Strain identifier

BacDive ID: 13222

Type strain: Yes

Species: Amycolatopsis azurea

Strain Designation: AM-3696

Strain history: KCC A-0275 <-- S. ?mura AM-3696.

NCBI tax ID(s): 1238180 (strain), 36819 (species)

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General

@ref: 11336

BacDive-ID: 13222

DSM-Number: 43854

keywords: genome sequence, 16S sequence, Bacteria, spore-forming, antibiotic compound production

description: Amycolatopsis azurea AM-3696 is a spore-forming bacterium that builds an aerial mycelium and produces antibiotic compounds.

NCBI tax id

NCBI tax idMatching level
1238180strain
36819species

strain history

@refhistory
11336<- T.H. Embley, Omura AM-3696 <- A. Henssen <- NRRL
67770KCC A-0275 <-- S. ?mura AM-3696.

doi: 10.13145/bacdive13222.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Pseudonocardiales
  • family: Pseudonocardiaceae
  • genus: Amycolatopsis
  • species: Amycolatopsis azurea
  • full scientific name: Amycolatopsis azurea (?mura et al. 1983) Henssen et al. 1987

  • synonyms

    • @ref: 20215
    • synonym: Pseudonocardia azurea

@ref: 11336

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Pseudonocardiaceae

genus: Amycolatopsis

species: Amycolatopsis azurea

full scientific name: Amycolatopsis azurea (?mura et al. 1983) Henssen et al. 1987 emend. Nouioui et al. 2018

strain designation: AM-3696

type strain: yes

Morphology

colony morphology

@refcolony colorincubation periodmedium used
19607Steel blue10-14 daysISP 2
1960710-14 daysISP 3
19607Red10-14 daysISP 4
19607Purple violet10-14 daysISP 5
1960710-14 daysISP 6
19607Purple violet10-14 daysISP 7

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
19607yesAerial MyceliumDistant blueISP 2
19607yesAerial MyceliumWhiteISP 3
19607yesAerial MyceliumWhiteISP 4
19607yesAerial MyceliumWhiteISP 5
19607noISP 6
19607yesAerial MyceliumRoseISP 7

multimedia

  • @ref: 11336
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_43854.jpg
  • caption: Medium 535 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11336TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
11336GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)yeshttps://mediadive.dsmz.de/medium/65Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water
19607ISP 2yesName: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
19607ISP 3yesName: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
19607ISP 4yesName: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
19607ISP 5yesName: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
19607ISP 6yesName: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
19607ISP 7yesName: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes

culture temp

@refgrowthtypetemperature
19607positiveoptimum30
11336positivegrowth28
67770positivegrowth28

Physiology and metabolism

oxygen tolerance

  • @ref: 69480
  • oxygen tolerance: aerobe
  • confidence: 90.489

spore formation

@refspore descriptiontype of sporespore formationconfidence
19607Formation of spores, spore surface smooth, fragmentationsporeyes
69481yes90

compound production

@refcompound
11336azureomycin
19607Octacosamicin A

halophily

  • @ref: 19607
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 5 %

observation

@refobservation
67770Bioconversion of AS1387392
67770quinones: MK-9(H4), MK-9(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1960717234glucose+
1960722599arabinose+
1960717992sucrose+
1960718222xylose-
1960717268myo-inositol+
1960729864mannitol-
1960728757fructose-
1960726546rhamnose-
1960716634raffinose+
1960762968cellulose-
6836817632nitrate-reduction
6836830849L-arabinose-fermentation
6836827613amygdalin-fermentation
6836828053melibiose-fermentation
6836817992sucrose-fermentation
6836862345L-rhamnose-fermentation
6836830911sorbitol-fermentation
6836817268myo-inositol-fermentation
6836816899D-mannitol-fermentation
6836817634D-glucose-fermentation
6836827897tryptophan-energy source

metabolite production

@refmetaboliteproductionChebi-ID
67770azureomycinyes
68368dinitrogenno17997
68368nitriteno16301
68368acetoinyes15688
68368indoleno35581
68368hydrogen sulfideno16136

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin+
6836835581indole-

enzymes

@refvalueactivityec
68368tryptophan deaminase-4.1.99.1
68382esterase (C 4)-
68382lipase (C 14)-
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382alpha-galactosidase-3.2.1.22
68382beta-glucuronidase-3.2.1.31
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
19607--+-+--++++-+-+++--
11336+/----+/----+/-------+---

