Skip to main content
SpringerLink
Log in

Practical Aspects of Working with Actinobacteria

  • Chapter
  • First Online:
Biology and Biotechnology of Actinobacteria

Abstract

More than other bacteria Actinobacteria, especially the mycelium forming ones impress by their appearance, the color of the aerial mycelium, of the substrate mycelium and also of pigments that diffuse into the agar (Cross 1989; Krasil’nikov 1979; Küster 1976) and the morphology of their differentiation stages (Gottlieb 1961) which will be described in the later chapters. The aerial mycelium which makes them look like a fungus and the often three dimensional shape of the colony. The color of the aerial mycelium has been used by many groups for a first classification (Flaig and Kutzner 1960; Ettlinger et al. 1958; Shirling and Gottlieb 1966; Tresner and Backus 1963). The main classification groups are: white, grey white, cream (Streptomyces albus); yellow-grey (Streptomyces griseus); rose, pale violet (Streptomyces fradiae, Microbispora rosea), rose-grey (Streptomyces lavendulae); pale brown, red brown (Streptomyces fragilis); pale blue, grey-blue (Streptomyces viridochromogenes); blue green (Streptomyces glaucescens, Actinomadura rubrobrunnea); pale green, green (Streptomyces prasinus, Microtetraspora viridis); pale grey, grey (Streptomyces violaceoruber, Microtetraspora glauca) (Blinov and Khokhlov 1970). By the description of the aerial mycelium color three points have to be kept in mind. The first is that the typical color is only expressed if the culture is also sporulating. Different species often sporulate on different media, so a number of agar cultures have to be prepared to get good results. The second is the diffusion of pigments from the substrate mycelium into the aerial mycelium which can have influences on the shade of the aerial mycelium. The third is the experience with many different Actinobacteria and their pigmentation, to do this grouping well. It is therefore very important to use the same media and culture conditions for all strains that will be compared. Over the years the use of the media from Shirling and Gottlieb (1966) from the “International Streptomyces Project/ISP” has been established in nearly all labs working with Actinobacteria (composition of media, see Sect. 11.2.1).

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Abdelmohsen UR, Cheng C, Viegelmann C, Zhang T, Grkovic T, Ahmed S, Quinn RJ, Hentschel U, Edrada-Ebel R (2014) Dereplication strategies for targeted isolation of new antitrypanosomal actinosporins A and B from a marine sponge associated-Actinokineospora sp. EG49. Mar Drugs 12(3):1220–1244

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ackermann BL, Regg BT, Colombo L, Stella S, Coutant JE (1996) Rapid analysis of antibiotic-containing mixtures from fermentation broths by using liquid chromatography-electrospray ionization-mass spectrometry and matrix-assisted laser desorption ionization-time-of-flight-mass spectrometry. J Am Soc Mass Spectrom 7(12):1227–1237

    Article  CAS  PubMed  Google Scholar 

  • Agarwal A, D’Souza P, Johnson TS, Dethe SM, Chandrasekaran C (2014) Use of in vitro bioassays for assessing botanicals. Curr Opin Biotechnol 25:39–44

    Article  CAS  PubMed  Google Scholar 

  • Ahlert J, Shepard E, Lomovskaya N, Zazopoulos E, Staffa A, Bachmann BO, Huang K, Fonstein L, Czisny A, Whitwam RE (2002) The calicheamicin gene cluster and its iterative type I enediyne PKS. Science 297(5584):1173–1176

    Article  CAS  PubMed  Google Scholar 

  • Alvi K, Peterson J, Hofmann B (1995) Rapid identification of elaiophylin and geldanamycin in Streptomyces fermentation broths using CPC coupled with a photodiode array detector and LC-MS methodologies. J Ind Microbiol 15(2):80–84

    Article  CAS  PubMed  Google Scholar 

  • Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215(3):403–410

    Google Scholar 

  • Baldacci E, Spalla C, Grein A (1954) The classification of the Actinomyces species (Streptomyces). Arch Microbiol 20:347–357

    CAS  Google Scholar 

  • Baldacci E, Farina G, Locci R (1966) Emendation of the genus Streptoverticillium Baldacci (1958) and revision of some species. G Microbiol 14:153–171

    Google Scholar 

  • Ball KD, Trevors J (2002) Bacterial genomics: the use of DNA microarrays and bacterial artificial chromosomes. J Microbiol Methods 49(3):275–284

    Article  CAS  PubMed  Google Scholar 

  • Bennedict RG, Pridham TG, Lindenfelser LA, Hall HH, Jackson RW (1955) Further studies in the evaluation of carbohydrate utilization tests as aids in the differentiation of species of Streptomyces. Appl Microbiol 3:1–6

