Strain identifier

BacDive ID: 13385

Type strain: Yes

Species: Pseudonocardia xinjiangensis

Strain Designation: XJ 45, XJ-4-5

Strain history: CIP <- 2002, W.J. Li, Yunnan Univ., Kunming, China: strain XJ-4-5 <- C.L. Jiang

NCBI tax ID(s): 75289 (species)

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General

@ref: 11857

BacDive-ID: 13385

DSM-Number: 44661

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

description: Pseudonocardia xinjiangensis XJ 45 is a mesophilic, Gram-positive, rod-shaped bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 75289
  • Matching level: species

strain history

@refhistory
11857<- W.-J. Li <- CIP <- CCTCC <- C.-L. Jiang; XJ 45
67770AS 4.1538 <-- C. L. Jiang XJ-45.
123987CIP <- 2002, W.J. Li, Yunnan Univ., Kunming, China: strain XJ-4-5 <- C.L. Jiang

doi: 10.13145/bacdive13385.20230509.8.1

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 xinjiangensis
  • full scientific name: Pseudonocardia xinjiangensis (Xu et al. 1999) Huang et al. 2002

  • synonyms

    • @ref: 20215
    • synonym: Actinobispora xinjiangensis

@ref: 11857

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Pseudonocardiaceae

genus: Pseudonocardia

species: Pseudonocardia xinjiangensis

full scientific name: Pseudonocardia xinjiangensis (Xu et al. 1999) Huang et al. 2002

strain designation: XJ 45, XJ-4-5

type strain: yes

Morphology

cell morphology

  • @ref: 123987
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11857GYM 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
33776MEDIUM 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)
123987CIP Medium 57yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=57

culture temp

@refgrowthtypetemperaturerange
11857positivegrowth28mesophilic
33776positivegrowth30mesophilic
67770positivegrowth28mesophilic
123987positivegrowth25-37mesophilic
123987nogrowth10psychrophilic
123987nogrowth41thermophilic
123987nogrowth45thermophilic

Physiology and metabolism

halophily

@refsaltgrowthtested relationconcentration
123987NaClpositivegrowth0 %
123987NaClnogrowth2 %
123987NaClnogrowth4 %
123987NaClnogrowth6 %
123987NaClnogrowth8 %
123987NaClnogrowth10 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1239874853esculin-hydrolysis
123987606565hippurate+hydrolysis
12398717632nitrate-reduction
12398716301nitrite-reduction
12398717632nitrate-respiration

metabolite production

  • @ref: 123987
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12398715688acetoin-
12398717234glucose-

enzymes

@refvalueactivityec
123987oxidase-
123987beta-galactosidase-3.2.1.23
123987alcohol dehydrogenase-1.1.1.1
123987gelatinase-
123987catalase+1.11.1.6
123987gamma-glutamyltransferase-2.3.2.2
123987lysine decarboxylase-4.1.1.18
123987ornithine decarboxylase-4.1.1.17
123987tryptophan deaminase-
123987urease+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
123987-+++-++---+----+----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
123987--------------------------------+------------------------------------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
11857soilXinjiang, Tolufan, grapy farmlandChinaCHNAsia
67770SoilTolufan, XinjiangChinaCHNAsia
123987Environment, SoilXinjiangChinaCHNAsia

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
118571Risk group (German classification)
1239872Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
67770Actinobispora xinjiangensis 16S ribosomal RNA gene, partial sequenceAF0567091563ena75289
67770Actinobispora xinjiangensis 16S ribosomal RNA gene, partial sequenceAF3257281325ena75289
67770Pseudonocardia xinjiangensis strain XJ 45 16S ribosomal RNA gene, partial sequenceEU7225201516ena75289

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudonocardia xinjiangensis strain JCM 1183975289.3wgspatric75289
67770Pseudonocardia xinjiangensis JCM 11839GCA_012911925contigncbi75289

GC content

  • @ref: 67770
  • GC-content: 71.5
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno89.053no
flagellatedno97.605no
gram-positiveyes88.102no
anaerobicno99.172no
aerobicyes92.462no
halophileno92.857no
spore-formingyes79.228no
glucose-utilyes83.731no
thermophileno99.399no
glucose-fermentno88.065no

External links

@ref: 11857

culture collection no.: DSM 44661, AS 4.1538, CCTCC AA 97020, CIP 107366, JCM 11839, BCRC 16358, CGMCC 4.1538, NBRC 105201

straininfo link

  • @ref: 82582
  • straininfo: 100472

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny10319514Three new species of the genus Actinobispora of the family Pseudonocardiaceae, Actinobispora alaniniphila sp. nov., Actinobispora aurantiaca sp. nov. and Actinobispora xinjiangensis sp. nov.Xu LH, Jin X, Mao PH, Lu ZF, Cui XL, Jiang CLInt J Syst Bacteriol10.1099/00207713-49-2-8811999Actinomycetales/*classification/cytology/genetics/physiology, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Genes, rRNA, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Spores, Bacterial/physiologyGenetics
Phylogeny28820114Pseudonocardia nigra sp. nov., isolated from Atacama Desert rock.Trujillo ME, Idris H, Riesco R, Nouioui I, Igual JM, Bull AT, Goodfellow MInt J Syst Evol Microbiol10.1099/ijsem.0.0020632017Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Chile, DNA, Bacterial/genetics, *Desert Climate, Fatty Acids/chemistry, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome
Phylogeny32931406Pseudonocardia acidicola sp. nov., a novel actinomycete isolated from peat swamp forest soil.Klaysubun C, Lipun K, Duangmal KInt J Syst Evol Microbiol10.1099/ijsem.0.0044592020Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Pseudonocardia/*classification/isolation & purification, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Thailand, Vitamin K 2/analogs & derivatives/chemistry, *WetlandsTranscriptome

Reference

@idauthorscataloguedoi/urltitle
11857Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44661)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44661
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
33776Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/4793
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/
68382Automatically annotated from API zym
82582Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID100472.1StrainInfo: A central database for resolving microbial strain identifiers
123987Curators of the CIPCollection of Institut Pasteur (CIP 107366)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107366