Abstract
The urgent need for new antimicrobials arises from antimicrobial resistance. Actinobacteria, especially Streptomyces genus, are responsible for production of numerous clinical antibiotics and anticancer agents. Genome mining reveals the biosynthetic gene clusters (BGCs) related to secondary metabolites and the genetic potential of a strain to produce natural products. However, this potential may not be expressed under laboratory conditions. In the present study, the Antarctic bacterium was taxonomically affiliated as Streptomyces albidoflavus ANT_B131 (CBMAI 1855). The crude extracts showed antimicrobial activity against both fungi, Gram-positive and Gram-negative bacteria and antiproliferative activity against five human tumor cell lines. Whole-genome sequencing reveals a genome size of 6.96 Mb, and the genome mining identified 24 BGCs, representing 13.3% of the genome. The use of three culture media and three extraction methods reveals the expression and recovery of 20.8% of the BGCs. The natural products identified included compounds, such as surugamide A, surugamide D, desferrioxamine B + Al, desferrioxamine E, and ectoine. This study reveals the potential of S. albidoflavus ANT_B131 as a natural product producer. Yet, the diversity of culture media and extraction methods could enhance the BGCs expression and recovery of natural products, and could be a strategy to intensify the BGC expression of natural products.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
Data availability
All relevant data are contained within the article.
References
Álvarez-Álvarez R, Botas A, Albillos SM et al (2015) Molecular genetics of naringenin biosynthesis, a typical plant secondary metabolite produced by Streptomyces clavuligerus. Microb Cell Fact 14:178. https://doi.org/10.1186/s12934-015-0373-7
Alves DA, Machado D, Melo A et al (2016) Preparation of thermosensitive gel for controlled release of levofloxacin and their application in the treatment of multidrug-resistant bacteria. BioMed Res Int 2016:1–10. https://doi.org/10.1155/2016/9702129
Angolini CFF, Gonçalves AB, Sigrist R et al (2016) Genome mining of endophytic Streptomyces wadayamensis reveals high antibiotic production capability. J Braz Chem Soc. https://doi.org/10.5935/0103-5053.20160180
Bérdy J (2005) Bioactive microbial metabolites: a personal view. J Antibiot 58:1–26. https://doi.org/10.1038/ja.2005.1
Blin K, Shaw S, Steinke K et al (2019) antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline. Nucleic Acids Res 47:W81–W87. https://doi.org/10.1093/nar/gkz310
Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120. https://doi.org/10.1093/bioinformatics/btu170
Brettin T, Davis JJ, Disz T et al (2015) RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Sci Rep 5:8365. https://doi.org/10.1038/srep08365
Carpenter DE, Anderson K, Citron DM et al (2018) Methods for antimicrobial susceptibility testing of anaerobic bacteria. Clin Lab Stand Inst 9:1–64
Chambers MC, Maclean B, Burke R et al (2012) A cross-platform toolkit for mass spectrometry and proteomics. Nat Biotechnol 30:918–920. https://doi.org/10.1038/nbt.2377
Chen S, Huang X, Zhou X et al (2003) Organizational and mutational analysis of a complete FR-008/Candicidin gene cluster encoding a structurally related polyene complex. Chem Biol 10:1065–1076. https://doi.org/10.1016/j.chembiol.2003.10.007
Clardy J, Fischbach MA, Currie CR (2009) The natural history of antibiotics. Curr Biol 19:R437–R441. https://doi.org/10.1016/j.cub.2009.04.001
CLSI. Performance standards for antimicrobial disk susceptibility tests; approved standard—11th ed. CLSI Document M02-A11. Wayne: Clinical and Laboratory Standards Institute, 2012
Cockerill FR, Clinical and Laboratory Standards Institute (eds) (2012) Performance standards for antimicrobial susceptibility tests: approved standard—eleventh edition. CLSI, Wayne, PA