    Google Scholar 

  • Besemer J, Borodovsky M (1999) Heuristic approach to deriving models for gene finding. Nucleic Acids Res 27(19):3911–3920

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Besemer J, Lomsadze A, Borodovsky M (2001) GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions. Nucleic Acids Res 29(12):2607–2618

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Beutler JA, Alvarado AB, Schaufelberger DE, Andrews P, McCloud TG (1990) Dereplication of phorbol bioactives: Lyngbya Majuscula and Croton Cuneatus. J Nat Prod 53(4):867–874

    Article  CAS  PubMed  Google Scholar 

  • Beyer S, Distler J, Piepersberg W (1996) Thestr gene cluster for the biosynthesis of 5′-hydroxystreptomycin inStreptomyces glaucescens GLA. 0 (ETH 22794): new operons and evidence for pathway-specific regulation by StrR. Mol Gen Genet MGG 250(6):775–784

    CAS  PubMed  Google Scholar 

  • Bland CE, Couch JN (1981) The family Actinoplanaceae. In: Starr MP, Stolp H, Trüper HG, Balons A, Schlegel HG (eds) TheProkaryotes – a handbook on habitats, isolation and identification of bacteria. Springer Verlag, Berlin, pp 2004–2010

    Google Scholar 

  • Blinov NO, Khokhlov AS (1970) Pigments and taxonomy of actinomycetales. In: Prauser H (ed) The Actinomycetales, Jena Int. Symp. Tax, vol 1968. VEB Fischer Verlag, Jena, pp 145–154

    Google Scholar 

  • Blunt J, Munro M, Laatsch H (2006) AntiMarin database. University of Canterbury, Christchurch

    Google Scholar 

  • Borodovsky M, McIninch J (1993) Recognition of genes in DNA sequence with ambiguities. Biosystems 30(1):161–171

    Article  CAS  PubMed  Google Scholar 

  • Cerdeño AM, Bibb MJ, Challis GL (2001) Analysis of the prodiginine biosynthesis gene cluster of Streptomyces Coelicolor A3 (2): new mechanisms for chain initiation and termination in modular multienzymes. Chem Biol 8(8):817–829

    Article  PubMed  Google Scholar 

  • Challis GL (2006) Engineering Escherichia Coli to produce nonribosomal peptide antibiotics. Nat Chem Biol 2(8):398–400

    Article  CAS  PubMed  Google Scholar 

  • Challis GL (2008) Mining microbial genomes for new natural products and biosynthetic pathways. Microbiology 154(6):1555–1569

    Article  CAS  PubMed  Google Scholar 

  • Chaudhuri RR, Loman NJ, Snyder LA, Bailey CM, Stekel DJ, Pallen MJ (2008) xBASE2: a comprehensive resource for comparative bacterial genomics. Nucleic Acids Res 36(suppl 1):D543–D546

    CAS  PubMed  Google Scholar 

  • Clos LJ II, Jofre MF, Ellinger JJ, Westler WM, Markley JL (2013) NMRbot: python scripts enable high-throughput data collection on current Bruker BioSpin NMR spectrometers. Metabolomics 9(3):558–563

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Corre C, Challis GL (2007) Heavy tools for genome mining. Chem Biol 14(1):7–9

    Article  CAS  PubMed  Google Scholar 

  • Crevelin E, de Moraes LB, de Melo IS (2010) Mass spectrometry in microbial metabolomic analysis as an analytical tool for dereplication strategy. Planta Med 76(12):P545

    Article  Google Scholar 

  • Crevelin EJ, Crotti AE, Zucchi TD, Melo IS, Moraes LA (2014) Dereplication of Streptomyces sp. AMC 23 polyether ionophore antibiotics by accurate-mass electrospray tandem mass spectrometry. J Mass Spectrom 49(11):1117–1126

    Article  CAS  PubMed  Google Scholar 

  • Cross T (1981) The monosporic Actinomycetes. In: Starr MP, Stolp H, Trüper HG, Balons A, Schlegel HG (eds) TheProkaryotes – a handbook on habitats, isolation and identification of bacteria. Springer Verlag, Berlin, pp 2091–2102

    Google Scholar 

  • Cross T (1989) Growth and examination of Actinomycetes-some guidelines. In: Williams ST, Sharpe ME, Holt JG (eds) Bergey’s manual of systematic becteriology, vol 4. Williams and Wilkins, Baltimore, pp 2340–2343

    Google Scholar 

  • Dashti Y, Grkovic T, Abdelmohsen UR, Hentschel U, Quinn RJ (2014) Production of induced secondary metabolites by a co-culture of sponge-associated actinomycetes, Actinokineospora sp. EG49 and nocardiopsis sp. RV163. Mar Drugs 12(5):3046–3059

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Davis L (2012) Basic methods in molecular biology. Elsevier, Amsterdam

