DOI: https://doi.org/10.18524/2307-4663.2020.3(50).219362
СІКВЕНС ГЕНОМУ BACILLUS PUMILUS ONU 554, ІЗОЛЬОВАНОГО З ГЛИБОКОВОДНИХ ДОННИХ ВІДКЛАДЕНЬ ЧОРНОГО МОРЯ
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Arndt D, Grant JR, Marcu A, Sajed T, Pon A, Liang Y, Wishart DS et al. PHASTER: a better, faster version of the PHAST phage search tool. Nucleic Acids Res. 2016;44(1):16-21.
Auch AF, von Jan M, Klenk HP, Göker M. Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Standards in genomic sciences. 2010;2(1):117-134.
Aunpad R, Panbangred W. Evidence for two putative holin-like peptides encoding genes of Bacillus pumilus strain WAPB4. Current microbiology. 2012;64(4):343-348.
Bertelli C, Laird MR, Williams KR, Lau BY, Hoad G et al. IslandViewer 4: Expanded prediction of genomic islands for larger-scale datasets. Nucleic Acids Research. 2017;45:30-35.
Blin K, Shaw S, Steinke K, Villebro R, Ziemert N, Lee S Y et al. antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline. Nucleic Acids Res. 2019;47(1):81-87.
De S, Kaur G, Roy A, Dogra G, Kaushik R, Yadav P et al. A Simple Method for the Efficient Isolation of Genomic DNA from Lactobacilli Isolated from Traditional Indian Fermented Milk (dahi). Indian J Microbiol. 2010;50(4):412-418.
Garcia-Ramon, DC et al. An in-depth characterization of the entomopathogenic strain Bacillus pumilus 15.1 reveals that it produces inclusion bodies similar to the parasporal crystals of Bacillus thuringiensis. Applied microbiology and biotechnology. 2016;100(8):3637-3654.
Ivanytsia VО, Shtenikov MD, Ostapchuk АМ. [Facultatively anaerobic sporeforming bacteria of deep-sea sediments of the Black sea]. Microbiology & Biotechnology. 2017;40(4):94-103. Ukrainian.
Joensen KG, Scheutz F, Lund O, Hasman H, Kaas RS, Nielsen EM et al. Real-time whole-genome sequencing for routine typing, surveillance, and outbreak detection of verotoxigenic Escherichia coli. J Clin. Micobiol. 2014;52(5):1501-1510.
Kemperman R, Kuipers A, Karsens H, Nauta A, Kuipers O, Kok J. Identification and characterization of two novel clostridial bacteriocins, circularin A and closticin 574. Applied and Environmental Microbiology. 2003;69(3):1589-1597.
Kovaleva VA, Shalovylo YI, Gorovik YN, Lagonenko A, Evtushenkov AN, Gout R. Bacillus pumilus – a new phytopathogen of Scots pine. Journal of Forest Science. 2015;61(3):131-137.
Kubicek CP, Steindorff AS, Chenthamara K, Manganiello G, Henrissat B, Zhang J. et al. Evolution and comparative genomics of the most common Trichoderma species. BMC genomics. (2019);20(1):485.
Kyrpides, NC. Fifteen years of microbial genomics: meeting the challenges and fulfilling the dream. Nature biotechnology. 2009;27(7):627-632.
Lee I, Kim YO, Park SC, Chun J OrthoANI: an improved algorithm and software for genome-based species definition of Bacteria and Archaea // 第 七届全国微生物资源学术暨国际微生物系统与分类学研讨会. 2015:180- 180.
Logan NA, De Vos P. Bacillus. In: Bergey's Manual of Systematics of Archaea and Bacteria Ed Whitman W B John Wiley & Sons, Inc, 2015. Режим доступу: http://onlinelibrary.wiley.com/doi/10.1002/9781118960608. gbm00530/abstract
Meier-Kolthoff JP, Göker M. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun. 2019;10(1):1 -10.
Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ, Disz T et al. The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic acids research. 2014; 42(1):206-214.
Shtenikov MD, Ostapchuk AM, Ivanytsia VO. Antagonistic activity of endosporeforming bacteria of deep water the Black Sea sediments. Microbiology & Biotechnology. 2018;43(3):82-89.