Convey P, Peck LS (2019) Antarctic environmental change and biological responses. Sci Adv 5:eaaz0888. https://doi.org/10.1126/sciadv.aaz0888
Cury GG, Mobilon C, Stehling EG et al (2009) Molecular typing of methicillin-resistant Staphylococcus aureus (MRSA) strains isolated in two metropolitan areas of São Paulo State, southeast Brazil. Braz J Infect Dis. https://doi.org/10.1590/S1413-86702009000300002
Danilovich ME, Sánchez LA, Acosta F, Delgado OD (2018) Antarctic bioprospecting: in pursuit of microorganisms producing new antimicrobials and enzymes. Polar Biol 41:1417–1433. https://doi.org/10.1007/s00300-018-2295-4
Darling AE, Mau B, Perna NT (2010) progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS ONE 5:e11147. https://doi.org/10.1371/journal.pone.0011147
Ernst M, Kang KB, Caraballo-Rodríguez AM et al (2019) MolNetEnhancer: enhanced molecular networks by integrating metabolome mining and annotation tools. Metabolites 9:144. https://doi.org/10.3390/metabo9070144
Ewing B, Green P (1998) Base-calling of automated sequencer traces using Phred. II. Error probabilities. Genome Res 8:186–194. https://doi.org/10.1101/gr.8.3.186
Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791. https://doi.org/10.1111/j.1558-5646.1985.tb00420.x
Fu G, Wang R, Ding J et al (2020) Micromonospora zhangzhouensis sp. nov., a novel actinobacterium isolated from mangrove soil, exerts a cytotoxic activity in vitro. Sci Rep 10:3889. https://doi.org/10.1038/s41598-020-60677-0
Gordon D, Abajian C, Green P (1998) Consed: a graphical tool for sequence finishing. Genome Res 8:195–202. https://doi.org/10.1101/gr.8.3.195
Grimm A, Madduri K, Ali A, Hutchinson CR (1994) Characterization of the Streptomyces peucetius ATCC 29050 genes encoding doxorubicin polyketide synthase. Gene 151:1–10. https://doi.org/10.1016/0378-1119(94)90625-4
Gurevich A, Saveliev V, Vyahhi N, Tesler G (2013) QUAST: quality assessment tool for genome assemblies. Bioinformatics 29:1072–1075. https://doi.org/10.1093/bioinformatics/btt086
Harvey AL, Edrada-Ebel R, Quinn RJ (2015) The re-emergence of natural products for drug discovery in the genomics era. Nat Rev Drug Discov 14:111–129. https://doi.org/10.1038/nrd4510
Hassan AME, Fahal AH, Ahmed AO et al (2001) The immunopathology of actinomycetoma lesions caused by Streptomyces somaliensis. Trans R Soc Trop Med Hyg 95:89–92. https://doi.org/10.1016/S0035-9203(01)90346-3
Hosotani N, Kumagai K, Nakagawa H et al (2005) Antimycins A10∼A16, seven new antimycin antibiotics produced by Streptomyces spp. SPA-10191 and SPA-8893. J Antibiot 58:460–467. https://doi.org/10.1038/ja.2005.61
Ivanova V, Laatsch H, Kolarova M, Aleksieva K (2013) Structure elucidation of a new natural diketopiperazine from a Microbispora aerata strain isolated from Livingston Island, Antarctica. Nat Prod Res 27:164–170. https://doi.org/10.1080/14786419.2012.665911
Jeon Y-J, Kim S, Kim JH et al (2019) The comprehensive roles of ATRANORIN, a secondary metabolite from the Antarctic lichen Stereocaulon caespitosum, in HCC tumorigenesis. Molecules 24:1414. https://doi.org/10.3390/molecules24071414
Kalinovskaya NI, Romanenko LA, Irisawa T et al (2011) Marine isolate Citricoccus sp. KMM 3890 as a source of a cyclic siderophore nocardamine with antitumor activity. Microbiol Res 166:654–661. https://doi.org/10.1016/j.micres.2011.01.004
Kautsar SA, Blin K, Shaw S et al (2019) MIBiG 2.0: a repository for biosynthetic gene clusters of known function. Nucleic Acids Res. https://doi.org/10.1093/nar/gkz882
Khalifa SAM, Elias N, Farag MA et al (2019) Marine natural products: a source of novel anticancer drugs. Mar Drugs 17:491. https://doi.org/10.3390/md17090491
