Strain identifier

BacDive ID: 10797

Type strain: Yes

Species: Nocardia xishanensis

Strain Designation: 276

Strain history: Z. Liu 276.

NCBI tax ID(s): 1210101 (strain), 238964 (species)

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General

@ref: 12180

BacDive-ID: 10797

DSM-Number: 44895

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

description: Nocardia xishanensis 276 is an aerobe, mesophilic, Gram-positive bacterium that builds an aerial mycelium and was isolated from soil.

NCBI tax id

NCBI tax idMatching level
238964species
1210101strain

strain history

@refhistory
12180<- Y. Mikami, IFM, Chiba University, Japan <- Z. Liu; 276
67770Z. Liu 276.

doi: 10.13145/bacdive10797.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Mycobacteriales
  • family: Nocardiaceae
  • genus: Nocardia
  • species: Nocardia xishanensis
  • full scientific name: Nocardia xishanensis Zhang et al. 2004

@ref: 12180

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardiaceae

genus: Nocardia

species: Nocardia xishanensis

full scientific name: Nocardia xishanensis Zhang et al. 2004

strain designation: 276

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
31251positiveovoid-shapedno
69480positive100

colony morphology

@refcolony colormedium used
69366ColourlessISP 2
69366ColourlessISP 3
69366Beige (1001)ISP 7
69366Beige (1001)suter with tyrosine
69366Beige (1001)suter without tyrosine
69366Ivory (1014)ISP 5
69366Ivory (1014)ISP 6

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
69366yesAerial myceliumCream (9001)ISP 2
69366yesAerial myceliumPure white (9010)ISP 3
69366noAerial myceliumISP 5
69366yesAerial myceliumCream (9001)ISP 6
69366noAerial myceliumISP 7
69366yesAerial myceliumLight ivory (1015)suter with tyrosine
69366noAerial myceliumsuter without tyrosine

pigmentation

@refproductionnamecolor
31251no
69366yesMelanin
69366yessoluble pigmentBrown beige (1011), ochre brown (8001)

multimedia

@refmultimedia contentcaptionintellectual property rights
69366DSM_44895_image3.jpegPlates (65, ISP2, ISP3, ISP4, ISP5, ISP7)Helmholtz-Zentrum für Infektionsforschung GmbH
69366DSM_44895_image4.jpegPlates (65, ISP2, ISP3, ISP4, ISP5, ISP7)Helmholtz-Zentrum für Infektionsforschung GmbH

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12180GPHF-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
12180GYM 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

culture temp

@refgrowthtypetemperaturerange
12180positivegrowth28mesophilic
31251positivegrowth22-38
31251positiveoptimum30mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
31251positivegrowth5.5-10alkaliphile
31251positiveoptimum7.75

Physiology and metabolism

oxygen tolerance

  • @ref: 31251
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
31251no
69481yes100
69480no97.989

halophily

@refsaltgrowthtested relationconcentration
31251NaClpositivegrowth0-3 %
31251NaClpositiveoptimum1.5 %
69366NaClpositivegrowth0-2.5 %

observation

  • @ref: 67770
  • observation: quinones: MK-8(H6, ω-cycl)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3125130089acetate+carbon source
3125117128adipate+carbon source
3125117057cellobiose+carbon source
3125128757fructose+carbon source
3125133984fucose+carbon source
3125128260galactose+carbon source
3125117234glucose+carbon source
3125117754glycerol+carbon source
3125124996lactate+carbon source
3125125115malate+carbon source
3125117306maltose+carbon source
3125137684mannose+carbon source
3125128053melibiose+carbon source
3125115361pyruvate+carbon source
3125126546rhamnose+carbon source
3125133942ribose+carbon source
3125117814salicin+carbon source
3125130911sorbitol+carbon source
3125130031succinate+carbon source
3125117992sucrose+carbon source
312514853esculin+hydrolysis
3125117632nitrate+reduction
6936622599arabinose-growth
6936662968cellulose-growth
6936628757fructose-growth
6936617234glucose+growth
6936617268inositol-growth
6936637684mannose-growth
6936616634raffinose-growth
6936626546rhamnose-growth
6936617992sucrose-growth
6936618222xylose-growth
683794853esculin-hydrolysis
683795291gelatin-hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837917992sucrose-fermentation
6837928087glycogen-fermentation

enzymes

@refvalueactivityec
31251catalase+1.11.1.6
31251urease+3.5.1.5
68379gelatinase-
68379beta-glucosidase-3.2.1.21
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379alpha-glucosidase+3.2.1.20
68379beta-galactosidase-3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase+3.1.3.1
68379pyrrolidonyl arylamidase-3.4.19.3
68379pyrazinamidase-3.5.1.B15
68382esterase lipase (C 8)+
68382leucine arylamidase+3.4.11.1
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
69366+/---+--+--+/----------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
69366+/-+/-++/-++/-+/-+/--++/----++/----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
12180soilBeijing, Xishan MountainChinaCHNAsia
67770SoilXishan Mountain, BeijingChinaCHNAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_2795.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_243;97_907;98_2166;99_2795&stattab=map
  • Last taxonomy: Nocardia
  • 16S sequence: GQ853067
  • Sequence Identity:
  • Total samples: 30
  • soil counts: 20
  • aquatic counts: 3
  • animal counts: 5
  • plant counts: 2

Safety information

risk assessment

  • @ref: 12180
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Nocardia xishanensis strain W9867 16S ribosomal RNA gene, partial sequenceGQ8530671441ena238964
31251Nocardia xishanensis 16S ribosomal RNA gene, partial sequenceAY333115.1411nuccore238964
12180Nocardia xishanensis 16S ribosomal RNA gene, partial sequenceAY3331151411ena238964

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardia xishanensis NBRC 1013581210101.4wgspatric1210101
66792Nocardia xishanensis NBRC 1013582731957752draftimg1210101
67770Nocardia xishanensis NBRC 101358GCA_001613365contigncbi1210101

GC content

@refGC-contentmethod
1218068.8
6777068.8thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno93.296yes
gram-positiveyes87.582yes
anaerobicno99.1no
aerobicyes90.516yes
halophileno93.914no
spore-formingyes85.398no
thermophileno99.133yes
glucose-utilyes87.156yes
flagellatedno98.118yes
glucose-fermentno92.483yes

External links

@ref: 12180

culture collection no.: DSM 44895, CGMCC 4.1860, IFM 10549, JCM 12160, NBRC 101358

straininfo link

  • @ref: 80062
  • straininfo: 134457

literature

  • topic: Phylogeny
  • Pubmed-ID: 15545475
  • title: Nocardia xishanensis sp. nov., a novel actinomycete isolated from soil.
  • authors: Zhang J, Liu Z, Goodfellow M
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.63133-0
  • year: 2004
  • mesh: Bacterial Typing Techniques, China, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Genes, rRNA, Molecular Sequence Data, Nocardia/*classification/genetics/*isolation & purification/metabolism, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology
  • topic2: Enzymology

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
12180Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44895)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44895
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
31251Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604127574
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/
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
69366Wink, J.https://cdn.dsmz.de/wink/DSM%2044895.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
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
80062Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID134457.1StrainInfo: A central database for resolving microbial strain identifiers