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16S phylogeny of the Streptomycetaceae

16S phylogeny of the Streptomycetaceae. Alan Ward. 16S phylogeny of the Streptomycetaceae. Outline. Motivation Streptomyces taxonomy 16S Whole genome sequencing A bigger 16S phylogeny Where is the diversity The type strains Uncultured diversity Where are: The whole genomes

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16S phylogeny of the Streptomycetaceae

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  1. 16S phylogeny of the Streptomycetaceae Alan Ward

  2. 16S phylogeny of the Streptomycetaceae Outline • Motivation • Streptomyces taxonomy • 16S • Whole genome sequencing • A bigger 16S phylogeny • Where is the diversity • The type strains • Uncultured diversity • Where are: • The whole genomes • Kitasatosporaand Streptacidiphilus • Marine actinomycetes • Thermophiles • The Streptomyces violaceusnigerclade • Who makes nigericin

  3. 16S phylogeny of the Streptomycetaceae Why? Hypothesis those claiming the same antibiotic in different species “are mistaken in species identification or the nature of the antibiotic” Krassilnikov5 best producers of natural product antibiotics are members of the actinomycetes, and according to Hugenholz et al. (1998), approximately 30% or more of these have been discovered at one time or another. This has been the result of some fifty years worth of intense antibiotic screening programs conducted by pharmaceutical industry natural products scientists Strohl, 2004 To address this hypothesis, for Streptomyces, need to be able to address the relationship of strains to one another For example, a survey of the literature linked the “species” names Streptomyces antibioticus, S. griseus and S. hygroscopicus, with the production of 13, 32, and 46 different structural types of natural products, respectively. Examples of compounds produced by strains characterized as S. hygroscopicus include rapamycin, spectinomycin, bialophos, hygromycin, and a variety of polyethers.Strohl 2004

  4. 16S phylogeny of the Streptomycetaceae

  5. 16S phylogeny of the Streptomycetaceae Stackebrandt and Goebel (1994) Int J SystBacteriol44, 846–849 - prokaryotes Stachet al. (2003) App Environ Microbiol 69, 6189-6200 - actinobacteria

  6. 16S phylogeny of the Streptomycetaceae more Whole genome projects • Streptomyces sp. CNS615 • Streptomyces sp. CNS335 • Streptomyces sp. CNT371 • Streptomyces sp. CNR698 • Streptomyces sp. CNB091 • Streptomyces sp. CNQ766 • Streptomyces sp. CNS335 • Streptomyces sp. CNS615 • Streptomyces sp. CNT302 • Streptomyces sp. CNT372 • Streptomyces sp. CNY228 • Streptomyces sp. CNY243 • Streptomyces sp. PVA 94-07 • Streptomyces sp. GBA 94-10 • Streptomyces sp. CNS606 • Streptomyces sp. CNT318 • Streptomyces sp. TAA204 • Streptomyces sp. CNQ329 • Streptomyces sp. CNT360 • Streptomyces sp. CNQ865 • Streptomyces sp. TAA486 • Streptomyces sp. CNH287 • Streptomyces sp. TAA040 • Streptomyces sp. CNQ-525 • Streptomyces sp. GXT6 • Streptomyces sp. PAMC26508 • … • Streptomyces sp. H668 • Streptomyces sp. 371 • Streptomyces sp. HGB0020 • Streptomyces sp. HPH0547 • Streptomyces sp. 118.1MFTsu1.1 • Streptomyces sp. 142MFCol3.1 • Streptomyces sp. 142MFCol3.1 • Streptomyces sp. 351MFTsu5.1 • Streptomyces sp. AP10 JX101691 • Streptomyces cinnamoneus • Streptomyces thermoviolaceus • Streptomyces sp. M17 • Streptomyces sp. M43 • Streptomyces sp. CNH099 • Streptomyces sp. CNH189 • Streptomyces sp. CNP082 • Streptomyces sp. CNS654

