Strain identifier

BacDive ID: 13238

Type strain: Yes

Species: Amycolatopsis tolypomycina

Strain Designation: B-2847, FH6113

Strain history: CIP <- 2003, DSMZ <- J. Wink, Aventis: strain FH6113 <- IFO

NCBI tax ID(s): 208445 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 11849

BacDive-ID: 13238

DSM-Number: 44544

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, antibiotic compound production

description: Amycolatopsis tolypomycina B-2847 is a facultative anaerobe, mesophilic bacterium that builds an aerial mycelium and produces antibiotic compounds.

NCBI tax id

  • NCBI tax id: 208445
  • Matching level: species

strain history

@refhistory
11849<- J. Wink, Aventis; FH6113 <- IFO
67770KCC S-0936 <-- Kyowa Hakko Kogyo Co., Ltd.; KY 1446 <-- ATCC 21177 <-- Takeda Chem. Ind., Ltd.; B2847.
123563CIP <- 2003, DSMZ <- J. Wink, Aventis: strain FH6113 <- IFO

doi: 10.13145/bacdive13238.20230509.8.1

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 tolypomycina
  • full scientific name: Amycolatopsis tolypomycina Wink et al. 2003

@ref: 11849

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Pseudonocardiaceae

genus: Amycolatopsis

species: Amycolatopsis tolypomycina

full scientific name: Amycolatopsis tolypomycina Wink et al. 2003 emend. Nouioui et al. 2018

strain designation: B-2847, FH6113

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no91.977
69480100positive
123563nopositiverod-shaped

colony morphology

@refcolony colorincubation periodmedium used
20071Pure orange (2004)10-14 daysISP 2
20071Melon yellow (1028)10-14 daysISP 3
20071Yellow orange (2000)10-14 daysISP 4
20071Colorless10-14 daysISP 5
2007110-14 daysISP 6
20071Yellow orange (2000)10-14 daysISP 7
123563

multicellular morphology

@refmedium nameforms multicellular complexcomplex namecomplex color
20071ISP 2
20071ISP 3yesAerial MyceliumWhite
20071ISP 4no
20071ISP 5yesAerial MyceliumWhite
20071ISP 6no
20071ISP 7yesAerial MyceliumWhite

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11849GYM 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
20071ISP 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
20071ISP 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:
20071ISP 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
20071ISP 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
20071ISP 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
20071ISP 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
33913MEDIUM 57 - for Streptomyces, Nocardioides, Lentzea albidocapillata and Streptoverticillium reticulumyesDistilled water make up to (1000.000 ml);Agar (15.000 g);Glucose (4.000g);Yeast extract (4.000 g);Malt extract (10.000 g);Calcium carbonate (2.000 g)
123563CIP Medium 57yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=57

culture temp

@refgrowthtypetemperaturerange
11849positivegrowth28mesophilic
20071positiveoptimum28mesophilic
33913positivegrowth30mesophilic
67770positivegrowth28mesophilic
123563positivegrowth25-37mesophilic
123563nogrowth10psychrophilic
123563nogrowth41thermophilic
123563nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 123563
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
20071no
69481yes94
69480yes100

compound production

@refcompound
11849rifamycin
11849tolypomycin
67770Tolypomycin

halophily

@refsaltgrowthtested relationconcentration
20071NaClpositivemaximum2.5 %
123563NaClpositivegrowth0-2 %
123563NaClnogrowth4 %
123563NaClnogrowth6 %
123563NaClnogrowth8 %
123563NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: MK-9(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2007117234glucose+
2007122599arabinose+
2007117992sucrose+
2007118222xylose-
2007117268myo-inositol+
2007129864mannitol+
2007128757fructose+
2007126546rhamnose+
2007116634raffinose-
2007162968cellulose-
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate+assimilation
6836818257ornithine+degradation
6836825094lysine+degradation
6836829016arginine+hydrolysis
12356316947citrate-carbon source
1235634853esculin+hydrolysis
123563606565hippurate+hydrolysis
12356317632nitrate+reduction
12356316301nitrite-reduction
12356317632nitrate+respiration
683794853esculin+hydrolysis
683795291gelatin+hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837928087glycogen-fermentation

antibiotic resistance

  • @ref: 123563
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno
12356335581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin-
6836835581indole-
12356315688acetoin-
12356317234glucose-

