Strain identifier

BacDive ID: 13403

Type strain: Yes

Species: Pseudonocardia babensis

Strain Designation: VN05A0561

Strain history: CIP <- 2010, NBRC <- VTCC and NITE: strain VN05A0561

NCBI tax ID(s): 663386 (species)

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General

@ref: 17666

BacDive-ID: 13403

DSM-Number: 45574

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

description: Pseudonocardia babensis VN05A0561 is an aerobe, spore-forming, mesophilic bacterium that was isolated from plant litter.

NCBI tax id

  • NCBI tax id: 663386
  • Matching level: species

strain history

@refhistory
17666<- NBRC <- D. V. Hop(VTCC) and K. Ando(NITE); VN05A0561
116695CIP <- 2010, NBRC <- VTCC and NITE: strain VN05A0561

doi: 10.13145/bacdive13403.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Pseudonocardiales
  • family: Pseudonocardiaceae
  • genus: Pseudonocardia
  • species: Pseudonocardia babensis
  • full scientific name: Pseudonocardia babensis Sakiyama et al. 2010

@ref: 17666

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Pseudonocardiaceae

genus: Pseudonocardia

species: Pseudonocardia babensis

full scientific name: Pseudonocardia babensis Sakiyama et al. 2010

strain designation: VN05A0561

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
29660positive01-02 µm0.3-0.5 µmrod-shapedno
116695positiverod-shapedno

pigmentation

  • @ref: 29660
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
17666GYM 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
40334MEDIUM 57 - for Streptomyces, Nocardioides, Lentzea albidocapillata and Streptoverticillium reticulumyesDistilled water make up to (1000.000 ml);Agar (15.000 g);Glucose (4.000g);Yeast extract (4.000 g);Malt extract (10.000 g);Calcium carbonate (2.000 g)
116695CIP Medium 57yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=57

culture temp

@refgrowthtypetemperaturerange
17666positivegrowth28mesophilic
29660positivegrowth10-45
29660positiveoptimum28mesophilic
40334positivegrowth30mesophilic

culture pH

@refabilitytypepH
29660positivegrowth7
29660positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 29660
  • oxygen tolerance: aerobe

spore formation

  • @ref: 29660
  • spore formation: yes

halophily

@refsaltgrowthtested relationconcentration
29660NaClpositivegrowth0-3 %
29660NaClpositiveoptimum0-3 %

observation

  • @ref: 29660
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2966022599arabinose+carbon source
2966018403L-arabitol+carbon source
2966017057cellobiose+carbon source
2966028757fructose+carbon source
2966028260galactose+carbon source
2966017234glucose+carbon source
2966017716lactose+carbon source
2966017306maltose+carbon source
2966029864mannitol+carbon source
2966028053melibiose+carbon source
2966016634raffinose+carbon source
2966026546rhamnose+carbon source
2966017814salicin+carbon source
2966030911sorbitol+carbon source
2966017992sucrose+carbon source
2966027082trehalose+carbon source
2966017151xylitol+carbon source
2966018222xylose+carbon source
296604853esculin+hydrolysis
11669517632nitrate-reduction
11669516301nitrite-reduction

metabolite production

  • @ref: 116695
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
116695oxidase-
116695catalase-1.11.1.6
116695urease-3.5.1.5
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

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
116695--+--+--------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
17666plant litterBa BE National Park, Back KanVietnamVNMAsia
116695Plant, LitterBa be National Park, Back KanVietnamVNMAsia

isolation source categories

Cat1Cat2Cat3
#Host#Plants
#Host Body Product#Plant#Plant litter (Forest)
#Host Body Product#Plant#Plant litter (Forest)

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
176661Risk group (German classification)
1166952Risk group (French classification)

Sequence information

16S sequences

  • @ref: 17666
  • description: Pseudonocardia babensis gene for 16S rRNA, partial sequence
  • accession: AB514449
  • length: 1454
  • database: ena
  • NCBI tax ID: 663386

GC content

  • @ref: 17666
  • GC-content: 73

External links

@ref: 17666

culture collection no.: DSM 45574, CIP 110219, NBRC 105793, VTCC A-1757

straininfo link

  • @ref: 82601
  • straininfo: 371021

literature

  • topic: Phylogeny
  • Pubmed-ID: 19933589
  • title: Pseudonocardia babensis sp. nov., isolated from plant litter.
  • authors: Sakiyama Y, Thao NKN, Vinh HV, Giang NM, Miyadoh S, Hop DV, Ando K
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.018127-0
  • year: 2009
  • mesh: Actinomycetales/*classification/cytology/genetics/*isolation & purification, Arabinose/analysis, Bacterial Typing Techniques, Cell Wall/chemistry, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Galactose/analysis, Microscopy, Electron, Scanning, Molecular Sequence Data, Phospholipids/analysis, Phylogeny, Plants/*microbiology, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Spores, Bacterial/cytology, Vietnam
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
17666Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45574)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45574
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
29660Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2604828776041
40334Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/8054
68382Automatically annotated from API zym
82601Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID371021.1StrainInfo: A central database for resolving microbial strain identifiers
116695Curators of the CIPCollection of Institut Pasteur (CIP 110219)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110219