Streptomyces sp. are actinobacteria, which are generally known to be prolific producers of antibiotics and various antimicrobial compounds. More than 90% of the reported Streptomyces sp. are known to be isolated from soil samples. Exploring the genomes of such actinobacteria has sparked interest in finding bioactive secondary metabolites after the remarkable breadth of biosynthetic gene clusters (BGCs) for antibacterial compounds was discovered. Streptomyces sp. PSAA01 was obtained from soil samples taken in Manas National Park, Assam, India. It was discovered that this strain and S. yatensis DSM 41771T are closely related. The strain PSAA01 has been found to harbour diverse biosynthetic gene clusters (BGCs), which might be responsible for the production of many significant bioactive secondary metabolites.
References
[1]
Jose, P.A. and Jha, B. (2016) New Dimensions of Research on Actinomycetes: Quest for Next Generation Antibiotics. FrontiersinMicrobiology, 7, Article No. 1295. https://doi.org/10.3389/fmicb.2016.01295
[2]
Jiang, Y., Li, Q., Chen, X. and Jiang, C. (2016) Isolation and Cultivation Methods of Actinobacteria. In: Actinobacteria—BasicsandBiotechnologicalApplications, InTech, 39-57. https://doi.org/10.5772/61457
[3]
van der Meij, A., Worsley, S.F., Hutchings, M.I. and van Wezel, G.P. (2017) Chemical Ecology of Antibiotic Production by Actinomycetes. FEMSMicrobiologyReviews, 41, 392-416. https://doi.org/10.1093/femsre/fux005
[4]
Prudence, S.M.M., Addington, E., Castaño-Espriu, L., Mark, D.R., Pintor-Escobar, L., Russell, A.H., et al. (2020) Advances in Actinomycete Research: An Actinobase Review of 2019. Microbiology, 166, 683-694. https://doi.org/10.1099/mic.0.000944
[5]
Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. (2020) List of Prokaryotic Names with Standing in Nomenclature (LPSN) Moves to the DSMZ. InternationalJournalofSystematicandEvolutionaryMicrobiology, 70, 5607-5612. https://doi.org/10.1099/ijsem.0.004332
[6]
Suga, T., Kimura, T., Inahashi, Y., Iwatsuki, M., Nonaka, K., Také, A., et al. (2018) Hamuramicins a and B, 22-Membered Macrolides, Produced by an Endophytic Actinomycete Allostreptomyces Sp. K12-0794. TheJournalofAntibiotics, 71, 619-625. https://doi.org/10.1038/s41429-018-0055-x
[7]
Bérdy, J. (2005) Bioactive Microbial Metabolites. TheJournalofAntibiotics, 58, 1-26. https://doi.org/10.1038/ja.2005.1
[8]
Barka, E.A., Vatsa, P., Sanchez, L., Gaveau-Vaillant, N., Jacquard, C., Klenk, H., et al. (2016) Taxonomy, Physiology, and Natural Products of Actinobacteria. MicrobiologyandMolecularBiologyReviews, 80, 1-43. https://doi.org/10.1128/mmbr.00019-15
[9]
Bentley, S.D., Chater, K.F., Cerdeño-Tárraga, A., Challis, G.L., Thomson, N.R., James, K.D., et al. (2002) Complete Genome Sequence of the Model Actinomycete Streptomyces Coelicolor A3(2). Nature, 417, 141-147. https://doi.org/10.1038/417141a
[10]
Bao, J., He, F., Li, Y., Fang, L., Wang, K., Song, J., et al. (2018) Cytotoxic Antibiotic Angucyclines and Actinomycins from the Streptomyces sp. Xzhg99t. TheJournalofAntibiotics, 71, 1018-1024. https://doi.org/10.1038/s41429-018-0096-1
[11]
Iliĉ, S.B., Konstantinoviĉ, S.S., Todoroviĉ, Z.B., Laziĉ, M.L., Veljkoviĉ, V.B., Jokoviĉ, N. and Radovanoviĉ, B.C. (2007) Characterization and Antimicrobial Activity of the Bioactive Metabolites in Streptomycete Isolates. Mikrobiologiia, 4, 480-487.
[12]
Law, J.W., Ser, H., Duangjai, A., Saokaew, S., Bukhari, S.I., Khan, T.M., et al. (2017) Streptomyces colonosanans Sp. Nov., a Novel Actinobacterium Isolated from Malaysia Mangrove Soil Exhibiting Antioxidative Activity and Cytotoxic Potential against Human Colon Cancer Cell Lines. FrontiersinMicrobiology, 8, Article No. 877. https://doi.org/10.3389/fmicb.2017.00877
[13]
Schneider, O., Simic, N., Aachmann, F.L., Rückert, C., Kristiansen, K.A., Kalinowski, J., et al. (2018) Genome Mining of Streptomyces sp. YIM 130001 Isolated from Lichen Affords New Thiopeptide Antibiotic. FrontiersinMicrobiology, 9, Article No. 3139. https://doi.org/10.3389/fmicb.2018.03139
[14]
Law, J.W., Chan, K., He, Y., Khan, T.M., Ab Mutalib, N., Goh, B., et al. (2019) Diversity of Streptomyces spp. from Mangrove Forest of Sarawak (Malaysia) and Screening of Their Antioxidant and Cytotoxic Activities. ScientificReports, 9, Article No. 15262. https://doi.org/10.1038/s41598-019-51622-x
[15]
Ventola, C.L. (2015) The Antibiotic Resistance Crisis: Part 1: Causes and Threats. P&T: A Peer-Reviewed Journal for Formulary Management, 4, 277-283.
