Strain identifier

BacDive ID: 13206

Type strain: Yes

Species: Actinokineospora auranticolor

Strain Designation: YU 961-1

Strain history: CIP <- 2003, NBRC <- M. Hayakawa, Yamanashi Univ., Kofu, Japan: strain YU 961-1

NCBI tax ID(s): 155976 (species)

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General

@ref: 11959

BacDive-ID: 13206

DSM-Number: 44650

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

description: Actinokineospora auranticolor YU 961-1 is an obligate aerobe, mesophilic, Gram-positive bacterium that was isolated from fallen leaves in a level-land forest.

NCBI tax id

  • NCBI tax id: 155976
  • Matching level: species

strain history

@refhistory
11959<- M. Otoguro; YU 961-1
67770IFO 16518 <-- M. Hayakawa YU 961-1.
116565CIP <- 2003, NBRC <- M. Hayakawa, Yamanashi Univ., Kofu, Japan: strain YU 961-1

doi: 10.13145/bacdive13206.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Pseudonocardiales
  • family: Pseudonocardiaceae
  • genus: Actinokineospora
  • species: Actinokineospora auranticolor
  • full scientific name: Actinokineospora auranticolor Otoguro et al. 2003

@ref: 11959

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Pseudonocardiaceae

genus: Actinokineospora

species: Actinokineospora auranticolor

full scientific name: Actinokineospora auranticolor Otoguro et al. 2003

strain designation: YU 961-1

type strain: yes

Morphology

cell morphology

  • @ref: 116565
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 116565

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11959GYM 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
36662MEDIUM 116 - for Streptomyces, Nocardia, Streptosporangium and Mycobacterium chlorophenolicumyesDistilled water make up to (1000.000 ml);Agar (20.000 g);Glucose (4.000g);Yeast extract (4.000 g);Malt extract (10.000 g)
116565CIP Medium 146yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=146
116565CIP Medium 116yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=116

culture temp

@refgrowthtypetemperaturerange
11959positivegrowth28mesophilic
36662positivegrowth30mesophilic
67770positivegrowth28mesophilic
116565positivegrowth10-37
116565nogrowth41thermophilic
116565nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 116565
  • oxygen tolerance: obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
116565NaClpositivegrowth0-2 %
116565NaClnogrowth4 %
116565NaClnogrowth6 %
116565NaClnogrowth8 %
116565NaClnogrowth10 %

observation

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

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371sucrose-builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose-builds acid from17306
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371esculin-builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose-builds acid from16024
68371D-fructose-builds acid from15824
68371D-glucose-builds acid from17634
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose-builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
68369malate-assimilation25115
68369adipate-assimilation17128
68369decanoate-assimilation27689
68369maltose-assimilation17306
68369N-acetylglucosamine-assimilation59640
68369D-mannitol-assimilation16899
68369D-mannose-assimilation16024
68369L-arabinose-assimilation30849
68369D-glucose-assimilation17634
68369gelatin+hydrolysis5291
68369esculin-hydrolysis4853
68369urea-hydrolysis16199
68369arginine-hydrolysis29016
68369D-glucose-fermentation17634
68369tryptophan-energy source27897
68369nitrate-reduction17632
116565citrate-carbon source16947
116565esculin-hydrolysis4853
116565hippurate+hydrolysis606565
116565nitrate-reduction17632
116565nitrite-reduction16301

antibiotic resistance

  • @ref: 116565
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
11656535581indoleno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-testmethylred-test
6836935581indole-
11656515688acetoin-
11656517234glucose-

enzymes

@refvalueactivityec
68369gelatinase+
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
116565oxidase-
116565beta-galactosidase+3.2.1.23
116565alcohol dehydrogenase-1.1.1.1
116565gelatinase+/-
116565amylase-
116565DNase-
116565caseinase-3.4.21.50
116565catalase+1.11.1.6
116565tween esterase+
116565gamma-glutamyltransferase+2.3.2.2
116565lecithinase-
116565lipase-
116565lysine decarboxylase-4.1.1.18
116565ornithine decarboxylase-4.1.1.17
116565phenylalanine ammonia-lyase-4.3.1.24
116565protease-
116565tryptophan deaminase-
116565urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
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
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
11959-++/-+/--+----+/-+/----+-+--
116565-+++-+----++---+-+--

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
11959------+-------+/------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
116565-------------------------------------------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
116565+--+-------------------------------------------------------++-+---------------+++--------++-------+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
11959fallen leaves in a level-land forestYamanashiJapanJPNAsia
67770Fallen leaves in a level-land forestJapanJPNAsia
116565Environment, Fallen leaves in level-land forestJapanJPNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Forest
#Host Body-Site#Plant#Leaf (Phyllosphere)

taxonmaps

  • @ref: 69479
  • File name: preview.99_121873.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_394;97_444;98_80846;99_121873&stattab=map
  • Last taxonomy: Actinokineospora auranticolor
  • 16S sequence: AB058396
  • Sequence Identity:
  • Total samples: 30
  • soil counts: 5
  • aquatic counts: 2
  • animal counts: 5
  • plant counts: 18

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
119591Risk group (German classification)
1165651Risk group (French classification)

Sequence information

16S sequences

  • @ref: 11959
  • description: Actinokineospora auranticolor gene for 16S rRNA, partial sequence
  • accession: AB058396
  • length: 1474
  • database: ena
  • NCBI tax ID: 155976

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Actinokineospora auranticolor DSM 446502731957505draftimg155976
67770Actinokineospora auranticolor YU 961-1GCA_002934265contigncbi155976

GC content

@refGC-contentmethod
1195971.3
6777071.3high performance liquid chromatography (HPLC)

External links

@ref: 11959

culture collection no.: DSM 44650, IFO 16518, NBRC 16518, JCM 11646, CIP 107896

straininfo link

  • @ref: 82414
  • straininfo: 88107

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny28820111Description of Actinokineospora acnipugnans sp. nov., an actinomycete isolated from soil, showing potential uses in cosmetics.Dahal RH, Shim DS, Kim JInt J Syst Evol Microbiol10.1099/ijsem.0.0020782017Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, Cosmetics, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, *Grassland, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny32618556Actinokineospora pegani sp. nov., an endophytic actinomycete isolated from the surface-sterilized root of Peganum harmala L.Lei YJ, Xia ZF, Luo XX, Zhang LLInt J Syst Evol Microbiol10.1099/ijsem.0.0042992020Actinobacteria/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Peganum/*microbiology, Phospholipids/chemistry, *Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11959Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44650)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44650
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
36662Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5457
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/
68369Automatically annotated from API 20NE
68371Automatically annotated from API 50CH acid
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
82414Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID88107.1StrainInfo: A central database for resolving microbial strain identifiers
116565Curators of the CIPCollection of Institut Pasteur (CIP 107896)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107896