    Google Scholar 

  • Delcher AL, Harmon D, Kasif S, White O, Salzberg SL (1999) Improved microbial gene identification with GLIMMER. Nucleic Acids Res 27(23):4636–4641

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Delcher AL, Bratke KA, Powers EC, Salzberg SL (2007) Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23(6):673–679

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Donadio S, Monciardini P, Alduina R, Mazza P, Chiocchini C, Cavaletti L, Sosio M, Puglia AM (2002) Microbial technologies for the discovery of novel bioactive metabolites. J Biotechnol 99(3):187–198

    Article  CAS  PubMed  Google Scholar 

  • Dorokhova LA, Agre NS, Kalakoutskii LV, Krasil’nikov NA (1969) Fine structure of sporulating hyphae and spores in a thermophilic actinomycete, Micropolyspora rectivirgula. J Microsc 8:845–854

    Google Scholar 

  • Doyle TW, Borders DB (1995) Enediyne antibiotics as antitumor agents. Marcel Dekker, New York

    Google Scholar 

  • Drechsler C (1919) Morphology of the genus Actinomyces II. Bot Gaz 67:147–168

    Article  Google Scholar 

  • Duché J (1934) Les actinomyces du groupe Albus. Encycl Mycol VI:1–375

    Google Scholar 

  • Ettlinger L, Corbaz R, Hütter R (1958) Zur Systematik der Actinomyceten. 4. Eine Arteinteilung der Gattung Streptomyces Waksman and Henricic. Arch Microbiol 31:326–358

    Google Scholar 

  • Farnet CM, Zazopoulos E (2005) Improving drug discovery from microorganisms. In: Natural products. Springer, Totowa, pp 95–106

    Chapter  Google Scholar 

  • Fiehn O (2001) Combining genomics, metabolome analysis, and biochemical modelling to understand metabolic networks. Comp Funct Genomics 2(3):155–168

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fischbach MA, Walsh CT (2006) Assembly-line enzymology for polyketide and nonribosomal peptide antibiotics: logic, machinery, and mechanisms. Chem Rev 106(8):3468–3496

    Article  CAS  PubMed  Google Scholar 

  • Flaig W, Kutzner H (1960) Beitrag zur Systematik der Gattung Streptomyces Waksman and Henrici. Arch Microbiol 35:105–138

    CAS  Google Scholar 

  • Forner D, Berrué F, Correa H, Duncan K, Kerr RG (2013) Chemical dereplication of marine actinomycetes by liquid chromatography–high resolution mass spectrometry profiling and statistical analysis. Anal Chim Acta 805:70–79

    Article  CAS  PubMed  Google Scholar 

  • Gauze GF, Preobrazhenskaya TP, Kudrina ES, Blinov NO, Ryabova ID, Sveshnikova MA (1957) Problems in the classification of antagonistic actinomycetes. State publishing house for medical literature (in Russian). Medzig, Moscow

    Google Scholar 

  • Gibbs AJ, McIntyre GA (1970) The diagram, a method for comparing sequences. FEBS J 16(1):1–11

    Google Scholar 

  • Gottlieb D (1961) An evaluation of criteria and procedures in the description and characterization of the Streptomycetes. Appl Microbiol 9:55–65

    CAS  PubMed  PubMed Central  Google Scholar 

  • Gross H, Stockwell VO, Henkels MD, Nowak-Thompson B, Loper JE, Gerwick WH (2007) The genomisotopic approach: a systematic method to isolate products of orphan biosynthetic gene clusters. Chem Biol 14(1):53–63

    Article  CAS  PubMed  Google Scholar 

  • Hakvåg S, Fjærvik E, Josefsen KD, Ian E, Ellingsen TE, Zotchev SB (2008) Characterization of Streptomyces spp. isolated from the sea surface microlayer in the Trondheim fjord, Norway. Mar Drugs 6(4):620–635

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Hao C, Huang S, Deng Z, Zhao C, Yu Y (2014) Mining of the pyrrolamide antibiotics analogs in Streptomyces netropsis reveals the amidohydrolase-dependent “iterative strategy” underlying the pyrrole polymerization. PLoS One 9(6):e99077

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Hara H, Ohnishi Y, Horinouchi S (2009) DNA microarray analysis of global gene regulation by A-factor in Streptomyces Griseus. Microbiology 155(7):2197–2210

    Article  CAS  PubMed  Google Scholar 

  • Haynes SW, Challis GL (2007) Non-linear enzymatic logic in natural product modular mega-synthases and-synthetases. Curr Opin Drug Discov Devel 10(2):203–218

    CAS  PubMed  Google Scholar 

  • Henssen A (1970) Spore formation in thermophilic Actinomycetes. In: Prauser H (ed) The Actinomycetales, Jena Int. Symp tax, vol 1968. VEB Fischer Verlag, Jena, pp 205–210