[16]
Ikeda, H., Ishikawa, J., Hanamoto, A., Shinose, M., Kikuchi, H., Shiba, T., et al. (2003) Complete Genome Sequence and Comparative Analysis of the Industrial Microorganism Streptomyces avermitilis. NatureBiotechnology, 21, 526-531. https://doi.org/10.1038/nbt820
[17]
Ohnishi, Y., Ishikawa, J., Hara, H., Suzuki, H., Ikenoya, M., Ikeda, H., et al. (2008) Genome Sequence of the Streptomycin-Producing Microorganism Streptomyces griseus IFO 13350. JournalofBacteriology, 190, 4050-4060. https://doi.org/10.1128/jb.00204-08
[18]
Cruz-Morales, P., Vijgenboom, E., Iruegas-Bocardo, F., Girard, G., Yáñez-Guerra, L.A., Ramos-Aboites, H.E., et al. (2013) The Genome Sequence of Streptomyceslividans 66 Reveals a Novel tRNA-Dependent Peptide Biosynthetic System within a Metal-Related Genomic Island. GenomeBiologyandEvolution, 5, 1165-1175. https://doi.org/10.1093/gbe/evt082
[19]
El-Nakeeb, M.A. and Lechevalier, H.A. (1963) Selective Isolation of Aerobic Actinomycetes. AppliedMicrobiology, 11, 75-77. https://doi.org/10.1128/am.11.2.75-77.1963
[20]
Küster, E. and Williams, S.T. (1964) Selection of Media for Isolation of Streptomycetes. Nature, 202, 928-929. https://doi.org/10.1038/202928a0
[21]
Shirling, E.B. and Gottlieb, D. (1966) Methods for Characterization of Streptomyces Species. InternationalJournalofSystematicBacteriology, 16, 313-340. https://doi.org/10.1099/00207713-16-3-313
[22]
Maiti, P.K. and Mandal, S. (2019) Majority of Actinobacterial Strains Isolated from Kashmir Himalaya Soil Are Rich Source of Antimicrobials and Industrially Important Biomolecules. AdvancesinMicrobiology, 9, 220-238. https://doi.org/10.4236/aim.2019.93016
[23]
Maiti, P.K., Das, S., Sahoo, P. and Mandal, S. (2020) Streptomyces sp SM01 Isolated from Indian Soil Produces a Novel Antibiotic Picolinamycin Effective against Multi Drug Resistant Bacterial Strains. ScientificReports, 10, Article No. 10092. https://doi.org/10.1038/s41598-020-66984-w
[24]
Marmur, J. (1961) A Procedure for the Isolation of Deoxyribonucleic Acid from Micro-Organisms. JournalofMolecularBiology, 3, 208-IN1. https://doi.org/10.1016/s0022-2836(61)80047-8
[25]
Yoon, S., Ha, S., Kwon, S., Lim, J., Kim, Y., Seo, H., et al. (2017) Introducing Ezbiocloud: A Taxonomically United Database of 16S rRNA Gene Sequences and Whole-Genome Assemblies. InternationalJournalofSystematicandEvolutionaryMicrobiology, 67, 1613-1617. https://doi.org/10.1099/ijsem.0.001755
[26]
Tamura, K., Stecher, G., Peterson, D., Filipski, A. and Kumar, S. (2013) MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0. MolecularBiologyandEvolution, 30, 2725-2729. https://doi.org/10.1093/molbev/mst197
[27]
Felsenstein, J. (1981) Evolutionary Trees from DNA Sequences: A Maximum Likelihood Approach. JournalofMolecularEvolution, 17, 368-376. https://doi.org/10.1007/bf01734359
[28]
Jukes, T.H. and Cantor, C.R. (1969) Evolution of Protein Molecules. In: MammalianProteinMetabolism, Elsevier, 21-132. https://doi.org/10.1016/b978-1-4832-3211-9.50009-7
[29]
Tamura K. (1992) Estimation of the Number of Nucleotide Substitutions When There Are Strong Transition-Transversion and G+C-Content Biases. MolecularBiologyandEvolution, 4, 678-687.
