Strain identifier

BacDive ID: 13245

Type strain: Yes

Species: Amycolatopsis kentuckyensis

Strain history: CIP <- 2003, P. Labeda, USDA, Peoria, Illinois, USA <- 1999, J. M. Donahue, LDDC, Kentucky Univ., USA

NCBI tax ID(s): 218823 (species)

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General

@ref: 11961

BacDive-ID: 13245

DSM-Number: 44652

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, spore-forming, mesophilic, animal pathogen

description: Amycolatopsis kentuckyensis DSM 44652 is an obligate aerobe, spore-forming, mesophilic animal pathogen that builds an aerial mycelium and was isolated from equine placenta.

NCBI tax id

  • NCBI tax id: 218823
  • Matching level: species

strain history

@refhistory
11961<- D. P. Labeda, NRRL
67770DSM 44652 <-- NRRL B-24129 <-- J. M. Donahue LDDC 9447-99.
120400CIP <- 2003, P. Labeda, USDA, Peoria, Illinois, USA <- 1999, J. M. Donahue, LDDC, Kentucky Univ., USA

doi: 10.13145/bacdive13245.20230509.8.1

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 kentuckyensis
  • full scientific name: Amycolatopsis kentuckyensis Labeda et al. 2003

@ref: 11961

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Pseudonocardiaceae

genus: Amycolatopsis

species: Amycolatopsis kentuckyensis

full scientific name: Amycolatopsis kentuckyensis Labeda et al. 2003

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no94.575
69480100positive
120400nopositiverod-shaped

colony morphology

@refcolony colorincubation periodmedium used
20085Ochre brown (8001)10-14 daysISP 2
20085Cream (9001)10-14 daysISP 3
20085Beige (1001)10-14 daysISP 4
20085Ochre brown (8001)10-14 daysISP 5
20085Beige (1001)10-14 daysISP 6
20085Ochre brown (8001)10-14 daysISP 7
120400

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
20085yesAerial MyceliumCream (9001)ISP 2
20085yesAerial MyceliumCream (9001)ISP 3
20085yesAerial MyceliumCream (9001)ISP 4
20085yesAerial MyceliumCream (9001)ISP 5
20085noISP 6
20085yesAerial MyceliumCream (9001)ISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11961GYM 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
11961N-Z-AMINE-MEDIUM (DSMZ Medium 554)yeshttps://mediadive.dsmz.de/medium/554Name: N-Z-AMINE-MEDIUM (DSMZ Medium 554) Composition: Starch 20.0 g/l Agar 20.0 g/l Glucose 10.0 g/l N-Z amine 5.0 g/l Yeast extract 5.0 g/l CaCO3 1.0 g/l Distilled water
20085ISP 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
20085ISP 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:
20085ISP 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
20085ISP 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
20085ISP 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
20085ISP 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
33908MEDIUM 56 - for Micromonospora purpureayesDistilled water make up to (1000.000 ml);Agar (15.000 g);Glucose (10.000g);Yeast extract (5.000 g);Starch maize (20.000 g);Calcium carbonate (1.000 g);Casamino acids (5.000 g)
120400CIP Medium 56yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=56

culture temp

@refgrowthtypetemperaturerange
11961positivegrowth28mesophilic
33908positivegrowth30mesophilic
67770positivegrowth28mesophilic
120400positivegrowth10-41
120400nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 120400
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481yes97
69480yes100

halophily

@refsaltgrowthtested relationconcentration
120400NaClpositivegrowth0-2 %
120400NaClnogrowth4 %
120400NaClnogrowth6 %
120400NaClnogrowth8 %
120400NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: MK-9(H2), MK-9(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2008517234glucose+
2008522599arabinose+
2008517992sucrose+
2008518222xylose-
2008517268myo-inositol+
2008529864mannitol+
2008528757fructose+
2008526546rhamnose+
2008562968cellulose+
2008516634raffinose+
6836830849L-arabinose-fermentation
6836827613amygdalin-fermentation
6836828053melibiose-fermentation
6836817992sucrose-fermentation
6836862345L-rhamnose-fermentation
6836830911sorbitol-fermentation
6836817268myo-inositol-fermentation
6836816899D-mannitol-fermentation
6836817634D-glucose-fermentation
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis
12040016947citrate+carbon source
1204004853esculin+hydrolysis
120400606565hippurate+hydrolysis
12040017632nitrate-reduction
12040016301nitrite-reduction
12040017632nitrate-respiration

antibiotic resistance

  • @ref: 120400
  • 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
12040035581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin-
6836835581indole-
12040015688acetoin-
12040017234glucose-