    Google Scholar 

  • Hesseltine CW, Bennedict RG, Pridham TG (1954) Useful criteria for species differentiation on the genus Streptomyces. Ann N Y Acad Sci 60:136–151

    Article  CAS  PubMed  Google Scholar 

  • Hou Y, Braun DR, Michel CR, Klassen JL, Adnani N, Wyche TP, Bugni TS (2012) Microbial strain prioritization using metabolomics tools for the discovery of natural products. Anal Chem 84(10):4277–4283

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hubert J, Nuzillard JM, Renault JH (2015) Dereplication strategies in natural product research: how many tools and methodologies behind the same concept? Phytochem Rev 16:1–41

    Google Scholar 

  • Hufsky F, Scheubert K, Böcker S (2014) Computational mass spectrometry for small-molecule fragmentation. Trends Anal Chem 53:41–48

    Article  CAS  Google Scholar 

  • Humble MW, King A, Phillips I (1977) API ZYM: a simple rapid system for the detection of bacterial enzymes. J Clin Pathol 30:275–277

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hütter R (1967) Systematik der Streptomyceten unter besonderer Berücksichtigung der von ihnen gebildeten Antibiotika. Bibl Microbiol 6:1–382

    PubMed  Google Scholar 

  • Ito T, Odake T, Katoh H, Yamaguchi Y, Aoki M (2011) High-throughput profiling of microbial extracts. J Nat Prod 74(5):983–988

    Article  CAS  PubMed  Google Scholar 

  • Jain SK, Pathania AS, Parshad R, Raina C, Ali A, Gupta AP, Kushwaha M, Aravinda S, Bhushan S, Bharate SB (2013) Chrysomycins A–C, antileukemic naphthocoumarins from Streptomyces sporoverrucosus. RSC Adv 3(43):21046–21053

    Article  CAS  Google Scholar 

  • Jensen HL (1930) Actinomycetes in Danish soils. Soil Sci 30:59–77

    Article  CAS  Google Scholar 

  • Jeunilaux C (1955) Production of exochitinase by Streptomyces. CR Soc Biol 149:1307–1308

    Google Scholar 

  • Ji Z, Wei S, Zhang J, Wu W, Wang M (2008) Identification of streptothricin class antibiotics in the early-stage of antibiotics screening by electrospray ionization mass spectrometry. J Antibiot 61(11):660

    Article  CAS  PubMed  Google Scholar 

  • Kameník Z, Hadacek F, Marečková M, Ulanova D, Kopecký J, Chobot V, Plháčková K, Olšovská J (2010) Ultra-high-performance liquid chromatography fingerprinting method for chemical screening of metabolites in cultivation broth. J Chromatogr A 1217(51):8016–8025

    Article  PubMed  CAS  Google Scholar 

  • Kersten RD, Yang YL, Xu Y, Cimermancic P, Nam SJ, Fenical W, Fischbach MA, Moore BS, Dorrestein PC (2011) A mass spectrometry–guided genome mining approach for natural product peptidogenomics. Nat Chem Biol 7(11):794–802

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kilian M (1978) Rapid identification of Actinomycetaceae and related bacteria. J Clin Microbiol 8:127–133

    CAS  PubMed  PubMed Central  Google Scholar 

  • Kleigrewe K, Almaliti J, Tian IY, Kinnel RB, Korobeynikov A, Monroe EA, Duggan BM, Di Marzo V, Sherman DH, Dorrestein PC (2015) Combining mass spectrometric metabolic profiling with genomic analysis: a powerful approach for discovering natural products from cyanobacteria. J Nat Prod 78(7):1671–1682

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Krainsky A (1914) Die Aktinomyceten und ihre Bedeutung in der Natur. Zentralbl Bacteriol Parasitenkd Infektionskr Hyg Abt II 41:649–688

    Google Scholar 

  • Krasil’nikov NA (1941) Guide to the bacteria and Actinomycetes (in Russian). Akad. Nauk SSSR, Moscow

    Google Scholar 

  • Krasil’nikov NA (1949) Guide to the bacteria and Actinomycetes. Akad. Nauk SSSR, Moscow

    Google Scholar 

  • Krasil’nikov NA (1979) Pigmentation of Actinomycetes and its significance in taxonomy. In: Prauser H (ed) The Actinomycetales, Jena Int. Symp. Tax, vol 1968. VEB Fischer Verlag, Jena, pp 123–131

    Google Scholar 

  • Küster E (1976) Chromogenicity of Actinomycetes. In: Arai T (ed) Actinomycetes: the boundary microorganisms. Toppan Company, Ltd., Tokyo, pp 43–54