Tyurin AP, Efimenko TA, Prokhorenko IA, Rogozhin EA, Malanicheva IA, Zenkova VA. Amicoumacins and Related Compounds: Chemistry and Biology. Studies in Natural Products Chemistry. Elsevier, 2018. 55:385-441.
van Heel AJ, de Jong A, Song C, Viel JH, Kok J, Kuipers O P. BAGEL4: a user-friendly web server to thoroughly mine RiPPs and bacteriocins. Nucleic Acids Res. 2018;46(1):278-281.
van Heel AJ, Montalban-Lopez M, Oliveau Q, Kuipers O P. Genomeguided identification of novel head-to-tail cyclized antimicrobial peptides, exemplified by the discovery of pumilarin. Microbial genomics. 2017;3(10). doi: 10.1099/mgen.0.000134
Wattam AR, Brettin T, Davis JJ, Gerdes S, Kenyon R, Machi D et al. Assembly, Annotation, and Comparative Genomics in PATRIC, the All Bacterial Bioinformatics Resource Center. In: Comparative Genomics. Methods Mol Biol. New York: Humana Press; 2018. p. 79-101.
Yoon SH, Ha SM, Lim JM, Kwon SJ, Chun, J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek. 2017;110(10):1281-1286.
Zankari E, Hasman H, Cosentino S, Vestergaard M, Rasmussen S, Lund O et al. Identification of acquired antimicrobial resistance genes. J Antimicrob Chemother. 2012;67(11):2640-2644.
Zhao X, Kuipers О P Identification and classification of known and putative antimicrobial compounds produced by a wide variety of Bacillales species. BMC Genomics. 2016;17(1):1-18.
Пристатейна бібліографія ГОСТ
Arndt D., Grant J.R., Marcu A., Sajed T., Pon A., Liang Y., Wishart D. S.et al. PHASTER: a better, faster version of the PHAST phage search tool. // Nucleic Acids Res. – 2016. – V. 44, N 1. – P. 16–21.
Auch A.F., von Jan M., Klenk H.P., Göker M. Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. // Standards in genomic sciences. – 2010. – V. 2, N 1. – C. 117–134.
Aunpad R., Panbangred W. Evidence for two putative holin-like peptides encoding genes of Bacillus pumilus strain WAPB4. // Current microbiology. – 2012. –V. 64, N 4. – C. 343–348.
Bertelli C., Laird M.R., Williams K.R., Lau B.Y., Hoad G et al.IslandViewer 4: Expanded prediction of genomic islands for larger-scale datasets. // Nucleic Acids Research. – 2017. – 45. – P. 30–35.
Blin K., Shaw S., Steinke K., Villebro R., Ziemert N., Lee S. Y.et al.antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline. // Nucleic Acids Res. – 2019. – V. 47, N 1 . – P. 81–87.
De S., Kaur G., Roy A., Dogra G., Kaushik R., Yadav P. et al. A Simple Method for the Efficient Isolation of Genomic DNA from Lactobacilli Isolated from Traditional Indian Fermented Milk (dahi). // Indian J Microbiol. – 2010. – V. 50, N 4. – P. 412–418.
Garcia-Ramon D.C., Molina C.A., Osuna A., Vílchez S. An in-depth characterization of the entomopathogenic strain Bacillus pumilus 15.1 reveals that it produces inclusion bodies similar to the рarasporal crystals of Bacillus thuringiensis.// Applied microbiology and biotechnology. – 2016. –V. 100, N 8. – P. 3637–3654.
Ivanytsia V.О., Shtenikov M.D., Ostapchuk А. М.[Facultatively anaerobic sporeforming bacteria of deep-sea sediments of the Black sea]. // Microbiology & Biotechnology. – 2017. – V. 40, N 4. – P. 94–103. Ukrainian.
Joensen K.G., Scheutz F., Lund O., Hasman H., Kaas R.S., Nielsen E.M. et al. Real-time whole-genome sequencing for routine typing, surveillance, and outbreak detection of verotoxigenic Escherichia coli.// J. Clin. Micobiol. – 2014. – V. 52, N 5. – P. 1501–1510.
