Strain identifier

BacDive ID: 13240

Type strain: Yes

Species: Amycolatopsis keratiniphila

Strain Designation: FH 1893

Strain history: DSM 44586 <-- J. Wink FH 1893 <-- Höchst India Ltd..

NCBI tax ID(s): 208442 (subspecies)

« 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: 11901

BacDive-ID: 13240

DSM-Number: 44586

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

description: Amycolatopsis keratiniphila FH 1893 is a spore-forming, mesophilic, Gram-positive bacterium that was isolated from soil sample.

NCBI tax id

  • NCBI tax id: 208442
  • Matching level: subspecies

strain history

@refhistory
11901<- J. Wink, Aventis; FH 1893 <- Höchst India Ltd.
67770DSM 44586 <-- J. Wink FH 1893 <-- Höchst India Ltd..

doi: 10.13145/bacdive13240.20230509.8.1

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 keratiniphila
  • full scientific name: Amycolatopsis keratiniphila Al-Musallam et al. 2003

  • synonyms

    • @ref: 20215
    • synonym: Amycolatopsis keratiniphila subsp. nogabecina

@ref: 11901

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Pseudonocardiaceae

genus: Amycolatopsis

species: Amycolatopsis keratiniphila subsp. keratiniphila

full scientific name: Amycolatopsis keratiniphila subsp. keratiniphila (Al-Musallam et al. 2003) Wink et al. 2003

strain designation: FH 1893

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: positive
  • confidence: 100

colony morphology

@refcolony colorincubation periodmedium used
20075Sand yellow (1002)10-14 daysISP 2
20075Sand yellow (1002)10-14 daysISP 3
20075Beige (1001)10-14 daysISP 4
20075Beige (1001)10-14 daysISP 5
20075Sand yellow (1002)10-14 daysISP 6
20075Beige (1001)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
20075noISP 2
20075noISP 3
20075noISP 4
20075noISP 5
20075noISP 6
20075noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11901GYM 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
20075ISP 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
20075ISP 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:
20075ISP 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
20075ISP 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
20075ISP 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
20075ISP 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

@refgrowthtypetemperaturerange
11901positivegrowth28mesophilic
20075positiveoptimum28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481yes90
69480yes100

compound production

@refcompound
11901nogabecin
20075Nogabecin (=Actinoidin B).
67770Nogabecin

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2007517234glucose+
2007522599arabinose+
2007517992sucrose+
2007518222xylose+
2007517268myo-inositol+
2007529864mannitol+
2007528757fructose+
2007526546rhamnose+
2007516634raffinose-
2007562968cellulose+
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate+assimilation
6836818257ornithine+degradation
6836825094lysine+degradation
6836829016arginine+hydrolysis
6837917632nitrate-reduction
683794853esculin+hydrolysis
6837916199urea+hydrolysis
683795291gelatin+hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837917992sucrose-fermentation
6837928087glycogen-fermentation

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

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

enzymes

@refvalueactivityec
68379gelatinase+
68379urease+3.5.1.5
68379beta-glucosidase+3.2.1.21
68379N-acetyl-beta-glucosaminidase+3.2.1.52
68379alpha-glucosidase+3.2.1.20
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
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)-
68382esterase lipase (C 8)+
68382lipase (C 14)+
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
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+
68382alpha-galactosidase+3.2.1.22
68382beta-galactosidase+3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase+3.2.1.21
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382alpha-mannosidase+3.2.1.24
68382alpha-fucosidase-3.2.1.51

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
20075--+++++++++--------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
20075+-+++++++++++-++++-

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
20075+++++-+---+

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
11901soil sampleIndiaINDAsia
67770SoilIndiaINDAsia

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: AJ508238
  • 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
119011Risk group (German classification)
200751German classification

Sequence information

16S sequences

  • @ref: 11901
  • description: Amycolatopsis nogabecetica 16S rRNA gene, type strain DSM 44586T
  • accession: AJ508238
  • length: 1471
  • database: ena
  • NCBI tax ID: 208442

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Amycolatopsis keratiniphila FH 1893GCA_900105855chromosomencbi129921
66792Amycolatopsis keratiniphila strain FH 1893129921.3completepatric129921
66792Amycolatopsis keratiniphila nogabecina DSM 445862634166275draftimg129921
67770Amycolatopsis keratiniphila subsp. nogabecina FH 1893GCA_001953855scaffoldncbi208442

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes90no
motileno93.44no
gram-positiveyes85.215no
anaerobicno99.501no
aerobicyes94.83no
halophileno91.289no
spore-formingyes93.299no
thermophileno98.988no
glucose-utilyes88.734no
flagellatedno96.925no
glucose-fermentno93.043no

External links

@ref: 11901

culture collection no.: DSM 44586, CIP 107964, JCM 12671, NRRL B-24206

straininfo link

  • @ref: 82445
  • straininfo: 97664

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
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
Phylogeny33598876Amycolatopsis pittospori sp. nov., an endophytic actinobacterium isolated from native apricot tree and genome mining revealed the biosynthesis potential as antibiotic producer and plant growth promoter.Kaewkla O, Franco CMMAntonie Van Leeuwenhoek10.1007/s10482-021-01519-52021*Actinomycetales/genetics, Amycolatopsis, Anti-Bacterial Agents, Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, Humans, Nucleic Acid Hybridization, Phylogeny, *Prunus armeniaca, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2Pathogenicity

Reference

@idauthorscataloguedoi/urltitle
11901Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44586)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44586
20075Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44586.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
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
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
82445Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID97664.1StrainInfo: A central database for resolving microbial strain identifiers