Strain identifier

BacDive ID: 13231

Type strain: Yes

Species: Amycolatopsis japonica

Strain Designation: MG 417-CF 17

Strain history: CIP <- 2000, JCM <- M. Hamada MG417-CF17 (IMC A-0199)

NCBI tax ID(s): 208439 (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: 11600

BacDive-ID: 13231

DSM-Number: 44213

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, spore-forming, mesophilic, Gram-positive

description: Amycolatopsis japonica MG 417-CF 17 is an obligate aerobe, spore-forming, mesophilic bacterium that builds an aerial mycelium.

NCBI tax id

  • NCBI tax id: 208439
  • Matching level: species

strain history

@refhistory
11600<- M. Goodfellow <- T. Takeuchi, MG 417-CF 17, (Amycolatopsis japonicum), Inst. of Micro. Chemistry, Tokyo
67770M. Hamada MG417-CF17 (IMC A-0199).
120312CIP <- 2000, JCM <- M. Hamada MG417-CF17 (IMC A-0199)

doi: 10.13145/bacdive13231.20230509.8.1

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 japonica
  • full scientific name: Amycolatopsis japonica corrig. Goodfellow et al. 1997

  • synonyms

    • @ref: 20215
    • synonym: Amycolatopsis japonicum

@ref: 11600

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Pseudonocardiaceae

genus: Amycolatopsis

species: Amycolatopsis japonica

full scientific name: Amycolatopsis japonica Goodfellow et al. 1997

strain designation: MG 417-CF 17

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480positive100
120312positiverod-shapedno

colony morphology

@refcolony colorincubation periodmedium usedhemolysis ability
19636Saffron yellow10-14 daysISP 2
1963610-14 daysISP 3
1963610-14 daysISP 4
1963610-14 daysISP 5
19636Saffron yellow10-14 daysISP 6
19636Saffron yellow10-14 daysISP 7
1203121

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
19636yesAerial MyceliumWhiteISP 2
19636yesAerial MyceliumWhiteISP 3
19636yesAerial MyceliumISP 4
19636yesAerial MyceliumWhiteISP 5
19636noISP 6
19636yesAerial MyceliumWhiteISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11600BENNETT'S AGAR (DSMZ Medium 548)yeshttps://mediadive.dsmz.de/medium/548Name: BENNETT'S AGAR (DSMZ Medium 548) Composition: Agar 15.0 g/l Glucose 10.0 g/l N-Z amine 2.0 g/l Yeast extract 1.0 g/l Beef extract 1.0 g/l Distilled water
19636ISP 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
19636ISP 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:
19636ISP 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
19636ISP 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
19636ISP 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
19636ISP 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
35992MEDIUM 128 - for Nocardia brevicatena, Nocardia flavorosea subsp. fusca and Streptomyces ambofaciensyesDistilled water make up to (1000.000 ml);Maltose (10.000 g);Agar (20.000g);Yeast extract (1.000 g);Beef extract (1.000 g);Casamino acids (2.000 g)
120312CIP Medium 129yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=129

culture temp

@refgrowthtypetemperaturerange
11600positivegrowth28mesophilic
19636positiveoptimum28mesophilic
35992positivegrowth30mesophilic
67770positivegrowth28mesophilic
120312positivegrowth10-45

Physiology and metabolism

oxygen tolerance

  • @ref: 120312
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481yes90
69480yes100

compound production

@refcompound
11600catalase
11600lipolytic enzymes

halophily

@refsaltgrowthtested relationconcentration
19636NaClpositivemaximum2.5 %
120312NaClpositivegrowth0-6 %
120312NaClnogrowth8 %
120312NaClnogrowth10 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1963617234glucose+
1963622599arabinose+
1963617992sucrose-
1963618222xylose-
1963617268myo-inositol+
1963629864mannitol+
1963628757fructose+
1963626546rhamnose-
1963616634raffinose+
1963662968cellulose-
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose-builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose-builds acid from
6837117992sucrose-builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117306maltose-builds acid from
6837117814salicin-builds acid from
683714853esculin+builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose-builds acid from
6837115824D-fructose-builds acid from
6837112936D-galactose-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837116988D-ribose-builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate+assimilation
6836818257ornithine+degradation
6836825094lysine+degradation
6836829016arginine+hydrolysis
1203124853esculin+hydrolysis
120312606565hippurate+hydrolysis
12031217632nitrate-reduction
12031216301nitrite-reduction
12031217632nitrate-respiration

antibiotic resistance

  • @ref: 120312
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

@refmetaboliteproductionChebi-ID
67770Ethylenediamine-N,N'-disuccinic acid (EDDS)yes
68368acetoinyes15688
68368indoleno35581
68368hydrogen sulfideno16136
120312indoleno35581