  7. 16S phylogeny of the Streptomycetaceae Whole genome phylogeny Mohammad TauqeerAlam, Maria Elena Merlo, Eriko Takano, Rainer Breitling(2010) Genome-based phylogenetic analysis of Streptomyces and its relatives.Molecular Phylogenetics and Evolution 54 763–772 Streptomyces acidiscabies 84-104 Streptomyces scabiei 87.22 Streptomyces bingchenggensis BCW-1 Streptomyces sp. S4 Streptomyces cattleya NRRL 8057 Streptomyces sp. SA3_actF Streptomyces chartreusis NRRL 12338 Streptomyces sp. SA3_actG Streptomyces chartreusis NRRL 3882 Streptomyces sp. SirexAA-E Streptomyces clavuligerus ATCC 27064 Streptomyces sp. TOR3209 Streptomyces coelicolor A3(2) Streptomyces sp. Tu6071 Streptomyces flavogriseus IAF45CD, ATCC 33331 Streptomyces sp. W007 Streptomyces griseoaurantiacus M045 Streptomyces sp. Wigar10 Streptomyces griseusgriseus NBRC 13350 Streptomyces sviceus ATCC 29083 Streptomyces griseus XyelbKG-1 1 Streptomyces tsukubaensis NRRL 18488 Streptomyces hygroscopicusjinggangensis 5008 Streptomyces turgidiscabies Car8 Streptomyces ipomoeae 91-03 Streptomyces venezuelaeATCC 10712 Streptomyces lysosuperificus ATCC 31396 Streptomyces violaceusnigerTu 4113 Streptomyces pristinaespiralis ATCC 25486 Streptomyces viridosporus T7A, ATCC 39115 Streptomyces roseosporus NRRL 11379

  8. 16S phylogeny of the Streptomycetaceae Tree generation • Downloaded 7,610 pre-aligned streptomycete 16S from RDP in Genbank FASTA format (in 2010) – remove 17 ambiguous sequences • Edit labels to exclude invalid characters and consist of a unique numeric code, the species name, the strain name, the culture collection number and the Genbank sequence code • Generate the pairwise alignment distance matrix • Calculate the RDP alignment distance matrix and compare the pairwise and multiple alignment distances • Repeat • Manually re-align and calculate the distance matrix • Calculate a tree (NJ-Jukes & Cantor initially then Maximum Likelihood) • Sort the sequences to tree order • Until the total distance in the distance matrix stops decreasing

  9. 16S phylogeny of the Streptomycetaceae Multiple alignment

  10. 16S phylogeny of the Streptomycetaceae

  11. 16S phylogeny of the Streptomycetaceae Whole genome projects

  12. 16S phylogeny of the Streptomycetaceae Higher order clusters? Streptacidiphilus Kitasatospora

  13. 16S phylogeny of the Streptomycetaceae

  14. 16S phylogeny of the Streptomycetaceae

  15. 16S phylogeny of the Streptomycetaceae Streptomycesviolaceusnigerclade

  16. 16S phylogeny of the Streptomycetaceae Streptomycesviolaceusnigerclade

  17. A B Ela Pen Aza Hex Gel 16S phylogeny of the Streptomycetaceae HPLC analysis of Streptomyces violaceusnigerclade Number of strains producing each secondary metabolite in different production media. HPLC-DAD chromatograms showing major metabolites produced by members of the S. violaceusnigerclade A, Streptomyces sp. DSM 4137 and B, WS-P18C9.Aza = azalomycin F, Ela = elaiophylin, Gel = geldanamycin, Hex = hexaenepolyene and Pen = pentaenepolyene.

  18. 16S phylogeny of the Streptomycetaceae Streptomycesviolaceusnigerclade

  19. Elaiophylin Lankacidin

  20. 16S phylogeny of the Streptomycetaceae Blastp analysis of AntiSMASHfor elaiophylin gene cluster

  21. 16S phylogeny of the Streptomycetaceae AntiSMASH Streptomyces himastatinicus

  22. 16S phylogeny of the Streptomycetaceae

  23. 16S phylogeny of the Streptomycetaceae Conclusions • Motivation • Streptomyces taxonomy • 16S • Whole genome sequencing • A bigger 16S phylogeny • Where is the diversity • The type strains • Uncultured diversity • Where are: • The whole genomes • Kitasatosporaand Streptacidiphilus • Marine actinomycetes • Thermophiles • The Streptomyces violaceusnigerclade • Who makes nigericin

  24. 16S phylogeny of the Streptomycetaceae Acknowledgements Stephen Haydock – for introducing us to Streptomyces DSM 4137 PorntipaAiemsum-ang and Yashawant Kumar – PhD students at Newcastle Peter Fiedler Ern Lacy The software developers The sequencers for Genbank/EMBL whole genomes and gene clusters databases/blast/PubMed/links RDP 16S data The chemists for SeaView molecules and structures ClustalX Muscle MAFFT PhyMLFastTree ESPRIT Culture collections/microbiologists for Dendroscope microorganisms antiSMASH

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