[30]
Kimura, M. (1980) A Simple Method for Estimating Evolutionary Rates of Base Substitutions through Comparative Studies of Nucleotide Sequences. JournalofMolecularEvolution, 16, 111-120. https://doi.org/10.1007/bf01731581
[31]
Nei, M. and Kumar S. (2000) Molecular Evolution and Phylogenetics. Oxford University Press.
[32]
Alikhan, N., Petty, N.K., Ben Zakour, N.L. and Beatson, S.A. (2011) BLAST Ring Image Generator (BRIG): Simple Prokaryote Genome Comparisons. BMCGenomics, 12, Article No. 402. https://doi.org/10.1186/1471-2164-12-402
[33]
Meier-Kolthoff, J.P. and Göker, M. (2019) TYGS Is an Automated High-Throughput Platform for State-of-the-Art Genome-Based Taxonomy. NatureCommunications, 10, Article No. 2182. https://doi.org/10.1038/s41467-019-10210-3
[34]
Aziz, R.K., Bartels, D., Best, A.A., DeJongh, M., Disz, T., Edwards, R.A., et al. (2008) The RAST Server: Rapid Annotations Using Subsystems Technology. BMCGenomics, 9, Article No. 75. https://doi.org/10.1186/1471-2164-9-75
[35]
Rodriguez-R, L.M. and Konstantinidis, K.T. (2016) The Enveomics Collection: A Toolbox for Specialized Analyses of Microbial Genomes and Metagenomes (No. e1900v1).
[36]
Meier-Kolthoff, J.P., Auch, A.F., Klenk, H. and Göker, M. (2013) Genome Sequence-Based Species Delimitation with Confidence Intervals and Improved Distance Functions. BMCBioinformatics, 14, Article No. 60. https://doi.org/10.1186/1471-2105-14-60
[37]
Blin, K., Shaw, S., Kloosterman, A.M., Charlop-Powers, Z., van Wezel, G.P., Medema, M.H., et al. (2021) antiSMASH 6.0: Improving Cluster Detection and Comparison Capabilities. NucleicAcidsResearch, 49, W29-W35. https://doi.org/10.1093/nar/gkab335
[38]
Skinnider, M.A., Johnston, C.W., Gunabalasingam, M., Merwin, N.J., Kieliszek, A.M., MacLellan, R.J., et al. (2020) Comprehensive Prediction of Secondary Metabolite Structure and Biological Activity from Microbial Genome Sequences. NatureCommunications, 11, Article No. 6058. https://doi.org/10.1038/s41467-020-19986-1
[39]
Blin, K., Shaw, S., Steinke, K., Villebro, R., Ziemert, N., Lee, S.Y., et al. (2019) Antismash 5.0: Updates to the Secondary Metabolite Genome Mining Pipeline. NucleicAcidsResearch, 47, W81-W87. https://doi.org/10.1093/nar/gkz310
[40]
Saintpierre, D., Amir, H., Pineau, R., Sembiring, L. and Goodfellow, M. (2003) Streptomyces yatensis sp. Nov., a Novel Bioactive Streptomycete Isolated from a New-Caledonian Ultramafic Soil. AntonievanLeeuwenhoek, 83, 21-26. https://doi.org/10.1023/a:1022906325397
[41]
Rong, X. and Huang, Y. (2010) Taxonomic Evaluation of the Streptomyces griseus Clade Using Multilocus Sequence Analysis and DNA-DNA Hybridization, with Proposal to Combine 29 Species and Three Subspecies as 11 Genomic Species. InternationalJournalofSystematicandEvolutionaryMicrobiology, 60, 696-703. https://doi.org/10.1099/ijs.0.012419-0
[42]
Richter, M. and Rosselló-Móra, R. (2009) Shifting the Genomic Gold Standard for the Prokaryotic Species Definition. ProceedingsoftheNationalAcademyofSciences, 106, 19126-19131. https://doi.org/10.1073/pnas.0906412106
[43]
Chun, J., Oren, A., Ventosa, A., Christensen, H., Arahal, D.R., da Costa, M.S., et al. (2018) Proposed Minimal Standards for the Use of Genome Data for the Taxonomy of Prokaryotes. InternationalJournalofSystematicandEvolutionaryMicrobiology, 68, 461-466. https://doi.org/10.1099/ijsem.0.002516
[44]
Liu, B., Ge, B., Ma, J., Wei, Q., Khan, A.A., Shi, L., et al. (2018) Identification of wysPII as an Activator of Morphological Development in Streptomyces albulus CK-15. FrontiersinMicrobiology, 9, Article No. 2550. https://doi.org/10.3389/fmicb.2018.02550
[45]
Yu, D., Xu, F., Valiente, J., Wang, S. and Zhan, J. (2013) An Indigoidine Biosynthetic Gene Cluster from Streptomyceschromofuscus ATCC 49982 Contains an Unusual IndB Homologue. JournalofIndustrialMicrobiologyandBiotechnology, 40, 159-168. https://doi.org/10.1007/s10295-012-1207-9