Strain identifier

BacDive ID: 13202

Type strain: Yes

Species: Actinokineospora inagensis

Strain history: IFO 15663 <-- T. Tamura YU4-1 <-- M. Hayakawa.

NCBI tax ID(s): 1120935 (strain), 103730 (species)

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General

@ref: 11630

BacDive-ID: 13202

DSM-Number: 44258

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

description: Actinokineospora inagensis DSM 44258 is an aerobe, spore-forming, mesophilic bacterium that was isolated from fallen leaves of a lakeside.

NCBI tax id

NCBI tax idMatching level
1120935strain
103730species

strain history

@refhistory
11630<- IFO <- T. Tamura, YU 4-1
67771<- IFO <- T. Tamura YU4-1 <- M.Hayakawa
67770IFO 15663 <-- T. Tamura YU4-1 <-- M. Hayakawa.

doi: 10.13145/bacdive13202.20230509.8.1

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

@ref: 11630

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Pseudonocardiaceae

genus: Actinokineospora

species: Actinokineospora inagensis

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

type strain: yes

Morphology

cell morphology

@refgram stainconfidence
67771positive
69480positive100

colony morphology

@refcolony colorincubation periodmedium used
19641Sand yellow10-14 daysISP 2
1964110-14 daysISP 3
19641Sand yellow10-14 daysISP 4
19641Sand yellow10-14 daysISP 5
19641Sand yellow10-14 daysISP 6
19641Sand yellow10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
19641noISP 2
19641noISP 3
19641noISP 4
19641noISP 5
19641noISP 6
19641noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11630GYM 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
19641ISP 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
19641ISP 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:
19641ISP 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
19641ISP 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
19641ISP 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
19641ISP 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

@refgrowthtypetemperaturerange
11630positivegrowth28mesophilic
67770positivegrowth28mesophilic
67771positivegrowth28mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 67771
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481yes100
69480yes100

halophily

  • @ref: 19641
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 10 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1964117234glucose+
1964122599arabinose-
1964117992sucrose-
1964118222xylose-
1964117268myo-inositol-
1964129864mannitol-
1964128757fructose-
1964126546rhamnose-
1964116634raffinose-
1964162968cellulose-
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate+assimilation
6836818257ornithine+degradation
6836825094lysine+degradation
6836829016arginine+hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin+
6836835581indole-

enzymes

@refvalueactivityec
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 (C 4)-
68382esterase lipase (C 8)+
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
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
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

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
19641+-+-+-++-++---+----

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19641-++++-+--++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
11630fallen leaves of a lakesideYamanashi PrefectureJapanJPNAsia
67770Fallen leaves on the shore of a lakeYamanashi Pref.JapanJPNAsia
67771Fallen leaves on the shore of a lakeYamanashi Pref.JapanJPNAsia

isolation source categories

  • Cat1: #Host Body-Site
  • Cat2: #Plant
  • Cat3: #Leaf (Phyllosphere)

taxonmaps

  • @ref: 69479
  • File name: preview.99_3774.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_394;97_2332;98_2877;99_3774&stattab=map
  • Last taxonomy: Actinokineospora inagensis subclade
  • 16S sequence: AF114799
  • Sequence Identity:
  • Total samples: 176
  • soil counts: 94
  • aquatic counts: 11
  • animal counts: 30
  • plant counts: 41

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
116301Risk group (German classification)
196411Risk group (German classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Actinokineospora inagensis strain NRRL B-24050T 16S ribosomal RNA gene, partial sequence
  • accession: AF114799
  • length: 1507
  • database: ena
  • NCBI tax ID: 103730

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Actinokineospora inagensis DSM 442581120935.3wgspatric1120935
66792Actinokineospora inagensis DSM 442582528768220draftimg1120935
67770Actinokineospora inagensis DSM 44258GCA_000482865scaffoldncbi1120935

GC content

@refGC-contentmethod
1163069.1
6777169.1high performance liquid chromatography (HPLC)
6777070.2genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno62.192no
flagellatedno90.932no
gram-positiveyes89.3no
anaerobicno98.708no
aerobicyes90.925no
halophileno95.193no
spore-formingyes90.945no
thermophileno97.143yes
glucose-utilyes86.619yes
glucose-fermentno92.427no

External links

@ref: 11630

culture collection no.: DSM 44258, IFO 15663, JCM 9923, KCTC 9571, MTCC 2685, NBRC 15663, NCIMB 13659, NRRL B-24050, VKM Ac-1982

straininfo link

  • @ref: 82410
  • straininfo: 50540

literature

  • topic: Phylogeny
  • Pubmed-ID: 25378048
  • title: Actinokineospora mzabensis sp. nov., a novel actinomycete isolated from Saharan soil.
  • authors: Aouiche A, Bouras N, Mokrane S, Zitouni A, Schumann P, Sproer C, Sabaou N, Klenk HP
  • journal: Antonie Van Leeuwenhoek
  • DOI: 10.1007/s10482-014-0328-8
  • year: 2014
  • mesh: Actinobacteria/*classification/genetics/*isolation & purification/physiology, Africa, Northern, Algeria, Bacterial Typing Techniques, Carbohydrates/analysis, Cell Wall/chemistry, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Hydrogen-Ion Concentration, Molecular Sequence Data, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Temperature, Vitamin K 2/analysis
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11630Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44258)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44258
19641Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44258.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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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
82410Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID50540.1StrainInfo: A central database for resolving microbial strain identifiers