Khan ST, Tamura T, Takagi M, Shin-ya K (2010) Streptomyces tateyamensis sp. nov., Streptomyces marinus sp. nov. and Streptomyces haliclonae sp. nov., isolated from the marine sponge Haliclona sp. Int J Syst Evol Microbiol 60:2775–2779. https://doi.org/10.1099/ijs.0.019869-0
Kim S, Park TI (2013) Naringenin: a partial agonist on estrogen receptor in T47D-KBluc breast cancer cells. Int J Clin Exp Med 6:890–899
Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120. https://doi.org/10.1007/BF01731581
Kiss T, Farkas E (1998) J Inclus Phenom Mol Recogn Chem 32:385–403. https://doi.org/10.1023/A:1008046330815
Kumar S, Stecher G, Li M et al (2018) MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 35:1547–1549. https://doi.org/10.1093/molbev/msy096
Labeda DP, Goodfellow M, Brown R et al (2012) Phylogenetic study of the species within the family Streptomycetaceae. Antonie Van Leeuwenhoek 101:73–104. https://doi.org/10.1007/s10482-011-9656-0
Labeda DP, Dunlap CA, Rong X et al (2017) Phylogenetic relationships in the family Streptomycetaceae using multi-locus sequence analysis. Antonie Van Leeuwenhoek 110:563–583. https://doi.org/10.1007/s10482-016-0824-0
Lamilla C, Pavez M, Santos A et al (2017) Bioprospecting for extracellular enzymes from culturable Actinobacteria from the South Shetland Islands, Antarctica. Polar Biol 40:719–726. https://doi.org/10.1007/s00300-016-1977-z
Lane D (1991) 16S/23S rRNA sequencing. In: Goodfellow M, Stackebrandt E (eds) Nucleic acid techniques in bacterial systematics. Wiley, Chichester, pp 115–147
Lavin PL, Yong ST, Wong CMVL, De Stefano M (2016) Isolation and characterization of Antarctic psychrotroph Streptomyces sp. strain INACH3013. Antarct Sci 28:433–442. https://doi.org/10.1017/S0954102016000250
Lewis K (2013) Platforms for antibiotic discovery. Nat Rev Drug Discov 12:371–387. https://doi.org/10.1038/nrd3975
Maansson M, Vynne NG, Klitgaard A et al (2016) An integrated metabolomic and genomic mining workflow to uncover the biosynthetic potential of bacteria. mSystems 1:e00028-e115. https://doi.org/10.1128/mSystems.00028-15
Maruyama HB, Azuma H, Kotoh Y, Suhara Y (1975) Desferrioxamine B, an inhibitor of Escherichia coli motility, reversing the stimulating effect of cyclic adenosine 3′,5′-monophosphate. Antimicrob Agents Chemother 7:377–380. https://doi.org/10.1128/AAC.7.3.377
Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M (2013) Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinform 14:60. https://doi.org/10.1186/1471-2105-14-60
Meier-Kolthoff JP, Klenk H-P, Göker M (2014) Taxonomic use of DNA G+C content and DNA–DNA hybridization in the genomic age. Int J Syst Evol Microbiol 64:352–356. https://doi.org/10.1099/ijs.0.056994-0
Monks A, Scudiero D, Skehan P et al (1991) Feasibility of a high-flux anticancer drug screen using a diverse panel of cultured human tumor cell lines. JNCI J Natl Cancer Inst 83:757–766. https://doi.org/10.1093/jnci/83.11.757
Mullis MM, Rambo IM, Baker BJ, Reese BK (2019) Diversity, ecology, and prevalence of antimicrobials in nature. Front Microbiol 10:2518. https://doi.org/10.3389/fmicb.2019.02518
Murray CJL, Ikuta KS, Sharara F et al (2022) Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis. Lancet 399:629–655. https://doi.org/10.1016/S0140-6736(21)02724-0
Núñez-Montero K, Lamilla C, Abanto M et al (2019) Antarctic Streptomyces fildesensis So13.3 strain as a promising source for antimicrobials discovery. Sci Rep 9:7488. https://doi.org/10.1038/s41598-019-43960-7
Padilla MA, Rodrigues RAF, Bastos JCS et al (2015) Actinobacteria from termite mounds show antiviral activity against bovine viral diarrhea virus, a surrogate model for hepatitis C virus. Evid-Based Complement Altern Med 2015:1–9. https://doi.org/10.1155/2015/745754