    Google Scholar 

  • Kutzner HJ (1981) The family Streptomycetaceae. In: Starr MP, Stolp H, Trüper HG, Balons A, Schlegel HG (eds) The prokaryotes: a handbook on habitats, isolation and identification of bacteria. Springer Verlag, Berlin, pp 2028–2090

    Google Scholar 

  • Kutzner HJ, Kroppensted RM, Korn-Wendisch F (1986) Methoden zur Untersuchung von Streptomyceten und einigen anderen Actinomyceten. 4 Auflage. Technische Universität, Darmstadt

    Google Scholar 

  • Kuznetsov VD, Yangulova JV (1970) Utilization of medium containing chitin for isolation and quantitative enumeration of actinomycetes from soil. Microbiologiya 39:902–906

    CAS  Google Scholar 

  • Lang G, Mayhudin NA, Mitova MI, Sun L, van der Sar S, Blunt JW, Cole AL, Ellis G, Laatsch H, Munro MH (2008) Evolving trends in the dereplication of natural product extracts: new methodology for rapid, small-scale investigation of natural product extracts. J Nat Prod 71(9):1595–1599

    Article  CAS  PubMed  Google Scholar 

  • Larsen TS, Krogh A (2003) EasyGene–a prokaryotic gene finder that ranks ORFs by statistical significance. BMC Bioinformatics 4(1):1

    Article  Google Scholar 

  • Lease RA, Belfort M (2000) A trans-acting RNA as a control switch in Escherichia Coli: DsrA modulates function by forming alternative structures. Proc Natl Acad Sci 97(18):9919–9924

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lee PS, Lee KH (2000) Genomic analysis. Curr Opin Biotechnol 11(2):171–175

    Article  PubMed  Google Scholar 

  • Liu W, Christenson SD, Standage S, Shen B (2002) Biosynthesis of the enediyne antitumor antibiotic C-1027. Science 297(5584):1170–1173

    Article  CAS  PubMed  Google Scholar 

  • Locci R (1971) On the spore formation process in Actinomycetes. IV. Examination by scanning electron microscopy of the genera Thermoactinomyces, Actinobifida and Thermomonospora. Riv Pat Vegetab Suppl 7:63–80

    Google Scholar 

  • MacFaddin JF (1980) Biochemical tests for the identification of medical bacteria, 2nd edn. Williams & Wilkins Co., Baltimore

    Google Scholar 

  • Macintyre L, Zhang T, Viegelmann C, Martinez IJ, Cheng C, Dowdells C, Abdelmohsen UR, Gernert C, Hentschel U, Edrada-Ebel R (2014) Metabolomic tools for secondary metabolite discovery from marine microbial symbionts. Mar Drugs 12(6):3416–3448

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Mahyudin NA, Blunt JW, Cole AL, Munro MH (2012) The isolation of a new S-methyl benzothioate compound from a marine-derived Streptomyces sp. Biomed Res Int 2012:894708

    Google Scholar 

  • Maizel JV, Lenk RP (1981) Enhanced graphic matrix analysis of nucleic acid and protein sequences. Proc Natl Acad Sci 78(12):7665–7669

    Google Scholar 

  • Malpartida F, Hopwood D (1984) Molecular cloning of the whole biosynthetic pathway of a Streptomyces antibiotic and its expression in a heterologous host. Nat Biotechnol 309:462–464

    CAS  Google Scholar 

  • Månsson M, Phipps RK, Gram L, Munro MH, Larsen TO, Nielsen KF (2010) Explorative solid-phase extraction (E-SPE) for accelerated microbial natural product discovery, dereplication, and purification. J Nat Prod 73(6):1126–1132

    Google Scholar 

  • Markowitz VM, Chen IMA, Palaniappan K, Chu K, Szeto E, Pillay M, Ratner A, Huang J, Woyke T, Huntemann M (2014) IMG 4 version of the integrated microbial genomes comparative analysis system. Nucleic Acids Res 42(D1):D560–D567

    Article  CAS  PubMed  Google Scholar 

  • Martin JF, Liras P (1989) Organization and expression of genes involved in the biosynthesis of antibiotics and other secondary metabolites. Annu Rev Microbiol 43(1):173–206

    Article  CAS  PubMed  Google Scholar 

  • Medema MH, Paalvast Y, Nguyen DD, Melnik A, Dorrestein PC, Takano E, Breitling R (2014) Pep2Path: automated mass spectrometry-guided genome mining of peptidic natural products. PLoS computational biololy 10(9):e1003822

    Article  CAS  Google Scholar 

  • Miyadoh S, Gakkai NH (1997) Atlas of Actinomycetes. Asakura Publishing Co, Tokyo

