Strain identifier

BacDive ID: 7843

Type strain: Yes

Species: Actinoplanes xinjiangensis

Strain Designation: 03-8772

Strain history: <- YQ Zhang, IMB, CAMS & Peking Union Medical College, China [6534]

NCBI tax ID(s): 512350 (species)

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General

@ref: 15646

BacDive-ID: 7843

DSM-Number: 45184

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

description: Actinoplanes xinjiangensis 03-8772 is an aerobe, spore-forming, mesophilic bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 512350
  • Matching level: species

strain history

@refhistory
15646<- Y.-Q. Zhang; 03-8772 <- Y.-Z. Wei and et al.
67770CCM 7527 <-- W. Sun et al. 03-8772.
67771<- YQ Zhang, IMB, CAMS & Peking Union Medical College, China [6534]

doi: 10.13145/bacdive7843.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micromonosporales
  • family: Micromonosporaceae
  • genus: Actinoplanes
  • species: Actinoplanes xinjiangensis
  • full scientific name: Actinoplanes xinjiangensis Sun et al. 2009

@ref: 15646

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micromonosporaceae

genus: Actinoplanes

species: Actinoplanes xinjiangensis

full scientific name: Actinoplanes xinjiangensis Sun et al. 2009

strain designation: 03-8772

type strain: yes

Morphology

cell morphology

@refgram stainmotilityconfidence
29303positiveyes
67771positive
125438positive90.117
125439positive99.8
125439no91

multimedia

  • @ref: 15646
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_45184.jpg
  • caption: Medium 553 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
15646GPHF-MEDIUM (DSMZ Medium 553)yeshttps://mediadive.dsmz.de/medium/553Name: 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
15646GYM 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
15646TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
15646BHI MEDIUM (DSMZ Medium 215)yeshttps://mediadive.dsmz.de/medium/215Name: BHI MEDIUM (DSMZ Medium 215) Composition: Brain heart infusion 37.0 g/l Distilled water

culture temp

@refgrowthtypetemperature
15646positivegrowth28
19922positiveoptimum28
29303positivegrowth10-37
67770positivegrowth28
67771positivegrowth28

culture pH

  • @ref: 29303
  • ability: positive
  • type: growth
  • pH: 6.5-8.5
  • PH range: alkaliphile

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
29303aerobe
67771aerobe
125439obligate aerobe97.5

spore formation

@refspore formationconfidence
29303yes
125439yes91.4

halophily

  • @ref: 29303
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-7 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2930330089acetate+carbon source
2930315963ribitol+carbon source
2930322599arabinose+carbon source
2930316947citrate+carbon source
2930328757fructose+carbon source
2930324265gluconate+carbon source
293035417glucosamine+carbon source
2930317234glucose+carbon source
2930337684mannose+carbon source
2930333942ribose+carbon source
2930330911sorbitol+carbon source
2930317992sucrose+carbon source
2930318222xylose+carbon source
293034853esculin+hydrolysis
2930317632nitrate+reduction

metabolite production

  • @ref: 29303
  • Chebi-ID: 16136
  • metabolite: hydrogen sulfide
  • production: yes

enzymes

@refvalueactivityec
29303acid phosphatase+3.1.3.2
29303alkaline phosphatase+3.1.3.1
29303gelatinase+
29303urease+3.5.1.5
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase+3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase+3.2.1.21
68382alpha-glucosidase-3.2.1.20
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-chymotrypsin+3.4.21.1
68382acid phosphatase+3.1.3.2
68382trypsin-3.4.21.4
68382valine arylamidase-
68382cystine arylamidase+3.4.11.3
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
19922+++-+-+-+++----+-+-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
15646soilXinjiang Uyghur Autonomous RegionChinaCHNAsia
67770SoilXinjiang Uyghur Autonomous Region, north-west ChinaChinaCHNAsia
67771From soilXinjiang ProvinceChinaCHNAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_27073.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_94;96_240;97_16361;98_20281;99_27073&stattab=map
  • Last taxonomy: Actinoplanes
  • 16S sequence: EU531457
  • Sequence Identity:
  • Total samples: 124
  • soil counts: 67
  • aquatic counts: 11
  • animal counts: 10
  • plant counts: 36

Safety information

risk assessment

  • @ref: 15646
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 15646
  • description: Actinoplanes xinjiangensis strain 03-8772 16S ribosomal RNA gene, partial sequence
  • accession: EU531457
  • length: 1444
  • database: nuccore
  • NCBI tax ID: 512350

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Actinoplanes xinjiangensis NBRC 106528GCA_016862475contigncbi512350
66792Actinoplanes xinjiangensis strain DSM 45184512350.3wgspatric512350
66792Actinoplanes xinjiangensis strain NBRC 106528512350.4wgspatric512350
66792Actinoplanes xinjiangensis DSM 451842695420963draftimg512350
67770Actinoplanes xinjiangensis DSM 45184GCA_003148685scaffoldncbi512350

GC content

@refGC-contentmethod
1564671.0thermal denaturation, midpoint method (Tm)
2930371
6777071thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes90.117no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no94.552yes
125438spore-formingspore-formingAbility to form endo- or exosporesyes89.089yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes88.553yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno95.25no
125438motile2+flagellatedAbility to perform flagellated movementno56.833no
125439BacteriaNetspore_formationAbility to form endo- or exosporesyes91.4
125439BacteriaNetmotilityAbility to perform movementno91
125439BacteriaNetgram_stainReaction to gram-stainingpositive99.8
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe97.5

External links

@ref: 15646

culture collection no.: DSM 45184, CCM 7527, KCTC 19461, JCM 16606, NBRC 106528

straininfo link

  • @ref: 77280
  • straininfo: 406599

literature

  • topic: Phylogeny
  • Pubmed-ID: 19625414
  • title: Actinoplanes sichuanensis sp. nov. and Actinoplanes xinjiangensis sp. nov.
  • authors: Sun W, Dong GX, Zhang YQ, Wei YZ, Li QP, Yu LY, Klenk HP, Zhang YQ
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.010561-0
  • year: 2009
  • mesh: DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Micromonosporaceae/*classification/genetics/*isolation & purification, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
15646Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45184)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45184
19922Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM45184.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
29303Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2571728776041
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
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
77280Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID406599.1StrainInfo: A central database for resolving microbial strain identifiers
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1