Strain identifier

BacDive ID: 24444

Type strain: Yes

Species: Amycolatopsis cihanbeyliensis

Strain Designation: BNT52

Strain history: <- Nevzat Sahin, Ondokuz Mayis Univ., Turkey

NCBI tax ID(s): 1128664 (species)

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General

@ref: 20306

BacDive-ID: 24444

DSM-Number: 45679

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

description: Amycolatopsis cihanbeyliensis BNT52 is an aerobe, spore-forming, mesophilic bacterium that was isolated from soil from a salt mine .

NCBI tax id

  • NCBI tax id: 1128664
  • Matching level: species

strain history

@refhistory
20306<- N. Sahin, Ondokuz Mayis Univ., Dept. of Biology, Samsun, Turkey; BNT52 <- M. Camas
67770DSM 45679 <-- N. Sahin; Ondokuz Mayis Univ., Turkey; BNT52 <-- M. Camas.
67771<- Nevzat Sahin, Ondokuz Mayis Univ., Turkey

doi: 10.13145/bacdive24444.20230509.8.1

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 cihanbeyliensis
  • full scientific name: Amycolatopsis cihanbeyliensis Tatar et al. 2013

@ref: 20306

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Pseudonocardiaceae

genus: Amycolatopsis

species: Amycolatopsis cihanbeyliensis

full scientific name: Amycolatopsis cihanbeyliensis Tatar et al. 2013

strain designation: BNT52

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
31059positiverod-shapedno
67771positive
69480no94.167
69480positive100

Culture and growth conditions

culture medium

  • @ref: 20306
  • name: GPHF-MEDIUM (DSMZ Medium 553)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/553
  • composition: Name: GPHF-MEDIUM (DSMZ Medium 553) Composition: Agar 20.0 g/l Glucose 10.0 g/l Beef extract 5.0 g/l Yeast extract 5.0 g/l Casein peptone 5.0 g/l CaCl2 x 2 H2O 0.74 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
20306positivegrowth28mesophilic
31059positivegrowth20-37
31059positiveoptimum28mesophilic
67770positivegrowth28mesophilic
67771positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
31059positivegrowth6.0-12alkaliphile
31059positiveoptimum7.2

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31059aerobe
67771aerobe

spore formation

@refspore formationconfidence
69481yes100
69480yes100

halophily

  • @ref: 31059
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-10 %

observation

@refobservation
67770quinones: MK-9(H4)
67771quinones: MK-9(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3105915963ribitol+carbon source
3105922599arabinose+carbon source
3105917057cellobiose+carbon source
3105923652dextrin+carbon source
3105928757fructose+carbon source
3105928260galactose+carbon source
3105915428glycine+carbon source
3105917716lactose+carbon source
3105917306maltose+carbon source
3105929864mannitol+carbon source
3105937684mannose+carbon source
3105917268myo-inositol+carbon source
3105928044phenylalanine+carbon source
3105926271proline+carbon source
3105917822serine+carbon source
3105930911sorbitol+carbon source
3105926986threonine+carbon source
3105917151xylitol+carbon source
3105918222xylose+carbon source
310594853esculin+hydrolysis
6836925115malate-assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836917306maltose-assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
683695291gelatin+hydrolysis
683694853esculin+hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
31059catalase+1.11.1.6
31059urease+3.5.1.5
68369gelatinase+
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
68382alkaline phosphatase+3.1.3.1
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382trypsin-3.4.21.4
68382alpha-chymotrypsin+3.4.21.1
68382acid phosphatase-3.1.3.2
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 zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
20306-++/-+/--++/-+/--+-+/------+--

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
20306-----++-+/----+/--+/----+/-+/-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
20306soil from a salt mine (38° 45' 50'' N 33° 09' 26'' E)central Anatolia region, Cihanbeyli Salt MineTurkeyTURAsia38.763933.1572
67770Cihanbeyli Salt Mine in the central Anatolia region of Turkey
67771From salternYavsanbeyli SalternTurkeyTURAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Other#Mine
#Environmental#Terrestrial#Soil
#Condition#Saline

Safety information

risk assessment

  • @ref: 20306
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 20306
  • description: Amycolatopsis cihanbeyliensis strain BNT52 16S ribosomal RNA gene, partial sequence
  • accession: JN989302
  • length: 1460
  • database: ena
  • NCBI tax ID: 1128664

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Amycolatopsis cihanbeyliensis strain DSM 456791128664.3wgspatric1128664
66792Amycolatopsis cihanbeyliensis DSM 456792806310631draftimg1128664
67770Amycolatopsis cihanbeyliensis DSM 45679GCA_006715045contigncbi1128664

GC content

@refGC-contentmethod
2030668.8fluorimetric
3105968.8
6777068.8thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno93.272yes
flagellatedno97.886no
gram-positiveyes91.294yes
anaerobicno99.349yes
aerobicyes93.118no
halophileno59.869no
spore-formingyes82.272no
thermophileno97.407yes
glucose-utilyes91.579no
glucose-fermentno93.226yes

External links

@ref: 20306

culture collection no.: DSM 45679, JCM 31029, KCTC 29065, NRRL B-24886

straininfo link

  • @ref: 88321
  • straininfo: 405290

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny23645018Amycolatopsis cihanbeyliensis sp. nov., a halotolerant actinomycete isolated from a salt mine.Tatar D, Sazak A, Guven K, Cetin D, Sahin NInt J Syst Evol Microbiol10.1099/ijs.0.050963-02013Actinomycetales/*classification/genetics/isolation & purification, Arabinose/analysis, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Galactose/analysis, *Mining, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Sodium Chloride, *Soil Microbiology, Turkey, Vitamin K 2/analogs & derivatives/analysisGenetics
Phylogeny34938275Amycolatopsis aidingensis sp. nov., a Halotolerant Actinobacterium, Produces New Secondary Metabolites.Li R, Wang M, Ren Z, Ji Y, Yin M, Zhou H, Tang SKFront Microbiol10.3389/fmicb.2021.7431162021
36445346Discovery of Efrotomycin Congeners and Heterologous Expression-Based Insights into the Self-Resistance Mechanism.Fang C, Zhang Q, Zhang W, Zhang C, Zhu YJ Nat Prod10.1021/acs.jnatprod.2c009862022

Reference

@idauthorstitledoi/urlcatalogueID_cross_referencepubmedjournal
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
20306Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-45679Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45679)
31059Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172738828776041
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa102533211880Nucleic Acids Res. 49: D498-D508 2020
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68369Automatically annotated from API 20NE
68382Automatically annotated from API zym
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
88321Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID405290.1