    Google Scholar 

  • Molyneux RJ, Schieberle P (2007) Compound identification: a journal of agricultural and food chemistry perspective. J Agric Food Chem 55(12):4625–4629

    Article  CAS  PubMed  Google Scholar 

  • Mount DW (2004) Bioinformatics: sequence and genome analysis, 2nd edn. Cold Spring Harbour Laboratory Press, Cold Spring Harbour

    Google Scholar 

  • Nett M, Ikeda H, Moore BS (2009) Genomic basis for natural product biosynthetic diversity in the actinomycetes. Nat Prod Rep 26(11):1362–1384

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nguyen DD, Wu CH, Moree WJ, Lamsa A, Medema MH, Zhao X, Gavilan RG, Aparicio M, Atencio L, Jackson C (2013) MS/MS networking guided analysis of molecule and gene cluster families. Proc Natl Acad Sci 110(28):E2611–E2620

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nielsen KF, Månsson M, Rank C, Frisvad JC, Larsen TO (2011) Dereplication of microbial natural products by LC-DAD-TOFMS. J Nat Prod 74(11):2338–2348

    Article  CAS  PubMed  Google Scholar 

  • Nitsch B, Kutzner HJ (1968) Bildung eines melanoiden Pigments durch Streptomyces griseus auf synthetischen Medien mit Tyrosin. Z Naturforsch 23b:566

    Google Scholar 

  • Nitsch B, Kutzner HJ (1973) Wachstum von Streptomyceten in Schüttelagarkulturen: eine neue Methode zur Feststellung des C-Qellen-Spektrums. Symp Tech Mikrobiol 3:481–486

    Google Scholar 

  • Ohnishi Y, Ishikawa J, Hara H, Suzuki H, Ikenoya M, Ikeda H, Yamashita A, Hattori M, Horinouchi S (2008) Genome sequence of the streptomycin-producing microorganism Streptomyces Griseus IFO 13350. J Bacteriol 190(11):4050–4060

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pauli GF, Chen SN, Lankin DC, Bisson J, Case RJ, Chadwick LR, Gödecke T, Inui T, Krunic A, Jaki BU (2014) Essential parameters for structural analysis and dereplication by 1H NMR spectroscopy. J Nat Prod 77(6):1473–1487

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pearson WR, Lipman DJ (1988) Improved tools for biological sequence comparison. Proc Natl Acad Sci 85(8):2444–2448

    Google Scholar 

  • Pridham TG, Gottlieb D (1948) The utilization of carbon compounds by some Actinomycetales as an aid for species determination. J Bacteriol 56:107–114

    CAS  PubMed  PubMed Central  Google Scholar 

  • Pridham TG, Hesseltine CW, Bennedict RG (1958) A guide for the classification of Streptomyces according to selected groups. Placement of strains in morphological sections. Appl Microbiol 6:52–79

    CAS  PubMed  PubMed Central  Google Scholar 

  • Proudnikov D, Timofeev E, Mirzabekov A (1998) Immobilization of DNA in polyacrylamide gel for the manufacture of DNA and DNA–oligonucleotide microchips. Anal Biochem 259(1):34–41

    Article  CAS  PubMed  Google Scholar 

  • Reynolds DM (1954) Exocellular chitinase from Streptomyces ssp. J Gen Microbiol 11:150–159

    Article  CAS  PubMed  Google Scholar 

  • Rick WY, Wang T, Bedzyk L, Croker KM (2001) Applications of DNA microarrays in microbial systems. J Microbiol Methods 47(3):257–272

    Article  Google Scholar 

  • Ritacco F, Haltli B, Janso J, Greenstein M, Bernan V (2003) Dereplication of Streptomyces soil isolates and detection of specific biosynthetic genes using an automated ribotyping instrument. J Ind Microbiol Biotechnol 30(8):472–479

    Article  CAS  PubMed  Google Scholar 

  • Salzberg SL, Delcher AL, Kasif S, White O (1998) Microbial gene identification using interpolated Markov models. Nucleic Acids Res 26(2):544–548

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Schena M, Shalon D, Davis RW, Brown PO (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270(5235):467

    Article  CAS  PubMed  Google Scholar 

  • Schiex T, Gouzy J, Moisan A, de Oliveira Y (2003) FrameD: a flexible program for quality check and gene prediction in prokaryotic genomes and noisy matured eukaryotic sequences. Nucleic Acids Res 31(13):3738–3741

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Schwecke T, Aparicio JF, Molnar I, König A, Khaw LE, Haydock SF, Oliynyk M, Caffrey P, Cortes J, Lester JB (1995) The biosynthetic gene cluster for the polyketide immunosuppressant rapamycin. Proc Natl Acad Sci 92(17):7839–7843

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shinobu R (1958) Physiological and cultural study for the identification of soil Actinomycetes species. Mem Osaka Univ Arts Educ B Natur Science 7:1–76

