Strain identifier

BacDive ID: 13511

Type strain: Yes

Species: Actinokineospora alba

Strain Designation: 03-9939

Strain history: <- YQ Zhang, Inst. Med. Biotechnol, China

NCBI tax ID(s): 504798 (species)

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General

@ref: 12354

BacDive-ID: 13511

DSM-Number: 45114

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

description: Actinokineospora alba 03-9939 is an aerobe, spore-forming, mesophilic bacterium that was isolated from soil sample.

NCBI tax id

  • NCBI tax id: 504798
  • Matching level: species

strain history

@refhistory
12354<- Y.-Q. Zhang, Chinese Acad. Med. Sciences & Peking Union Medical College; 03-9939 <- Y.-Z. Wei et al.
67770CCM 7461 <-- Y.-Q. Zhang 03-9939.
67771<- YQ Zhang, Inst. Med. Biotechnol, China

doi: 10.13145/bacdive13511.20230509.8.1

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 alba
  • full scientific name: Actinokineospora alba (Yuan et al. 2010) Nouioui et al. 2018

  • synonyms

    • @ref: 20215
    • synonym: Alloactinosynnema album

@ref: 12354

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Pseudonocardiaceae

genus: Actinokineospora

species: Actinokineospora alba

full scientific name: Actinokineospora alba (Yuan et al. 2010) Nouioui et al. 2018

strain designation: 03-9939

type strain: yes

Morphology

cell morphology

@refgram stain
29314positive
67771positive

colony morphology

@refcolony colorincubation periodmedium used
20165Sand yellow (1002)10-14 daysISP 2
20165Ivory (1014)10-14 daysISP 3
20165Beige (1001)10-14 daysISP 4
20165Green beige (1000)10-14 daysISP 5
20165Sand yellow (1002)10-14 daysISP 6
20165Beige (1001)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
20165noISP 2
20165noISP 3
20165noISP 4
20165noISP 5
20165noISP 6
20165noISP 7

pigmentation

  • @ref: 29314
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12354GYM 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
20165ISP 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
20165ISP 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:
20165ISP 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
20165ISP 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
20165ISP 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
20165ISP 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
12354positivegrowth28mesophilic
20165positiveoptimum28mesophilic
29314positivegrowth20-37
29314positiveoptimum30mesophilic
67770positivegrowth28mesophilic
67771positivegrowth28mesophilic

culture pH

@refabilitytypepH
29314positivegrowth06-08
29314positiveoptimum7.25

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
29314aerobe
67771aerobe

spore formation

  • @ref: 29314
  • spore formation: yes

halophily

  • @ref: 29314
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-3 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2016517234glucose-
2016522599arabinose-
2016517992sucrose+
2016518222xylose-
2016517268myo-inositol-
2016529864mannitol+
2016528757fructose+
2016526546rhamnose-
2016516634raffinose-
2016562968cellulose-
2931416947citrate+carbon source
293145417glucosamine+carbon source
2931415792malonate+carbon source
2931437684mannose+carbon source
2931428053melibiose+carbon source
2931428044phenylalanine+carbon source
2931426546rhamnose+carbon source
2931433942ribose+carbon source
2931430911sorbitol+carbon source
2931417992sucrose+carbon source
2931427082trehalose+carbon source
2931418222xylose+carbon source
293144853esculin+hydrolysis
2931417632nitrate+reduction

enzymes

@refvalueactivityec
29314acid phosphatase+3.1.3.2
29314alkaline phosphatase+3.1.3.1
29314alpha-galactosidase+3.2.1.22
29314gelatinase+
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
20165+++++++++++-++++++-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
12354soil sampleXinjiang ProvinceChinaCHNAsia
67770SoilXinjiang ProvinceChinaCHNAsia
67771From forest soilXinjiang ProvinceChinaCHNAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_943.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_394;97_640;98_739;99_943&stattab=map
  • Last taxonomy: Actinokineospora
  • 16S sequence: EU438907
  • Sequence Identity:
  • Total samples: 519
  • soil counts: 228
  • aquatic counts: 14
  • animal counts: 14
  • plant counts: 263

Safety information

risk assessment

  • @ref: 12354
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 12354
  • description: Alloactinosynnema album strain 03-9939 16S ribosomal RNA gene, partial sequence
  • accession: EU438907
  • length: 1442
  • database: ena
  • NCBI tax ID: 504798

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Alloactinosynnema album strain DSM 45114504798.7wgspatric504798
66792Actinokineospora alba DSM 451142775506708draftimg504798
67770Actinokineospora alba CPCC 201030GCA_900099755scaffoldncbi504798
67770Actinokineospora alba DSM 45114GCA_004362515contigncbi504798

GC content

@refGC-contentmethod
1235468.2thermal denaturation, midpoint method (Tm)
2931468.2
6777069.7genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
gram-positiveyes87.548yes
anaerobicno99.002yes
halophileno89.04no
spore-formingyes91.382no
glucose-utilyes89.388no
aerobicyes92.674yes
thermophileno96.304yes
motileno93.386no
flagellatedno97.126no
glucose-fermentno93.567no

External links

@ref: 12354

culture collection no.: DSM 45114, CCM 7461, KCTC 19294, JCM 17965, NBRC 106985

straininfo link

  • @ref: 82703
  • straininfo: 404688

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19648319Alloactinosynnema album gen. nov., sp. nov., a member of the family Actinosynnemataceae isolated from soil.Yuan LJ, Zhang YQ, Yu LY, Liu HY, Guan Y, Lee JC, Kim CJ, Zhang YQInt J Syst Evol Microbiol10.1099/ijs.0.010744-02009Actinomycetales/*classification/genetics/*isolation & purification/metabolism, Base Composition, China, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil MicrobiologyMetabolism
Phylogeny24408526Alloactinosynnema iranicum sp. nov., a rare actinomycete isolated from a hypersaline wetland, and emended description of the genus Alloactinosynnema.Nikou MM, Ramezani M, Amoozegar MA, Fazeli SAS, Schumann P, Sproer C, Sanchez-Porro C, Ventosa AInt J Syst Evol Microbiol10.1099/ijs.0.049189-02014Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Iran, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Salinity, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry, *WetlandsGenetics
Phylogeny33674994Actinokineospora xionganensis sp. nov., a filamentous actinomycete isolated from the lakeside soil of Baiyangdian.Wang Y, Shi J, Liu T, Zhang Y, Zhang L, Zhang XAntonie Van Leeuwenhoek10.1007/s10482-021-01532-82021*Actinobacteria/genetics, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil, Soil MicrobiologyTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
12354Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45114)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45114
20165Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM45114.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
29314Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2572728776041
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 updates33211880Nucleic 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
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
82703Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID404688.1StrainInfo: A central database for resolving microbial strain identifiers