Parrilli E, Tedesco P, Fondi M et al (2021) The art of adapting to extreme environments: the model system Pseudoalteromonas. Phys Life Rev 36:137–161. https://doi.org/10.1016/j.plrev.2019.04.003
Parte AC, Sardà Carbasse J, Meier-Kolthoff JP et al (2020) List of prokaryotic names with standing in nomenclature (LPSN) moves to the DSMZ. Int J Syst Evol Microbiol 70:5607–5612. https://doi.org/10.1099/ijsem.0.004332
Pastor JM, Salvador M, Argandoña M et al (2010) Ectoines in cell stress protection: uses and biotechnological production. Biotechnol Adv 28:782–801. https://doi.org/10.1016/j.biotechadv.2010.06.005
Pluháček T, Lemr K, Ghosh D et al (2016) Characterization of microbial siderophores by mass spectrometry: mass spectrometry of siderophores. Mass Spec Rev 35:35–47. https://doi.org/10.1002/mas.21461
Pospiech A (1995) A versatile quick-prep of genomic DNA from Gram-positive bacteria. Trends Genet 11:217–218. https://doi.org/10.1016/S0168-9525(00)89052-6
Prabhu J, Schauwecker F, Grammel N et al (2004) Functional expression of the ectoine hydroxylase gene (thpD) from Streptomyces chrysomallus in Halomonas elongata. Appl Environ Microbiol 70:3130–3132. https://doi.org/10.1128/AEM.70.5.3130-3132.2004
Raines DJ, Sanderson T, Wilde E, Duhme-Klair AK (2015) Siderophores. ISBN:9780124095472
Rex JH, Alexander BD, Andes D et al (2008) Reference method for broth dilution antifungal susceptibility testing of yeasts. Clin Lab Stand Inst 28:1–46
Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J (2016) JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 32:929–931. https://doi.org/10.1093/bioinformatics/btv681
Rizzo C, Lo Giudice A (2020) The variety and inscrutability of polar environments as a resource of biotechnologically relevant molecules. Microorganisms 8:1422. https://doi.org/10.3390/microorganisms8091422
Saitou N, Nei N (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. https://doi.org/10.1093/oxfordjournals.molbev.a040454
Sajjad W, Din G, Rafiq M et al (2020) Pigment production by cold-adapted bacteria and fungi: colorful tale of cryosphere with wide range applications. Extremophiles 24:447–473. https://doi.org/10.1007/s00792-020-01180-2
Schöller CEG, Gürtler H, Pedersen R et al (2002) Volatile metabolites from actinomycetes. J Agric Food Chem 50:2615–2621. https://doi.org/10.1021/jf0116754
Simão FA, Waterhouse RM, Ioannidis P et al (2015) BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31:3210–3212. https://doi.org/10.1093/bioinformatics/btv351
Soldatou S, Eldjarn GH, Huerta-Uribe A et al (2019) Linking biosynthetic and chemical space to accelerate microbial secondary metabolite discovery. FEMS Microbiol Lett 366:fnz142. https://doi.org/10.1093/femsle/fnz142
Stehling EG, Silveira WDD, Leite DDS (2008) Study of biological characteristics of Pseudomonas aeruginosa strains isolated from patients with cystic fibrosis and from patients with extra-pulmonary infections. Braz J Infect Dis 12:86–88. https://doi.org/10.1590/S1413-86702008000100018
Takada K, Ninomiya A, Naruse M et al (2013) Surugamides A-E, cyclic octapeptides with four d-amino acid residues, from a marine Streptomyces sp.: LC–MS-aided inspection of partial hydrolysates for the distinction of d- and l-amino acid residues in the sequence. J Org Chem 78:6746–6750. https://doi.org/10.1021/jo400708u
Tatusova T, DiCuccio M, Badretdin A et al (2016) NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 44:6614–6624. https://doi.org/10.1093/nar/gkw569
Thankachan D, Fazal A, Francis D et al (2019) A trans-acting cyclase offloading strategy for nonribosomal peptide synthetases. ACS Chem Biol 14:845–849. https://doi.org/10.1021/acschembio.9b00095
Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucl Acids Res 22:4673–4680. https://doi.org/10.1093/nar/22.22.4673