    Google Scholar 

  • Shirling EB, Gottlieb D (1966) Methods for characterization of Streptomyces species. Int J Syst Bacteriol 16:313–340

    Article  Google Scholar 

  • Singh SB, Pelaez F (2008) Biodiversity, chemical diversity and drug discovery. In: Petersen F, Amstutz R (eds) Natural compounds as drugs, vol 1. Springer, Basel, pp 141–174

    Chapter  Google Scholar 

  • Sladič G, Urukalo M, Kirn M, Lešnik U, Magdevska V, Benički N, Pelko M, Gasparič A, Raspor P, Polak T (2014) Identification of lipstatin-producing ability in Streptomyces virginiae CBS 314.55 using dereplication approach. Food Technol Biotechnol 52(3):276–284

    Google Scholar 

  • Stafsnes MH, Dybwad M, Brunsvik A, Bruheim P (2013) Large scale MALDI-TOF MS based taxa identification to identify novel pigment producers in a marine bacterial culture collection. Antonie Van Leeuwenhoek 103(3):603–615

    Article  CAS  PubMed  Google Scholar 

  • Stavri M, Schneider R, O’Donnell G, Lechner D, Bucar F, Gibbons S (2004) The antimycobacterial components of hops (Humulus Lupulus) and their dereplication. Phytother Res 18(9):774–776

    Article  CAS  PubMed  Google Scholar 

  • Suter MA (1978) Isolierung von Melanin-negativen Mutanten aus Streptomyces glaucescens, vol 6276. Diss ETH Zürich, Zurich

    Google Scholar 

  • Tanghe A, Teunissen A, Van Dijck P, Thevelein J (2000) Identification of genes responsible for improved cryoresistance in fermenting yeast cells. Int J Food Microbiol 55(1):259–262

    Article  CAS  PubMed  Google Scholar 

  • Tresner HD, Backus EJ (1963) System for color wheels for streptomycete taxonomy. Appl Microbiol 11:335–338

    CAS  PubMed  PubMed Central  Google Scholar 

  • Tresner HD, Davies MV, Backus EJ (1961) Electron microscopy of Streptomyces spore morphology and its role in species differentiation. J Bacteriol 81:70–80

    CAS  PubMed  PubMed Central  Google Scholar 

  • Van Der Werf MJ, Jellema RH, Hankemeier T (2005) Microbial metabolomics: replacing trial-and-error by the unbiased selection and ranking of targets. J Ind Microbiol Biotechnol 32(6):234–252

    Article  PubMed  CAS  Google Scholar 

  • Viegelmann C, Margassery LM, Kennedy J, Zhang T, O’Brien C, O’Gara F, Morrissey JP, Dobson AD, Edrada-Ebel R (2014) Metabolomic profiling and genomic study of a marine sponge-associated Streptomyces sp. Mar Drugs 12(6):3323–3351

    Google Scholar 

  • Vobis G (1985) Spore development in sporangia-forming Actinomycetes. In: Szabo G, Biró S, Goodfellow M (eds.), Proceedings of the Sixth International Symposium on Actinomycetes Biology, Debrecen, Hungary, 26–30 August, 1985, pp 443–452

    Google Scholar 

  • Vobis G, Kothe HW (1985) Sporogenesis in sporangiate Actinomycetes. In: Pathak NC, Singh VP (eds) Frontiers in applied microbiology, vol 1. Print House, Lucknow

    Google Scholar 

  • Waksman SA (1919) Cultural studies of species of Actinomycetes. Soil Sci 8:71–215

    Article  CAS  Google Scholar 

  • Waksman SA (1961) The Actinomycetes. II. Classification, identification and description of genera and species. The Williams and Wilkins Co., Baltimore, p 363

    Google Scholar 

  • Waksman SA, Curtis RE (1916) The actinomyces of the soil. Soil Sci I 1(2):99–134

    Article  CAS  Google Scholar 

  • Wildermuth H (1972) The surface structure of spores and aerial hyphae in Streptomyces viridochromogenes. Arch Microbiol 81:309–320

    CAS  Google Scholar 

  • Williams ST, Bradshaw RM, Colsterton JW, Forge A (1972) Fine structure of the sheath of some Streptomyces species. J Gen Microbiol 72:249–258

    Article  CAS  PubMed  Google Scholar 

  • Williams ST, Goodfellow M, Alderson G (1989) Genus Streptomyces Waksman and Henrici 1943, 339AL. In: Williams ST, Sharpe ME, Holt JG (eds) Bergey’s manual of systematic becteriology, vol 4. Williams and Wilkins, Baltimore, pp 2452–2492

