Strain identifier

BacDive ID: 13391

Type strain: Yes

Species: Pseudonocardia spinosispora

Strain Designation: LM 141

Strain history: CIP <- 2003, KCTC <- SD Lee, Seoul Natl Univ

NCBI tax ID(s): 1123025 (strain), 103441 (species)

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General

@ref: 11984

BacDive-ID: 13391

DSM-Number: 44797

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

description: Pseudonocardia spinosispora LM 141 is an aerobe, spore-forming, mesophilic bacterium that was isolated from soil from gold mine cave.

NCBI tax id

NCBI tax idMatching level
1123025strain
103441species

strain history

@refhistory
11984<- KCTC <- S. D. Lee; LM 141
331912003, KCTC
67770IMSNU 50581 <-- S. D. Lee LM 141.
67771<- SD Lee, Seoul Natl Univ
123262CIP <- 2003, KCTC <- SD Lee, Seoul Natl Univ

doi: 10.13145/bacdive13391.20230509.8.1

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 spinosispora
  • full scientific name: Pseudonocardia spinosispora Lee et al. 2002

@ref: 11984

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Pseudonocardiaceae

genus: Pseudonocardia

species: Pseudonocardia spinosispora

full scientific name: Pseudonocardia spinosispora Lee et al. 2002

strain designation: LM 141

type strain: yes

Morphology

cell morphology

@refgram stainmotilityconfidencecell shape
67771positive
69480no92.156
69480positive100
123262positivenorod-shaped

colony morphology

  • @ref: 123262

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11984GPHF-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
33191MEDIUM 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)
123262CIP Medium 57yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=57

culture temp

@refgrowthtypetemperaturerange
11984positivegrowth28mesophilic
33191positivegrowth30mesophilic
67770positivegrowth28mesophilic
67771positivegrowth30mesophilic
123262positivegrowth25-30mesophilic
123262nogrowth10psychrophilic
123262nogrowth41thermophilic
123262nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
67771aerobe
123262obligate aerobe

spore formation

@refspore formationconfidence
69481yes100
69480yes98.605

halophily

@refsaltgrowthtested relationconcentration
123262NaClpositivegrowth0-6 %
123262NaClnogrowth8 %
123262NaClnogrowth10 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12326216947citrate-carbon source
1232624853esculin-hydrolysis
123262606565hippurate-hydrolysis
12326217632nitrate+reduction
12326216301nitrite-reduction
123262132112sodium thiosulfate-builds gas from
12326217632nitrate-respiration

antibiotic resistance

  • @ref: 123262
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 123262
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12326215688acetoin-
12326217234glucose-

enzymes

@refvalueactivityec
123262oxidase+
123262alcohol dehydrogenase+1.1.1.1
123262gelatinase-
123262amylase-
123262DNase-
123262caseinase-3.4.21.50
123262catalase+1.11.1.6
123262tween esterase-
123262gamma-glutamyltransferase-2.3.2.2
123262lecithinase-
123262lipase-
123262lysine decarboxylase-4.1.1.18
123262ornithine decarboxylase-4.1.1.17
123262phenylalanine ammonia-lyase-4.3.1.24
123262tryptophan deaminase-
123262urease+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
123262--+--++---++--------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
123262-++-++--------------+-----+-----++--++----------++-----------+++--+--------+--+++++----++++++-++-++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
11984soil from gold mine caveKorea, Kongju CityRepublic of KoreaKORAsia
67770Soil at a gold mine cavenear Kongju CityRepublic of KoreaKORAsia
67771From soilRepublic of KoreaKORAsia
123262Environment, SoilKongjuRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Other#Mine
#Environmental#Terrestrial#Soil

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
119841Risk group (German classification)
1232622Risk group (French classification)

Sequence information

16S sequences

  • @ref: 11984
  • description: Pseudonocardia spinospora partial 16S rRNA gene, isolate LM 141T
  • accession: AJ249206
  • length: 1512
  • database: ena
  • NCBI tax ID: 103441

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudonocardia spinosispora DSM 447971123025.3wgspatric1123025
66792Pseudonocardia spinosispora DSM 447972524614769draftimg1123025
67770Pseudonocardia spinosispora DSM 44797GCA_000429025scaffoldncbi1123025

GC content

  • @ref: 11984
  • GC-content: 70.4

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno93.592no
flagellatedno98.181no
gram-positiveyes89.053no
anaerobicno99.261yes
halophileno88.275no
spore-formingyes76.945no
glucose-utilyes88.253no
aerobicyes94.577yes
thermophileno98.249no
glucose-fermentno91.935no

External links

@ref: 11984

culture collection no.: DSM 44797, IMSNU 50581, JCM 11935, KCTC 9991, NRRL B-24156, BCRC 16382, CIP 108013

straininfo link

  • @ref: 82588
  • straininfo: 100892

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12361262Pseudonocardia spinosispora sp. nov., isolated from Korean soil.Lee SD, Kim ES, Kang SO, Hah YCInt J Syst Evol Microbiol10.1099/00207713-52-5-16032002Actinomycetales/*classification/genetics/*isolation & purification/metabolism, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Korea, Microscopy, Electron, Scanning, Molecular Sequence Data, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Soil Microbiology, Terminology as TopicGenetics
Phylogeny19502340Pseudonocardia acaciae sp. nov., isolated from roots of Acacia auriculiformis A. Cunn. ex Benth.Duangmal K, Thamchaipenet A, Matsumoto A, Takahashi YInt J Syst Evol Microbiol10.1099/ijs.0.007724-02009Acacia/classification/genetics/*microbiology/physiology, Actinomycetales/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA Gyrase/genetics, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genotype, Molecular Sequence Data, Phenotype, Phylogeny, Plant Roots/*microbiology, Polymerase Chain Reaction/methods, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity, ThailandGenetics
Phylogeny20418409Pseudonocardia eucalypti sp. nov., an endophytic actinobacterium with a unique knobby spore surface, isolated from roots of a native Australian eucalyptus tree.Kaewkla O, Franco CMMInt J Syst Evol Microbiol10.1099/ijs.0.022327-02010Actinomycetales/*classification/genetics/*isolation & purification/physiology, Australia, Bacterial Typing Techniques, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Eucalyptus/*microbiology, Molecular Sequence Data, Phylogeny, Plant Roots/microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spores, Bacterial/cytologyGenetics

Reference

@idauthorscataloguedoi/urltitle
11984Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44797)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44797
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
33191Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5589
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
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
82588Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID100892.1StrainInfo: A central database for resolving microbial strain identifiers
123262Curators of the CIPCollection of Institut Pasteur (CIP 108013)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108013