Bacillus spp. are important producers of bioactive natural products with potential applications in medicine and agriculture. Bacillus sp. SCSIO 05476 from a deep-sea sediment exhibits broad-spectrum antimicrobial activities and strong cytotoxic activity. Here, an integrative approach combining genome mining and metabolic profiling has been applied to decipher the chemical origins of this strain’s varied and significant biological activities. First, genome mining revealed 19 candidate gene clusters encoding the biosynthesis of diverse secondary metabolites. Then, a series of bacillibactins, fengycins, bacillomycins, surfactins, bacillaenes, macrolactins, and related species were found by LC-DAD-MS. Finally, three new linear bacillibactins, linbacillibactins A–C (1–3), along with 11 known secondary metabolites, bacillibactin (4), normal-C13 Val7 surfactin (5), anteiso-C13 Leu7 surfactin (6), iso-C14 Leu7 surfactin (7), normal-C14 Leu7 surfactin (8), anteiso-C14 Leu7 surfactin (9), macrolactin D (10), normal-C14 bacillomycin D (11), iso-C16 bacillomycin D (12), normal-C17 bacillomycin D (13), and iso-C17 bacillomycin D (14), were obtained and elucidated by bioactivity and structure-guided isolation from the fermentation of strain SCSIO 05746. Among them, new compounds 1–3 show significant siderophore activities comparable to that of bacillibactin (4), compounds 13 and 14 exhibit strong cytotoxic activity. At the same time, the strain classification status was confirmed by genomic analyses, and the complete genome sequence of Bacillus siamensis was presented firstly. This study provides a foundation for understanding the mechanisms driving SCSIO 05746’s multiple bioactivities and demonstrates a successful way of discovering bioactive metabolites using a combination of genome mining and metabolic profiling methods.
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We are also truly grateful to Ms. Sun, Ms. Xiao, Ms. Zhang, and Mr. Li of the analytical facility of the South China Sea Institute of Oceanology for recording NMR and MS spectra.
This research was supported by the National Natural Science Foundation of China (41576136, 81425022, 31872036 and U1501223), the Key Laboratory of Tropical Marine Bio-resources and Ecology Program of CAS (LMB151005), the Science and Technology Innovation Program for the Youth Talents of Shenyang (RC170266), and the Youth Innovation Promotion Association CAS (2018229).
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Conflict of interest
The authors declare that they have no conflict of interest.
This article does not contain any studies with human participants or animals performed by any of the authors.
Alanjary M, Kronmiller B, Adamek M, Blin K, Weber T, Huson D, Philmus B, Ziemert N (2017) The Antibiotic Resistant Target Seeker (ARTS), an exploration engine for antibiotic cluster prioritization and novel drug target discovery. Nucleic Acids Res 45(W1):W42–W48. https://doi.org/10.1093/nar/gkx360Google Scholar
Dunlap CA, Kim SJ, Kwon SW, Rooney AP (2015) Phylogenomic analysis shows that Bacillus amyloliquefaciens subsp. plantarum is a later heterotypic synonym of Bacillus methylotrophicus. Int J Syst Evol Micr 65:2104–2109. https://doi.org/10.1099/ijs.0.000226Google Scholar
Dunlap CA, Bowman MJ, Schisler DA, Rooney AP (2016) Genome analysis shows Bacillus axarquiensis is not a later heterotypic synonym of Bacillus mojavensis; reclassification of Bacillus malacitensis and Brevibacterium halotolerans as heterotypic synonyms of Bacillus axarquiensis. Int J Syst Evol Micr 66:2438–2443. https://doi.org/10.1099/ijsem.0.001048Google Scholar
Jeong H, Jeong DE, Kim SH, Song GC, Park SY, Ryu CM, Park SH, Choi SK (2012) Draft genome sequence of the plant growth-promoting bacterium Bacillus siamensis KCTC 13613T. J Bacteriol 194(15):4148-4149. https://doi.org/10.1128/jb.00805-12
Jorgensen JH (1993) Antimicrobial susceptibility testing of bacteria that grow aerobically. Infect Dis Clin N Am 7(2):393–409Google Scholar
Koren S, Schatz MC, Walenz BP, Martin J, Howard JT, Ganapathy G, Wang Z, Rasko DA, McCombie WR, Jarvis ED, Phillippy AM (2012) Hybrid error correction and de novo assembly of single-molecule sequencing reads. Nat Biotech 30(7):693–700. https://doi.org/10.1038/nbt.2280
Pan H-Q, Yu S-Y, Song C-F, Wang N, Hua H-M, Hu J-C, Wang S-J (2015) Identification and characterization of the antifungal substances of a novel Streptomyces cavourensis NA4. J Microbiol Biotechnol 25(3):353–357. https://doi.org/10.4014/jmb.1407.07025Google Scholar
Shang H, Wang Q, Gu H, Wu L (2016) New Bacillus siamensis strain LYLB4, useful for preventing and treating pear fruit rot caused by pear ring rot and soft rot. CN105505834-A,Google Scholar
Sumpavapol P, Tongyonk L, Tanasupawat S, Chokesajjawatee N, Luxanani P, Visessanguan W (2010) Bacillus siamensis sp. nov., isolated from salted crab (poo-khem) in Thailand. Int J Syst Evol Micr 60:2364–2370. https://doi.org/10.1099/ijs.0.018879-0Google Scholar
Tanaka K, Ishihara A, Nakajima H (2014) Isolation of anteiso-C17, iso-C17, iso-C16, and iso-C15 bacillomycin D from Bacillus amyloliquefaciens SD-32 and their antifungal activities against plant pathogens. J Agr Food Chem 62(7):1469–1476. https://doi.org/10.1021/jf404531tGoogle Scholar
Tatusov RL, Natale DA, Garkavtsev IV, Tatusova TA, Shankavaram UT, Rao BS, Kiryutin B, Galperin MY, Fedorova ND, Koonin EV (2001) The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res 29(1):22–28. https://doi.org/10.1093/nar/29.1.22Google Scholar
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(W1):W237–W243. https://doi.org/10.1093/nar/gkv437Google Scholar
Zhang S, Shan J, Qiao L, Song H, Zhai X (2013) New Bacillus siamensis L13 strain having preservation number of CGMCC NO: 7285, for treating tobacco disease e.g. tobacco brown spot disease and preparing disinfectant, fermentation-promoting agent and micro-organism seaweed fertilizer. CN103215210-B,Google Scholar
Zhao C, Lv X, Fu J, He C, Hua H, Yan Z (2016) In vitro inhibitory activity of probiotic products against oral Candida species. J Appl Microbiol 121(1):254–262. https://doi.org/10.1111/jam.13138
1.Institute of Applied EcologyChinese Academy of SciencesShenyangPeople’s Republic of China
2.CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of OceanologyChinese Academy of SciencesGuangzhouPeople’s Republic of China