Tracanna V, De Jong A, Medema MH, Kuipers OP (2017) Mining prokaryotes for antimicrobial compounds: from diversity to function. FEMS Microbiol Rev 41:417–429. https://doi.org/10.1093/femsre/fux014
Wang M, Carver JJ, Phelan VV et al (2016) Sharing and community curation of mass spectrometry data with global natural products social molecular networking. Nat Biotechnol 34:828–837. https://doi.org/10.1038/nbt.3597
Wang Q, Garrity GM, Tiedje JM, Cole JR (2007) Naïve Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73:5261–5267. https://doi.org/10.1128/AEM.00062-07
Wang X, Shaaban KA, Elshahawi SI et al (2014) Mullinamides A and B, new cyclopeptides produced by the Ruth Mullins coal mine fire isolate Streptomyces sp. RM-27-46. J Antibiot 67:571–575. https://doi.org/10.1038/ja.2014.37
Wattam AR, Davis JJ, Assaf R et al (2017) Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center. Nucleic Acids Res 45:D535–D542. https://doi.org/10.1093/nar/gkw1017
Weinstein MP, Patel JB, Burnham CA et al (2018) Methods for dilution antimicrobial susceptibility tests for bacteria that grow aerobically. Clin Lab Stand Inst 12:1–112
Xu F, Nazari B, Moon K et al (2017) Discovery of a cryptic antifungal compound from Streptomyces albus J1074 using high-throughput elicitor screens. J Am Chem Soc 139:9203–9212. https://doi.org/10.1021/jacs.7b02716
Yagüe P, Lopez-Garcia MT, Rioseras B et al (2012) New insights on the development of Streptomyces and their relationships with secondary metabolite production. Curr Trends Microbiol 8:65–73
Yang Z, Kuboyama T, Tohda C (2017) A systematic strategy for discovering a therapeutic drug for Alzheimer’s disease and its target molecule. Front Pharmacol 8:340. https://doi.org/10.3389/fphar.2017.00340
Yoon S-H, Ha S-M, Kwon S et al (2017) Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 67:1613–1617. https://doi.org/10.1099/ijsem.0.001755
Zhang C, Straight PD (2019) Antibiotic discovery through microbial interactions. Curr Opin Microbiol 51:64–71. https://doi.org/10.1016/j.mib.2019.06.006
Ziemert N, Weber T, Medema MH (2020) Genome mining approaches to bacterial natural product discovery, 3rd edn. Elsevier Inc., Amsterdam, pp 19–33
Acknowledgements
The authors would like to thank Prof. Itamar Soares Melo and Prof. Eduardo Carlos Hadju for the contribution to the collection of marine Antarctic samples.
Funding
This work was supported by Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, Brazil, Code 001, and Fundação de Amparo à Pesquisa do Estado de São Paulo, Brazil, under Grant 2013/05961-9.
Author information
Authors and Affiliations
Contributions
All authors contributed to the study conception and design. Material preparation, data collection, and analysis were performed by PdF, JHC, TPF, ML, and ALTGR. The first draft of the manuscript was written by PdF, and all authors commented on the previous version of the manuscript. FF-G was responsible for supervision, funding acquisition, and resources. All authors have read and agreed to the published version of the manuscript.
Corresponding authors
Ethics declarations
Conflict of interest
The authors declare that they have no conflict of interest in the publication.
Additional information
Communicated by Yusuf Akhter.
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Supplementary Information
Below is the link to the electronic supplementary material.
Rights and permissions
Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.
About this article
Cite this article
de França, P., Costa, J.H., Fill, T.P. et al. Genome mining reveals secondary metabolites of Antarctic bacterium Streptomyces albidoflavus related to antimicrobial and antiproliferative activities. Arch Microbiol 205, 354 (2023). https://doi.org/10.1007/s00203-023-03691-w
Received:
Revised:
Accepted:
Published:
DOI: https://doi.org/10.1007/s00203-023-03691-w