Strain identifier

BacDive ID: 13204

Type strain: Yes

Species: Actinokineospora terrae

Strain history: IFO 15668 <-- T. Tamura YU6-3 <-- M. Hayakawa.

NCBI tax ID(s): 155974 (species)

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General

@ref: 11632

BacDive-ID: 13204

DSM-Number: 44260

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

description: Actinokineospora terrae DSM 44260 is an aerobe, spore-forming, Gram-positive bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 155974
  • Matching level: species

strain history

@refhistory
11632<- IFO <- T. Tamura, YU 6-3
67771<- IFO <- T. Tamura YU6-3 <- M. Hayakawa
67770IFO 15668 <-- T. Tamura YU6-3 <-- M. Hayakawa.

doi: 10.13145/bacdive13204.20240916.9.1

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 terrae
  • full scientific name: Actinokineospora terrae Tamura et al. 1995

@ref: 11632

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Pseudonocardiaceae

genus: Actinokineospora

species: Actinokineospora terrae

full scientific name: Actinokineospora terrae Tamura et al. 1995 emend. Nouioui et al. 2018

type strain: yes

Morphology

cell morphology

  • @ref: 67771
  • gram stain: positive

colony morphology

@refcolony colorincubation periodmedium used
19857Golden yellow10-14 daysISP 2
19857Ivory10-14 daysISP 3
19857Maize yellow10-14 daysISP 4
19857Signal yellow10-14 daysISP 5
19857Signal yellow10-14 daysISP 6
19857Light ivory10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
19857noISP 2
19857noISP 3
19857noISP 4
19857noISP 5
19857noISP 6
19857noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11632GYM 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
19857ISP 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
19857ISP 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:
19857ISP 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
19857ISP 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
19857ISP 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
19857ISP 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

@refgrowthtypetemperature
11632positivegrowth28
67770positivegrowth28
67771positivegrowth28

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
67771aerobe
69480aerobe91.009

halophily

  • @ref: 19857
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 2.5 %

observation

@refobservation
67770quinones: MK-9(H4)
67771quinones: MK-9(H_4_)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1985717234glucose+
1985722599arabinose-
1985717992sucrose+
1985718222xylose-
1985717268myo-inositol-
1985729864mannitol-
1985728757fructose+
1985726546rhamnose-
1985716634raffinose-
1985762968cellulose-
6836925115malate-assimilation
6836927689decanoate-assimilation
6836924265gluconate+assimilation
6836917306maltose-assimilation
6836916899D-mannitol-assimilation
6836917634D-glucose+assimilation
683695291gelatin+hydrolysis
683694853esculin+hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate+assimilation
6836818257ornithine+degradation
6836825094lysine+degradation
6836829016arginine+hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-test
6836935581indole-
6836815688acetoin-
6836835581indole-

enzymes

@refvalueactivityec
68369gelatinase+
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
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 lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382acid phosphatase+3.1.3.2
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControlbeta- Glucuronidase
19857+-+-+++++++---+---
11632+++-++/--+/--+---+------

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19857-++++-+----

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
11632-----+++++/-+/--+/--+-+/--+/--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
11632soilYamanashi PrefectureJapanJPNAsia
67770Soil around a pondYamanashi Pref.JapanJPNAsia
67771From soil around a pondYamanashi Pref.JapanJPNAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_119928.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_394;97_444;98_80846;99_119928&stattab=map
  • Last taxonomy: Actinokineospora
  • 16S sequence: AB058394
  • Sequence Identity:
  • Total samples: 113
  • soil counts: 62
  • aquatic counts: 7
  • animal counts: 12
  • plant counts: 32

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
116321Risk group (German classification)
198571Risk group (German classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Actinokineospora terrae gene for 16S rRNA, partial sequence
  • accession: AB058394
  • length: 1471
  • database: nuccore
  • NCBI tax ID: 155974

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Actinokineospora terrae strain DSM 44260155974.4wgspatric155974
66792Actinokineospora terrae DSM 442602616644847draftimg155974
67770Actinokineospora terrae DSM 44260GCA_900111175scaffoldncbi155974

GC content

@refGC-contentmethod
1163270.0
6777170.0high performance liquid chromatography (HPLC)
6777071genome sequence analysis
6777070high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69480gram-positivegram-positivePositive reaction to Gram-stainingyes85.657yes
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no95.697yes
69480spore-formingspore-formingAbility to form endo- or exosporesyes84.53no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes91.009no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno97.5yes
69480flagellatedmotile2+Ability to perform flagellated movementno58.333no

External links

@ref: 11632

culture collection no.: DSM 44260, IFO 15668, JCM 9924, KCTC 9572, MTCC 2688, NBRC 15668, IMSNU 22094, NCIMB 13660, NRRL B-24049, VKM Ac-1983

straininfo link

  • @ref: 82412
  • straininfo: 50541

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19933586Actinokineospora baliensis sp. nov., Actinokineospora cibodasensis sp. nov. and Actinokineospora cianjurensis sp. nov., isolated from soil and plant litter.Lisdiyanti P, Otoguro M, Ratnakomala S, Lestari Y, Hastuti RD, Triana E, Katsuhiko A, Widyastuti YInt J Syst Evol Microbiol10.1099/ijs.0.013276-02009Actinomycetales/chemistry/*classification/genetics/*isolation & purification, Carbohydrates/analysis, Cell Wall/chemistry, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Indonesia, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/analysis, Phospholipids/analysis, Phylogeny, Plants/*microbiology, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil MicrobiologyGenetics
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

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11632Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44260)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44260
19857Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44260.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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
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/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68368Automatically annotated from API 20E
68369Automatically annotated from API 20NE
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)
82412Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID50541.1StrainInfo: A central database for resolving microbial strain identifiers