Strain identifier

BacDive ID: 132521

Type strain: Yes

Species: Nocardia donostiensis

Strain Designation: Stamm 1, X1654

Strain history: <- M. Bell, Centers for Disease, Atlanta; X1654 <- M. Arana <- J. Larruskain

NCBI tax ID(s): 1538463 (species)

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General

@ref: 24310

BacDive-ID: 132521

DSM-Number: 46814

keywords: genome sequence, 16S sequence, Bacteria, mesophilic, pigmented

description: Nocardia donostiensis Stamm 1 is a mesophilic bacterium that builds an aerial mycelium and has a Salmon pink , mahogany brown pigmentation.

NCBI tax id

  • NCBI tax id: 1538463
  • Matching level: species

strain history

  • @ref: 24310
  • history: <- M. Bell, Centers for Disease, Atlanta; X1654 <- M. Arana <- J. Larruskain

doi: 10.13145/bacdive132521.20230509.8.1

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 donostiensis
  • full scientific name: Nocardia donostiensis Ercibengoa et al. 2020

@ref: 24310

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardiaceae

genus: Nocardia

species: Nocardia donostiensis

full scientific name: Nocardia donostiensis Ercibengoa et al. 2016

strain designation: Stamm 1, X1654

type strain: yes

Morphology

colony morphology

@refcolony colormedium used
69474ColourlessISP 4
69474Ivory (1014)ISP 5
69474Ivory (1014)suter without tyrosine
69474Light ivory (1015)ISP 7
69474Maize yellow (1006)ISP 6
69474Nut brown (8011)suter with tyrosine
69474Oyster white(1013)ISP 3
69474Sand yellow (1002)ISP 2

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
69474yesAerial myceliumTraffic white (9016)ISP 2
69474noAerial myceliumISP 3
69474noAerial myceliumISP 4
69474yesAerial myceliumTraffic white (9016)ISP 5
69474yesAerial myceliumTraffic white (9016)ISP 6
69474yesAerial myceliumTraffic white (9016)ISP 7
69474yesAerial myceliumSilk grey (7044)suter with tyrosine
69474yesAerial myceliumSignal white (9003)suter without tyrosine

pigmentation

  • @ref: 69474
  • production: yes
  • color: Salmon pink (3022), mahogany brown (8016)
  • name: soluble pigment

multimedia

  • @ref: 24310
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_46814.jpg
  • caption: Medium 535 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
24310GPHF-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
24310TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water

culture temp

  • @ref: 24310
  • growth: positive
  • type: growth
  • temperature: 28
  • range: mesophilic

Physiology and metabolism

halophily

  • @ref: 69474
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6947422599arabinose+growth
6947462968cellulose+growth
6947428757fructose-growth
6947417234glucose+growth
6947417268inositol-growth
6947437684mannose-growth
6947416634raffinose+growth
6947426546rhamnose+growth
6947417992sucrose+growth
6947418222xylose+growth
6837917632nitrate-reduction
683794853esculin-hydrolysis
6837916199urea-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
68379gelatinase-
68379urease-3.5.1.5
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)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
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
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 coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
69474-------------------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
69474+/-+/-+-++/----++/----+/-+---

Isolation, sampling and environmental information

isolation

  • @ref: 24310
  • sample type: sputum of 77-year-old male patient with chronic obstructive pulmonary disease (COPD)
  • geographic location: University Hospital Donosia in San Sebastian
  • country: Spain
  • origin.country: ESP
  • continent: Europe

isolation source categories

Cat1Cat2Cat3
#Infection#Inflammation
#Infection#Patient
#Host Body Product#Fluids#Sputum
#Host#Human#Male

taxonmaps

  • @ref: 69479
  • File name: preview.99_1609.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_243;97_907;98_1269;99_1609&stattab=map
  • Last taxonomy: Nocardia
  • 16S sequence: KM233637
  • Sequence Identity:
  • Total samples: 50
  • soil counts: 29
  • aquatic counts: 1
  • animal counts: 18
  • plant counts: 2

Sequence information

16S sequences

  • @ref: 24310
  • description: Nocardia sp. X1654 16S ribosomal RNA gene, partial sequence
  • accession: KM233637
  • length: 1441
  • database: ena
  • NCBI tax ID: 1538463

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardia donostiensis X1654GCA_002081715contigncbi1538463
66792Nocardia donostiensis X16542865871275draftimg1538463

GC content

  • @ref: 24310
  • GC-content: 66.7
  • method: sequence analysis

External links

@ref: 24310

culture collection no.: DSM 46814, CECT 8839

straininfo link

  • @ref: 90847
  • straininfo: 403874

literature

  • topic: Phylogeny
  • Pubmed-ID: 26914251
  • title: Nocardia donostiensis sp. nov., isolated from human respiratory specimens.
  • authors: Ercibengoa M, Bell M, Marimon JM, Humrighouse B, Klenk HP, Potter G, Perez-Trallero E
  • journal: Antonie Van Leeuwenhoek
  • DOI: 10.1007/s10482-016-0667-8
  • year: 2016
  • mesh: Adolescent, Aged, Bacterial Typing Techniques, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Humans, Male, Nocardia/*classification/genetics/*isolation & purification, Nocardia Infections/*microbiology, Phenotype, Phylogeny, Pneumonia, Bacterial/*microbiology, RNA, Ribosomal, 16S/genetics, Respiratory System/*microbiology
  • topic2: Pathogenicity

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
24310Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-46814Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 46814)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
69474Wink, J.Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweighttps://cdn.dsmz.de/wink/DSM%2046814.pdf
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
90847Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID403874.1