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin+
6836835581indole-
12031215688acetoin-
12031217234glucose-

enzymes

@refvalueactivityec
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
120312oxidase+
120312beta-galactosidase+3.2.1.23
120312alcohol dehydrogenase-1.1.1.1
120312gelatinase+
120312amylase-
120312DNase-
120312caseinase+3.4.21.50
120312catalase+1.11.1.6
120312tween esterase+
120312gamma-glutamyltransferase+2.3.2.2
120312lecithinase-
120312lipase-
120312lysine decarboxylase-4.1.1.18
120312ornithine decarboxylase-4.1.1.17
120312phenylalanine ammonia-lyase-4.3.1.24
120312tryptophan deaminase-
120312urease+3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382leucine arylamidase+3.4.11.1
68382cystine arylamidase+3.4.11.3
68382trypsin+3.4.21.4
68382alpha-chymotrypsin+3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382beta-glucosidase+3.2.1.21
68382N-acetyl-beta-glucosaminidase+3.2.1.52

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
19636+++++++++++++++++++
120312+++-+-+++++----++---

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19636+++++-+--++

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
120312+/-+/------+/---+/-----------+/---+-+/---------+/-+/-------+/---+/---

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
116001Risk group (German classification)
196361Risk group (German classification)
1203121Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
11600Amycolatopsis japonica 16S rRNA gene, type strain DSM 44213TAJ5082361485ena208439
67770Amycolatopsis.sp (MG 417) 16S rRNA geneX779591471ena37632

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Amycolatopsis japonica strain MG417-CF17 (=DSM 44213)208439.3completepatric208439
66792Amycolatopsis japonica strain MG417-CF17 strain DSM 44213208439.7plasmidpatric208439
66792Amycolatopsis japonica MG417-CF17, DSM 442132585427649completeimg208439
67770Amycolatopsis japonica DSM 44213GCA_000732925completencbi208439

GC content

@refGC-contentmethod
1160069.5
6777068.89genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes90no
motileno92.267no
gram-positiveyes85.614no
anaerobicno99.488no
aerobicyes94.898no
halophileno89.839no
spore-formingyes91.369no
glucose-utilyes89.092yes
flagellatedno96.269no
thermophileno99.024yes
glucose-fermentno93.894no

External links

@ref: 11600

culture collection no.: DSM 44213, JCM 10140, CIP 106801, KCTC 9817, NRRL B-24138

straininfo link

  • @ref: 82436
  • straininfo: 50525

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Genetics25193710Complete genome sequence of the actinobacterium Amycolatopsis japonica MG417-CF17(T) (=DSM 44213T) producing (S,S)-N,N'-ethylenediaminedisuccinic acid.Stegmann E, Albersmeier A, Spohn M, Gert H, Weber T, Wohlleben W, Kalinowski J, Ruckert CJ Biotechnol10.1016/j.jbiotec.2014.08.0342014Actinomycetales/*genetics, Base Composition/genetics, Genome, Bacterial/*genetics, Molecular Sequence Data, Succinates/*metabolismMetabolism
Metabolism33974270Microparticles enhance the formation of seven major classes of natural products in native and metabolically engineered actinobacteria through accelerated morphological development.Kuhl M, Ruckert C, Glaser L, Beganovic S, Luzhetskyy A, Kalinowski J, Wittmann CBiotechnol Bioeng10.1002/bit.278182021Anti-Bacterial Agents/*biosynthesis, *Metabolic Engineering, *Microorganisms, Genetically-Modified/genetics/metabolism, *Peptides, Cyclic/biosynthesis/genetics, *Streptomyces lividans/genetics/metabolism

Reference

@idauthorscataloguedoi/urltitle
11600Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44213)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44213
19636Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44213.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
35992Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18971
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
68371Automatically annotated from API 50CH acid
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
82436Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID50525.1StrainInfo: A central database for resolving microbial strain identifiers
120312Curators of the CIPCollection of Institut Pasteur (CIP 106801)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106801