    Google Scholar 

  • Williams ST, Wellington EMH (1981) The genera Actinomadura, Actinopolyspora, Excellospora, Microbispora, Micropolyspora, Microtetraspora, Nocardiopsis, Saccharopolyspora, andPseudonocardia. In: Starr MP, Stolp H, Trüper HG, Balons A, Schlegel HG (eds) TheProkaryotes: a handbook on habitats, isolation and identification of bacteria. Springer Verlag, Berlin, pp 2103–2117

    Google Scholar 

  • Wink J (2003) Polyphasic taxonomy and antibiotic formation in some closely related genera of the family Pseudonocardiaceae. In: Pandalai SG (ed) Recent research developments in antibiotics. Transworld Research Network, Trivandrum, pp 97–140

    Google Scholar 

  • Wink J (2016) Compendium of Actinobacteria from Dr. Joachim M. Wink University of Braunschweig Copyright Dr. Joachim M. Wink, Helmholtz-Zentrum für Infektionsforschung http://www.dsmz.de/bacterial-diversity/compendium-of-actinobacteria.html

  • Wink J, Gandhi J, Kroppenstedt RM, Seibert G, Straubler B, Schumann P, Stackebrandt E (2004) Amycolatopsis decaplanina sp. nov., a novel member of the genus with unusual morphology. Int J Syst Evol Microbiol 54:235–239

    Article  CAS  PubMed  Google Scholar 

  • Witt D, Stackebrandt E (1990) Unification of the genera Streptoverticillium and Streptomyces, and emendation of Streptomyces Waksman and Henrici 1943, 339al. Syst Appl Microbiol 13:361–371

    Article  CAS  Google Scholar 

  • Wolfender JL (2009) HPLC in natural product analysis: the detection issue. Planta Med 75(7):719–734

    Article  CAS  PubMed  Google Scholar 

  • Xie P, Ma M, Rateb ME, Shaaban KA, Yu Z, Huang SX, Zhao LX, Zhu X, Yan Y, Peterson RM (2014) Biosynthetic potential-based strain prioritization for natural product discovery: a showcase for diterpenoid-producing actinomycetes. J Nat Prod 77(2):377–387

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yang JY, Sanchez LM, Rath CM, Liu X, Boudreau PD, Bruns N, Glukhov E, Wodtke A, De Felicio R, Fenner A (2013) Molecular networking as a dereplication strategy. J Nat Prod 76(9):1686–1699

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zähner H, Ettlinger L (1957) Zur Systematik der Aktinomyceten. 3. Die Verwertung verschiedener Kohlenstoffquellen als Hilfsmittel zur Artbestimmung innerhalb der Gattung Streptomyces. Arch Mikrobiol 26:307–328

    Article  PubMed  Google Scholar 

  • Zazopoulos E, Huang K, Staffa A, Liu W, Bachmann BO, Nonaka K, Ahlert J, Thorson JS, Shen B, Farnet CM (2003) A genomics-guided approach for discovering and expressing cryptic metabolic pathways. Nat Biotechnol 21(2):187–190

    Article  CAS  PubMed  Google Scholar 

  • Zhao L-X, Huang S-X, Tang S-K, Jiang C-L, Duan Y, Beutler JA, Henrich CJ, McMahon JB, Schmid T, Blees JS (2011) Actinopolysporins A–C and tubercidin as a Pdcd4 stabilizer from the halophilic actinomycete Actinopolyspora erythraea YIM 90600. J Nat Prod 74(9):1990–1995

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Helmholtz Centre for Infection Research, Braunschweig, Germany

    Joachim Wink

  2. Department of Microbial Biotechnology, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, 14155-6455, Tehran, Iran

    Fatemeh Mohammadipanah & Hamed Kazemi Shariat Panahi

Authors
  1. Joachim Wink
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Fatemeh Mohammadipanah
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Hamed Kazemi Shariat Panahi
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Joachim Wink or Fatemeh Mohammadipanah .

Editor information

Editors and Affiliations

  1. Microbial Strain Collection; Helmholtz-Centre for Infection Research, Braunschweig, Germany

    Joachim Wink

  2. College of Science, University of Tehran, Tehran, Iran

    Fatemeh Mohammadipanah

  3. College of Science, University of Tehran, Tehran, Iran

    Javad Hamedi

Rights and permissions

Reprints and permissions

Copyright information

© 2017 Springer International Publishing AG

About this chapter

Cite this chapter

Wink, J., Mohammadipanah, F., Kazemi Shariat Panahi, H. (2017). Practical Aspects of Working with Actinobacteria. In: Wink, J., Mohammadipanah, F., Hamedi, J. (eds) Biology and Biotechnology of Actinobacteria. Springer, Cham. https://doi.org/10.1007/978-3-319-60339-1_11

Download citation

Publish with us

Policies and ethics

Search

Navigation