Kemperman R., Kuipers A., Karsens H., Nauta A., Kuipers O., Kok J. Identification and characterization of two novel clostridial bacteriocins, circularin A and closticin 574. // Applied and Environmental Microbiology. – 2003. – V. 69, N 3. – P. 1589–1597.
Kovaleva V.A., Shalovylo Y.I., Gorovik Y.N., Lagonenko A., Evtushenkov A. N., Gout R. Bacillus pumilus – a new phytopathogen of Scots pine. // Journal of Forest Science. – 2015. – V. 61, N 3. – P. 131–137.
Kubicek C.P., Steindorff A.S., Chenthamara K., Manganiello G., Henrissat B., Zhang J. et al. Evolution and comparative genomics of the most common Trichoderma species. // BMC genomics. – 2019. – V. 20, N 1. – P. 485.
Kyrpides N.C. Fifteen years of microbial genomics: meeting the challenges and fulfilling the dream. // Nature biotechnology. – 2009. – V. 27, N 7. – P. 627–632.
Lee I., Kim Y. O., Park S.C., Chun J.OrthoANI: an improved algorithm and software for genome-based species definition of Bacteria and Archaea // 第 七届全国微生物资源学术暨国际微生物系统与分类学研讨会. – 2015. – P. 180–180.
Logan N.A, De Vos P. Bacillus. In: Bergey’s Manual of Systematics of Archaea and Bacteria Ed Whitman WB. John Wiley & Sons, Inc, 2015. Режим доступу: http://onlinelibrary.wiley.com/doi/10.1002/9781118960608. gbm00530/abstract
Meier-Kolthoff J.P., Göker M. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. // Nat Commun. – 2019. – V. 10, N 1. – P. 1–10.
Overbeek R., Olson R., Pusch G.D., Olsen G.J., Davis J.J., Disz T. et al.The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). // Nucleic acids research. – 2014. – V. 42, N 1. – P. 206– 214.
Shtenikov M.D., Ostapchuk A.M., Ivanytsia V.O. Antagonistic activity of endosporeforming bacteria of deep water the Black Sea sediments. // Microbiology & Biotechnology. – 2018. – V. 43, N 3. – P. 82–89.
Tyurin A.P., Efimenko T.A., Prokhorenko I.A., Rogozhin E.A., Malanicheva I.A., Zenkova V.A. Amicoumacins and Related Compounds: Chemistry and Biology. // Studies in Natural Products Chemistry. – Elsevier, 2018. – 55. – P. 385–441.
van Heel A.J., de Jong A., Song C., Viel J. H., Kok J., Kuipers O.P. BAGEL4: a user-friendly web server to thoroughly mine RiPPs and bacteriocins. // Nucleic Acids Res. – 2018. – V. 46, N 1. – P. 278–281.
van Heel A.J., Montalban-Lopez M., Oliveau Q., Kuipers O.P. Genomeguided identification of novel head-to-tail cyclized antimicrobial peptides, exemplified by the discovery of pumilarin. // Microbial genomics. – 2017. – Vol. 3. – № 10. doi: 10.1099/mgen.0.000134
Wattam A.R., Brettin T., Davis J.J., Gerdes S., Kenyon R., Machi D. et al. Assembly, Annotation, and Comparative Genomics in PATRIC, the All Bacterial Bioinformatics Resource Center. In: Comparative Genomics. Methods Mol Biol. New York: Humana Press; 2018. p. 79–101.
Yoon S.H., Ha S.M., Lim J.M., Kwon S. J.,Chun, J. A large-scale evaluation of algorithms to calculate average nucleotide identity. // Antonie van Leeuwenhoek. – V. 2017. – V. 110, N 10. – P. 1281–1286.
Zankari E., Hasman H., Cosentino S., Vestergaard M., Rasmussen S., Lund O. et al. Identification of acquired antimicrobial resistance genes. // J Antimicrob Chemother. – 2012. – V. 67, N 11. – P. 2640–2644.
Zhao X., Kuipers О.P. Identification and classification of known and putative antimicrobial compounds produced by a wide variety of Bacillales species. // BMC Genomics. – 2016. – V. 17, N 1. – P. 1–18.

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ISSN 2076-0558 (Print); 2307-4663 (Online)
DOI 10.18524/2307-4663