E41 and B. anthracis F34, were isolated from a salt lake in Aïn M’lila-Oum El Bouaghi, eastern Algeria, and Ain Baida-Ouargla, southern Algeria, respectively. Their genomes display genes for the production of several bioactive secondary metabolites, including polyhydroxyalkanoate, iron siderophores, lipopeptides, and bacteriocins.
B
acillus is a large and ubiquitous genus commonly isolated from soil and sediment habitats. Bacillus spp. are aerobic or facultative anaerobic Gram-positive rodshaped bacteria capable of forming spores, which allows them to persist and disperse in diverse habitats. Bacillus spp. also produce a variety of bioactive small molecules, and we report here the genome sequences of two isolates, which encode the production of polyhydroxyalkanoate, iron siderophores, lipopeptides, and bacteriocins. Genomic DNA was extracted from single-colony isolates using the DNeasy blood and tissue kit (Qiagen), according to the manufacturer’s protocol. Sequencing libraries from the genomic DNA extracts were prepared using the Nextera XT DNA library preparation kit (Illumina). Whole-genome sequencing was performed using the MiSeq reagent kit version 2 (2 ⫻ 250 cycles) and MiSeq sequencing technology (Illumina), generating 150-bp paired-end reads. De novo assembly of the reads into contiguous sequences (contigs) was done using the CLC Genomics Workbench version 7.5.2 (CLC bio, Aarhus, Denmark). All of the genomes sequenced exceeded 300⫻ coverage. The draft genomes of E41 and F34 yielded 29 and 66 contigs, respectively. The draft genomes were then annotated using RAST version 2.0 (1) or PGAP (http://www.ncbi .nlm.nih.gov/genome/annotation_prok). Species identities were determined by an average nucleotide identity (ANI) of ⬎97% using JSpecies version 1.2.1 (2) with previously sequenced genomes in the GenBank database. Secondary metabolites were predicted using antiSMASH version 4 (3). The potential to produce bacteriocins was detected using BAGEL3 (4). Genome annotation by the NCBI PGAP predicted 5,779 genes, including 5,492 coding sequences (CDSs), 12 rRNAs, and 98 tRNAs, in the genome of Bacillus cereus E41, and 6,265 genes, including 5,866 CDSs, 10 rRNAs, and 76 tRNAs, in the genome of Bacillus anthracis F34. Both Bacillus spp. have the complete gene cluster for polyhydroxyalkanoate biosynthesis that is used for the production of bioplastics. They are also predicted to produce the siderophore petrobactin (asbABCDEF) (5). In addition, they both contain the bacillibactin nonribosomal peptide synthetase (NRPS) operon dhbACEF and the corresponding iron-bacillibactin uptake cluster feuABCD-yuiI (6). Volume 5 Issue 20 e00383-17
Received 29 March 2017 Accepted 30 March 2017 Published 18 May 2017 Citation Daas MS, Rosana ARR, Acedo JZ, Nateche F, Kebbouche-Gana S, Vederas JC, Case RJ. 2017. Draft genome sequences of Bacillus cereus E41 and Bacillus anthracis F34 isolated from Algerian salt lakes. Genome Announc 5:e00383-17. https://doi.org/10.1128/ genomeA.00383-17. Copyright © 2017 Daas et al. This is an openaccess article distributed under the terms of the Creative Commons Attribution 4.0 International license. Address correspondence to Rebecca J. Case, [email protected]. M.S.D. and A.R.R.R. contributed equally to this work.
genomea.asm.org 1
Daas et al.
The B. cereus E41 genome contains a complete gene cluster for the lantibiotic thusin (thsA1TM1A2A2=M2FE) (7). Furthermore, the genome contains biosynthetic gene clusters for surfactin, polyoxypeptin, as well as sugar compounds, such as S-glycan and exopolysaccharides. Accession number(s). The whole-genome shotgun projects have been deposited in DDBJ/ENA/GenBank for B. cereus E41 (MTAT00000000) and B. anthracis F34 (MTAU00000000). ACKNOWLEDGMENTS We gratefully acknowledge the help of Georgina McIntyre from the Applied Genomic Core, University of Alberta for assisting in library preparation and wholegenome sequencing. We thank Fabini D. Orata for assistance in bioinformatics analysis. This work was performed under the auspices of the Natural Sciences and Engineering Research Council of Canada to R.J.C. and J.C.V. This work, including the efforts of A.R.R.R. and J.Z.A., was funded by Alberta Innovates–Technology Futures and Alberta Innovates–Health Solutions, respectively. M.S.D. is funded by Agence Universitaire de la Francophonie, France. M.S.D., F.N. and S.K.-G. were supported by the National Fund for Scientific Research of Algeria.
REFERENCES 1. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O. 2008. The RAST server: rapid annotations using subsystems technology. BMC Genomics 9:75. https://doi.org/10.1186/1471-2164-9-75. 2. Richter M, Rosselló-Móra R. 2009. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 106: 19126 –19131. https://doi.org/10.1073/pnas.0906412106. 3. Weber T, Blin K, Duddela S, Krug D, Kim HU, Bruccoleri R, Lee SY, Fischbach MA, Müller R, Wohlleben W, Breitling R, Takano E, Medema MH. 2015. antiSMASH 3.0 —a comprehensive resource for the genome mining of biosynthetic gene clusters. Nucleic Acids Res 43:W237–W243. https:// doi.org/10.1093/nar/gkv437. 4. van Heel AJ, de Jong A, Montalbán-López M, Kok J, Kuipers OP. 2013. BAGEL3: automated identification of genes encoding bacteriocins and (non-)bactericidal posttranslationally modified peptides. Nucleic Acids Res 41:W448 –W453. https://doi.org/10.1093/nar/gkt391.
Volume 5 Issue 20 e00383-17
5. Read TD, Peterson SN, Tourasse N, Baillie LW, Paulsen IT, Nelson KE, Tettelin H, Fouts DE, Eisen JA, Gill SR, Holtzapple EK, Okstad OA, Helgason E, Rilstone J, Wu M, Kolonay JF, Beanan MJ, Dodson RJ, Brinkac LM, Gwinn M, DeBoy RT, Madpu R, Daugherty SC, Durkin AS, Haft DH, Nelson WC, Peterson JD, Pop M, Khouri HM, Radune D, Benton JL, Mahamoud Y, Jiang L, Hance IR, Weidman JF, Berry KJ, Plaut RD, Wolf AM, Watkins KL, Nierman WC. 2003. The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria. Nature 423:81– 86. https://doi.org/10 .1038/nature01586. 6. Hotta K, Kim CY, Fox DT, Koppisch AT. 2010. Siderophore-mediated iron acquisition in Bacillus anthracis and related strains. Microbiology 156: 1918 –1925. https://doi.org/10.1099/mic.0.039404-0. 7. Xin B, Zheng J, Liu H, Li J, Ruan L, Peng D, Sajid M, Sun M. 2016. Thusin, a novel two-component lantibiotic with potent antimicrobial activity against several Gram-positive pathogens. Front Microbiol 7:1115. https:// doi.org/10.3389/fmicb.2016.01115.
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