enzymes

@refvalueactivityec
68379gelatinase+
68379beta-glucosidase+3.2.1.21
68379N-acetyl-beta-glucosaminidase+3.2.1.52
68379beta-galactosidase+3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase+3.1.3.1
68379pyrrolidonyl arylamidase+3.4.19.3
68379pyrazinamidase-3.5.1.B15
68368gelatinase+
68368tryptophan deaminase-4.1.99.1
68368urease+3.5.1.5
68368ornithine decarboxylase+4.1.1.17
68368lysine decarboxylase+4.1.1.18
68368arginine dihydrolase+3.5.3.6
68368beta-galactosidase+3.2.1.23
123563oxidase-
123563beta-galactosidase+3.2.1.23
123563alcohol dehydrogenase-1.1.1.1
123563gelatinase+
123563amylase-
123563DNase-
123563caseinase+3.4.21.50
123563catalase+1.11.1.6
123563tween esterase-
123563gamma-glutamyltransferase+2.3.2.2
123563lecithinase-
123563lipase-
123563lysine decarboxylase-4.1.1.18
123563ornithine decarboxylase-4.1.1.17
123563phenylalanine ammonia-lyase-4.3.1.24
123563tryptophan deaminase-
123563urease+3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382leucine arylamidase+3.4.11.1
68382acid phosphatase+3.1.3.2
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382alpha-fucosidase-3.2.1.51

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYGControl
20071--++-+-++++------+-
11849+-++-++++-+---------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
20071+-++++++++-++-++++-
11849++/-+/--++/--+/--++-+/--+-++/---
123563+++-++-+-+--+-+-+---

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
20071+++++-+---+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
11849soilTokyoJapanJPNAsia
67770SoilTokyoJapanJPNAsia
123563Environment, SoilJapanJPNAsia

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
118491Risk group (German classification)
200711German classification
1235631Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
11849Amycolatopsis tolypophora 16S rRNA gene, type strain DSM 44544TAJ5082411408ena208445
67770Amycolatopsis tolypophorous partial 16S rRNA gene, strain IMSNU 20061TAJ2937571512ena208445

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Amycolatopsis tolypomycina strain DSM 44544208445.6wgspatric208445
66792Amycolatopsis tolypomycina DSM 445442634166899draftimg208445
67770Amycolatopsis tolypomycina DSM 44544GCA_900105945contigncbi208445

GC content

  • @ref: 67770
  • GC-content: 71.7
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes94no
motileno90.451no
gram-positiveyes84.802no
anaerobicno99.285no
aerobicyes89.443no
halophileno92.679no
spore-formingyes91.804no
glucose-utilyes90.724yes
flagellatedno96.855no
thermophileno98.096yes
glucose-fermentno92.271yes

External links

@ref: 11849

culture collection no.: DSM 44544, ATCC 21177, CIP 108212, IFO 14664, NBRC 14664, NRRL B-24205, JCM 4936, CBS 242.71, CGMCC 4.5590, IFO 12554, IMSNU 20061, NBRC 12554

straininfo link

  • @ref: 82443
  • straininfo: 44580

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12747408Three new antibiotic producing species of the genus Amycolatopsis, Amycolatopsis balhimycina sp. nov., A. tolypomycina sp. nov., A. vancoresmycina sp. nov., and description of Amycolatopsis keratiniphila subsp. keratiniphila subsp. nov. and A. keratiniphila subsp. nogabecina subsp. nov.Wink JM, Kroppenstedt RM, Ganguli BN, Nadkarni SR, Schumann P, Seibert G, Stackebrandt ESyst Appl Microbiol10.1078/0723202033223372902003Actinomycetales/*classification/genetics/metabolism/ultrastructure, Anti-Bacterial Agents/*biosynthesis, Culture Media/chemistry, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/analysis/genetics, Soil MicrobiologyGenetics
Phylogeny25744584Amycolatopsis rhabdoformis sp. nov., an actinomycete isolated from a tropical forest soil.Souza WR, Silva RE, Goodfellow M, Busarakam K, Figueiro FS, Ferreira D, Rodrigues-Filho E, Moraes LAB, Zucchi TDInt J Syst Evol Microbiol10.1099/ijs.0.0001762015Actinomycetales/*classification/genetics/isolation & purification, Bacteria, Aerobic/genetics, Bacterial Typing Techniques, Brazil, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Forests, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryGenetics

Reference

@idauthorscataloguedoi/urltitle
11849Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44544)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44544
20071Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44544.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
33913Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5810
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
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
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
82443Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID44580.1StrainInfo: A central database for resolving microbial strain identifiers
123563Curators of the CIPCollection of Institut Pasteur (CIP 108212)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108212