Strain identifier

BacDive ID: 13402

Type strain: Yes

Species: Pseudonocardia parietis

Strain Designation: 04-St-002

Strain history: CCM 7582 <-- P. Kämpfer 04-St-002.

NCBI tax ID(s): 570936 (species)

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General

@ref: 15898

BacDive-ID: 13402

DSM-Number: 45256

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

description: Pseudonocardia parietis 04-St-002 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from wall of a house colonized with moulds.

NCBI tax id

  • NCBI tax id: 570936
  • Matching level: species

strain history

@refhistory
15898<- P. Kämpfer; 04-St-002 <- T. Gabrio
67770CCM 7582 <-- P. Kämpfer 04-St-002.

doi: 10.13145/bacdive13402.20230509.8.1

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 parietis
  • full scientific name: Pseudonocardia parietis Schäfer et al. 2009

@ref: 15898

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Pseudonocardiaceae

genus: Pseudonocardia

species: Pseudonocardia parietis

full scientific name: Pseudonocardia parietis Schäfer et al. 2009

strain designation: 04-St-002

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
29272positiverod-shaped
69480no91.257
69480positive100

colony morphology

  • @ref: 61142
  • incubation period: 3-4 days

multimedia

  • @ref: 15898
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_45256.jpg
  • caption: Medium 65 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

  • @ref: 15898
  • name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/65
  • composition: Name: 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

culture temp

@refgrowthtypetemperaturerange
15898positivegrowth28mesophilic
29272positivegrowth25-30
29272positiveoptimum28
61142positivegrowth30
67770positivegrowth28mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 61142
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
29272no
69481yes100

halophily

  • @ref: 29272
  • salt: NaCl
  • growth: positive
  • tested relation: optimum
  • concentration: 0.90 %

observation

  • @ref: 67770
  • observation: quinones: MK-8(H4), MK-8(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2927228757fructose+carbon source
2927228260galactose+carbon source
2927217306maltose+carbon source
2927229864mannitol+carbon source
2927237684mannose+carbon source
29272506227N-acetylglucosamine+carbon source
2927230911sorbitol+carbon source
2927217992sucrose+carbon source
2927227082trehalose+carbon source
2927253426tween 80+carbon source

enzymes

@refvalueactivityec
29272catalase+1.11.1.6
29272cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
15898wall of a house colonized with mouldsStuttgartGermanyDEUEurope
611422000
67770Wall of an indoor environment colonized with mouldsStuttgartGermanyDEUEurope

isolation source categories

Cat1Cat2Cat3
#Engineered#Built environment#House
#Host#Fungi

taxonmaps

  • @ref: 69479
  • File name: preview.99_71198.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_175;97_189;98_49921;99_71198&stattab=map
  • Last taxonomy: Pseudonocardia
  • 16S sequence: FM863703
  • Sequence Identity:
  • Total samples: 876
  • soil counts: 65
  • aquatic counts: 42
  • animal counts: 129
  • plant counts: 640

Safety information

risk assessment

  • @ref: 15898
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 15898
  • description: Pseudonocardia parietis partial 16S rRNA gene, type strain 04-St-002T
  • accession: FM863703
  • length: 1407
  • database: ena
  • NCBI tax ID: 570936

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudonocardia parietis DSM 45256GCA_017876315contigncbi570936
66792Pseudonocardia parietis strain DSM 45256570936.3wgspatric570936
66792Pseudonocardia parietis DSM 452562918313847draftimg570936

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
gram-positiveyes90.253yes
anaerobicno99.134no
halophileno79.124no
spore-formingyes67.976yes
glucose-utilyes89.001no
thermophileno99.246yes
flagellatedno98.249no
aerobicyes91.063no
motileno92.341no
glucose-fermentno91.91no

External links

@ref: 15898

culture collection no.: DSM 45256, CCM 7582, CCUG 56962, JCM 16609

straininfo link

@refstraininfo
82599400011
82600409550

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19622655Pseudonocardia parietis sp. nov., from the indoor environment.Schafer J, Busse HJ, Kampfer PInt J Syst Evol Microbiol10.1099/ijs.0.009993-02009Actinomycetales/classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, *Environmental Microbiology, Fatty Acids/chemistry/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/geneticsMetabolism
Phylogeny22805759Pseudonocardia antimicrobica sp. nov., a novel endophytic actinomycete associated with Artemisia annua L. (sweet wormwood).Zhao GZ, Li J, Qin YL, Miao CP, Wei DQ, Zhang S, Xu LH, Li WJJ Antibiot (Tokyo)10.1038/ja.2012.562012Actinomycetales/genetics/*isolation & purification/ultrastructure, Artemisia annua/*microbiology, Base Composition/genetics, Base Sequence, DNA, Fungal/chemistry/genetics, Microscopy, Electron, Scanning, Molecular Sequence Data, Phenotype, Phylogeny, Polymerase Chain Reaction, RNA, Ribosomal, 16S/chemistry/genetics, Sequence Alignment, Spores, Fungal/genetics/ultrastructureGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
15898Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45256)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45256
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
29272Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2568928776041
61142Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 56962)https://www.ccug.se/strain?id=56962
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/
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
82599Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID400011.1StrainInfo: A central database for resolving microbial strain identifiers
82600Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID409550.1StrainInfo: A central database for resolving microbial strain identifiers