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARANO2N2
19607+++++-+--++
11336---------+------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
11336soilYamagata Pref.JapanJPNAsia
67770SoilYamagata Pref.JapanJPNAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_4024.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_408;97_462;98_1734;99_4024&stattab=map
  • Last taxonomy: Amycolatopsis
  • 16S sequence: AJ400709
  • Sequence Identity:
  • Total samples: 1433
  • soil counts: 689
  • aquatic counts: 30
  • animal counts: 79
  • plant counts: 635

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
113361Risk group (German classification)
196071Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Amycolatopsis azurea partial 16S rRNA gene, strain IMSNU 20053TAJ4007091460nuccore36819
20218Amycolatopsis azurea 16S rRNA (part.)X531991300nuccore36819

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Amycolatopsis azurea DSM 438541238180.3wgspatric1238180
66792Amycolatopsis azurea DSM 43854 strain DSM 438541238180.7wgspatric1238180
66792Amycolatopsis azurea DSM 438542537562147draftimg1238180
67770Amycolatopsis azurea DSM 43854GCA_000340415contigncbi1238180
67770Amycolatopsis azurea DSM 43854GCA_001995215scaffoldncbi1238180

GC content

@refGC-contentmethod
6777066thermal denaturation, midpoint method (Tm)
6777068.9genome sequence analysis

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesyes90no
69480gram-positivegram-positivePositive reaction to Gram-stainingyes87.583no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no97.414no
69480spore-formingspore-formingAbility to form endo- or exosporesyes84.508yes
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes90.489no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno97.6yes
69480flagellatedmotile2+Ability to perform flagellated movementno86.9no

External links

@ref: 11336

culture collection no.: DSM 43854, ATCC 51273, FERM P-4738, IFO 14573, JCM 3275, KCC A-0275, NBRC 14573, NRRL 11412, VKM Ac-1418, BCRC 13413, HUT 6555, IMSNU 20053, KACC 20058, KCCM 40242, KCTC 9154, NCIMB 14805

straininfo link

  • @ref: 82429
  • straininfo: 88624

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny528377Studies on bacterial cell wall inhibitors. VII. Azureomycins A and B, new antibiotics produced by Pseudonocardia azurea nov. sp. Taxonomy of the producing organism, isolation, characterization and biological properties.Omura S, Tanaka H, Tanaka Y, Spiri-Nakagawa P, Oiwa R, Takahashi Y, Matsuyama K, Iwai YJ Antibiot (Tokyo)10.7164/antibiotics.32.9851979Actinomycetales/classification/*metabolism/ultrastructure, Animals, Anti-Bacterial Agents/*biosynthesis/isolation & purification/pharmacology, Bacteria/drug effects, Chemical Phenomena, Chemistry, Fermentation, Mice, Peptide Biosynthesis, Peptides/isolation & purification/pharmacology, Time FactorsEnzymology
Metabolism20924384Bioconversion of AS1387392: bioconversion studies involving Amycolatopsis azurea JCM 3275.Sasamura S, Ohsumi K, Takase S, Yamada T, Muramatsu H, Fujie A, Mori H, Fujii T, Hino M, Sakamoto K, Hashimoto MJ Antibiot (Tokyo)10.1038/ja.2010.1082010Actinomycetales/*metabolism, Carbon/chemistry, Culture Media/chemistry, Hydrogen-Ion Concentration, Hydroxylation, Immunosuppressive Agents/*metabolism, Nitrogen/chemistry, Peptides, Cyclic/*metabolism, TemperatureCultivation
Phylogeny22771685Amycolatopsis magusensis sp. nov., isolated from soil.Camas M, Sahin N, Sazak A, Sproer C, Klenk HPInt J Syst Evol Microbiol10.1099/ijs.0.042770-02012Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Cyprus, DNA, Bacterial/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/analysisGenetics
Genetics26484067Genome sequencing and annotation of Amycolatopsis azurea DSM 43854(T).Khatri I, Subramanian S, Mayilraj SGenom Data10.1016/j.gdata.2013.12.0032014

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11336Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 43854)https://www.dsmz.de/collection/catalogue/details/culture/DSM-43854
19607Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM43854.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68368Automatically annotated from API 20E
68382Automatically annotated from API zym
69479João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.https://microbeatlas.org/MicrobeAtlas 1.0 beta
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
82429Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID88624.1StrainInfo: A central database for resolving microbial strain identifiers