Strain identifier

BacDive ID: 13242

Type strain: Yes

Species: Amycolatopsis keratiniphila

Strain Designation: D2

Strain history: CIP <- 2003, DSMZ <- Kuwait Univ., Safat, Kuwait: strain D2

NCBI tax ID(s): 129921 (species)

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General

@ref: 11742

BacDive-ID: 13242

DSM-Number: 44409

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic, Gram-positive, rod-shaped

description: Amycolatopsis keratiniphila D2 is an obligate aerobe, mesophilic, Gram-positive bacterium that builds an aerial mycelium and was isolated from soil sample from Omariya Agricultural Station.

NCBI tax id

  • NCBI tax id: 129921
  • Matching level: species

strain history

@refhistory
11742<- S. Al-Zarban, Univ. of Kuwait; D2
67770CIP 107963 <-- DSM 44409 <-- S. Al-Zarban D2.
120404CIP <- 2003, DSMZ <- Kuwait Univ., Safat, Kuwait: strain D2

doi: 10.13145/bacdive13242.20230509.8.1

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: 11742

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: D2

type strain: yes

Morphology

cell morphology

  • @ref: 120404
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: no

colony morphology

@refcolony colorincubation periodmedium used
20056Sand yellow (1002)10-14 daysISP 2
20056Sand yellow (1002)10-14 daysISP 3
20056Sand yellow (1002)10-14 daysISP 4
20056Sand yellow (1002)10-14 daysISP 5
20056Sand yellow (1002)10-14 daysISP 6
20056Sand yellow (1002)10-14 daysISP 7
120404

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
20056yesAerial MyceliumWhiteISP 2
20056yesAerial MyceliumWhiteISP 3
20056yesAerial MyceliumWhiteISP 4
20056noISP 5
20056noISP 6
20056noISP 7

multimedia

  • @ref: 11742
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_44409.jpg
  • caption: Medium 65 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11742GYM 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
20056ISP 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
20056ISP 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:
20056ISP 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
20056ISP 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
20056ISP 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
20056ISP 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
39972MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
120404CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
120404CIP Medium 116yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=116

culture temp

@refgrowthtypetemperaturerange
11742positivegrowth28mesophilic
20056positiveoptimum28mesophilic
39972positivegrowth30mesophilic
67770positivegrowth28mesophilic
120404positivegrowth25-41
120404nogrowth10psychrophilic
120404nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 120404
  • oxygen tolerance: obligate aerobe

halophily

  • @ref: 120404
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-10 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2005617234glucose+
2005622599arabinose+
2005617992sucrose+
2005618222xylose+
2005617268myo-inositol+
2005629864mannitol+
2005628757fructose+
2005626546rhamnose-
2005616634raffinose+
2005662968cellulose+
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-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
6837128087glycogen-builds acid from
6837128017starch-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
6837117057cellobiose-builds acid from
6837117814salicin-builds acid from
683714853esculin+builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
6837159640N-acetylglucosamine-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
6837117634D-glucose-builds acid from
6837112936D-galactose-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-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
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate+assimilation
6836818257ornithine+degradation
6836825094lysine+degradation
6836829016arginine+hydrolysis
12040416947citrate-carbon source
1204044853esculin+hydrolysis
120404606565hippurate+hydrolysis
12040417632nitrate+reduction
12040416301nitrite-reduction
12040417632nitrate-respiration
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

antibiotic resistance

  • @ref: 120404
  • 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
12040435581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin-
6836835581indole-
12040415688acetoin-
12040417234glucose+

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
120404oxidase-
120404beta-galactosidase+3.2.1.23
120404alcohol dehydrogenase-1.1.1.1
120404gelatinase+
120404amylase-
120404DNase-
120404caseinase+3.4.21.50
120404catalase+1.11.1.6
120404tween esterase-
120404gamma-glutamyltransferase+2.3.2.2
120404lecithinase+
120404lipase-
120404lysine decarboxylase-4.1.1.18
120404ornithine decarboxylase-4.1.1.17
120404phenylalanine ammonia-lyase-4.3.1.24
120404protease+
120404tryptophan deaminase-
120404urease+3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382trypsin+3.4.21.4
68382alpha-chymotrypsin+3.4.21.1
68382acid phosphatase+3.1.3.2
68382alpha-galactosidase-3.2.1.22
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
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
20056--++-++++++------+-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
20056++++++++++--+-+++--
120404+++-++-++++---+-+---

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
20056+++++-+---+

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
120404------------------------+------------------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
120404+++++-+-++-+---+++++++--+-+----+++---+-++-------++----+-++++++++---------+++---++-+-+---+++++++++++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
11742soil sample from Omariya Agricultural StationDesert AreaKuwaitKWTAsia
67770Marsh soilKuwaitKWTAsia
120404Environment, SoilKuwaitKWTAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture
#Environmental#Terrestrial#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: AJ278496
  • 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
117421Risk group (German classification)
200561German classification
1204041Risk group (French classification)

Sequence information

16S sequences

  • @ref: 11742
  • description: Amycolatopsis keratinophila 16S rRNA gene, strain DSM 44409T
  • accession: AJ278496
  • length: 1405
  • database: ena
  • NCBI tax ID: 129921

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Amycolatopsis keratiniphila subsp. keratiniphila strain DSM 44409227715.4wgspatric227715
66792Amycolatopsis keratiniphila keratiniphila DSM 444092772190668draftimg227715
67770Amycolatopsis keratiniphila subsp. keratiniphila DSM 44409GCA_001620365scaffoldncbi227715

GC content

  • @ref: 67770
  • GC-content: 69
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno92.243no
gram-positiveyes87.493no
anaerobicno99.486no
aerobicyes95.433no
halophileno90.006no
spore-formingyes93.667no
glucose-utilyes88.246no
flagellatedno96.839no
thermophileno99.058yes
glucose-fermentno93.439yes

External links

@ref: 11742

culture collection no.: DSM 44409, CIP 107963, NRRL B-24117, JCM 12683, BCRC 16375, NCIMB 14256

straininfo link

  • @ref: 82447
  • straininfo: 87928

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
Phylogeny12807215Amycolatopsis keratiniphila sp. nov., a novel keratinolytic soil actinomycete from Kuwait.Al-Musallam AA, Al-Zarban SS, Fasasi YA, Kroppenstedt RM, Stackebrandt EInt J Syst Evol Microbiol10.1099/ijs.0.02515-02003Actinomycetales/chemistry/*classification/genetics/isolation & purification, Animals, Bacterial Typing Techniques, Culture Media, DNA, Ribosomal/analysis, Genotype, Keratins/*metabolism, Kuwait, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Wool/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/urltitlejournalpubmed
11742Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44409)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44409
20056Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44409.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
39972Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5532
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68368Automatically annotated from API 20E
68371Automatically annotated from API 50CH acid
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
82447Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID87928.1StrainInfo: A central database for resolving microbial strain identifiers
120404Curators of the CIPCollection of Institut Pasteur (CIP 107963)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107963