enzymes

@refvalueactivityec
68368cytochrome oxidase-1.9.3.1
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
120400oxidase-
120400beta-galactosidase+3.2.1.23
120400alcohol dehydrogenase+1.1.1.1
120400gelatinase+/-
120400amylase+
120400DNase-
120400caseinase+3.4.21.50
120400catalase+1.11.1.6
120400tween esterase-
120400gamma-glutamyltransferase+2.3.2.2
120400lecithinase-
120400lipase-
120400lysine decarboxylase-4.1.1.18
120400ornithine decarboxylase-4.1.1.17
120400tryptophan deaminase-
120400urease+3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase+3.4.11.3
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

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
20085++++++++++--+-+++++
120400++--+++--++---+-+---

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
11961----------+----------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
120400+++++-++-+++++-+++++++-++-+----+++++-+-+--+++--+++++-+++++-++-+++-----+++++++--++---+-+-+++++++++++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
11961equine placentaKentucky, LexingtonUSAUSANorth America
67770Equine placentasLexington, KYUSAUSANorth America
120400Animal, Equine, placentaLexington, KentuckyUnited States of AmericaUSANorth America1999

isolation source categories

Cat1Cat2Cat3
#Host#Mammals#Equidae (Horse)
#Host Body Product#Urogenital tract

taxonmaps

  • @ref: 69479
  • File name: preview.99_660.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_408;97_462;98_532;99_660&stattab=map
  • Last taxonomy: Amycolatopsis
  • 16S sequence: AY183357
  • Sequence Identity:
  • Total samples: 5860
  • soil counts: 4583
  • aquatic counts: 156
  • animal counts: 306
  • plant counts: 815

Safety information

risk assessment

@refpathogenicity animalbiosafety levelbiosafety level comment
11961yes2Risk group (German classification)
200851German classification
1204001Risk group (French classification)

Sequence information

16S sequences

  • @ref: 11961
  • description: Amycolatopsis kentuckyensis 16S ribosomal RNA gene, partial sequence
  • accession: AY183357
  • length: 1506
  • database: ena
  • NCBI tax ID: 218823

Genome sequences

  • @ref: 67770
  • description: Amycolatopsis kentuckyensis NRRL B-24129
  • accession: GCA_002155975
  • assembly level: scaffold
  • database: ncbi
  • NCBI tax ID: 218823

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes97no
flagellatedno98.028no
gram-positiveyes86.67no
anaerobicno99.271no
halophileno89.226no
spore-formingyes89.144no
thermophileno98.27yes
glucose-utilyes91.414yes
aerobicyes92.622no
motileno90.658no
glucose-fermentno92.545yes

External links

@ref: 11961

culture collection no.: DSM 44652, JCM 12670, LDDC 9447-99, NRRL B-24129, CIP 108186

straininfo link

  • @ref: 82449
  • straininfo: 97717

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny13130055Amycolatopsis kentuckyensis sp. nov., Amycolatopsis lexingtonensis sp. nov. and Amycolatopsis pretoriensis sp. nov., isolated from equine placentas.Labeda DP, Donahue JM, Williams NM, Sells SF, Henton MMInt J Syst Evol Microbiol10.1099/ijs.0.02691-02003Actinomycetales/*classification/genetics/*isolation & purification/metabolism, Animals, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Female, Horses/*microbiology, Kentucky, Molecular Sequence Data, Phenotype, Phylogeny, Placenta/*microbiology, Pregnancy, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, South AfricaGenetics
Phylogeny15280283Reclassification of Amycolatopsis mediterranei DSM 46095 as Amycolatopsis rifamycinica sp. nov.Bala S, Khanna R, Dadhwal M, Prabagaran SR, Shivaji S, Cullum J, Lal RInt J Syst Evol Microbiol10.1099/ijs.0.02901-02004Actinomycetales/chemistry/*classification/genetics/physiology, Bacterial Typing Techniques, DNA Fingerprinting, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry, Electrophoresis, Gel, Pulsed-Field, Fatty Acids/analysis/isolation & purification, Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis/isolation & purification, Phylogeny, Polymorphism, Restriction Fragment Length, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Rifamycins/biosynthesis, Sequence Analysis, DNA, Sequence HomologyEnzymology

Reference

@idauthorscataloguedoi/urltitle
11961Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44652)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44652
20085Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44652.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
33908Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5780
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
82449Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID97717.1StrainInfo: A central database for resolving microbial strain identifiers
120400Curators of the CIPCollection of Institut Pasteur (CIP 108186)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108186