Strain identifier

BacDive ID: 23157

Type strain: Yes

Species: Nocardia grenadensis

Strain Designation: GW5-5797

Strain history: CIP <- 2011, P. Kämpfer, J. Liebig Giessen Univ., Giessen, Germany: strain GW5-5797

NCBI tax ID(s): 1223546 (strain), 931537 (species)

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General

@ref: 19134

BacDive-ID: 23157

DSM-Number: 45869

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

description: Nocardia grenadensis GW5-5797 is an aerobe, mesophilic, Gram-positive bacterium that builds an aerial mycelium and was isolated from sea sand.

NCBI tax id

NCBI tax idMatching level
1223546strain
931537species

strain history

@refhistory
19134<- CCUG; CCUG 60970 <- P. Kämpfer; GW5-5797
67770CCUG 60970 <-- P. Kämpfer GW5-5797.
119737CIP <- 2011, P. Kämpfer, J. Liebig Giessen Univ., Giessen, Germany: strain GW5-5797

doi: 10.13145/bacdive23157.20230509.8.1

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 grenadensis
  • full scientific name: Nocardia grenadensis Kämpfer et al. 2012

@ref: 19134

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardiaceae

genus: Nocardia

species: Nocardia grenadensis

full scientific name: Nocardia grenadensis Kämpfer et al. 2012

strain designation: GW5-5797

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
30205positiverod-shaped
69480no92.572
69480positive100
119737positiverod-shapedno

colony morphology

@refcolony colormedium usedincubation period
69450Deep orange (2011)ISP 4
69450Dahlia yellow (1022)suter without tyrosine
69450Bright red orange (2008)ISP 2
625072-3 days
69450Pastel orange (2003)ISP 7
69450Pastel yellow (1034)ISP 3
69450Pastel yellow (1034)ISP 5
69450Pastel yellow (1034)ISP 6
69450Saffron yellow (1017)suter with tyrosine

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
69450yesAerial myceliumSignal white (9003)ISP 2
69450noAerial myceliumISP 3
69450noAerial myceliumISP 4
69450yesAerial myceliumPure white (9010)ISP 5
69450noAerial myceliumISP 6
69450yesAerial myceliumCream (9004)ISP 7
69450yesAerial myceliumCream (9001)suter with tyrosine
69450yesAerial myceliumPastel yellow (1034)suter without tyrosine

pigmentation

@refproductionnamecolor
30205yes
69450noMelanin
69450yessoluble pigmentPastel yellow (1034), saffron yellow (1017), sand yellow (1022), sand yellow (1002)

multimedia

@refmultimedia contentcaptionintellectual property rights
69450DSM_45869_image3.jpegPlates (5006, ISP2, ISP3, ISP4, ISP5, ISP7)Helmholtz-Zentrum für Infektionsforschung GmbH
69450DSM_45869_image4.jpegPlates (5006, ISP2, ISP3, ISP4, ISP5, ISP7)Helmholtz-Zentrum für Infektionsforschung GmbH

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
19134GYM 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
19134BHI MEDIUM (DSMZ Medium 215)yeshttps://mediadive.dsmz.de/medium/215Name: BHI MEDIUM (DSMZ Medium 215) Composition: Brain heart infusion 37.0 g/l Distilled water
119737CIP Medium 57yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=57

culture temp

@refgrowthtypetemperaturerange
19134positivegrowth37mesophilic
30205positiveoptimum25-30mesophilic
62507positivegrowth37mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
30205aerobe
62507microaerophile
119737obligate aerobe

spore formation

@refspore formationconfidence
30205no
69481yes100
69480no98.556
119737no

halophily

  • @ref: 69450
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-7.5 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
30205161933-hydroxybenzoate+carbon source
3020515963ribitol+carbon source
3020516449alanine+carbon source
3020522599arabinose+carbon source
3020535391aspartate+carbon source
3020517057cellobiose+carbon source
3020528757fructose+carbon source
3020528260galactose+carbon source
3020527570histidine+carbon source
3020525115malate+carbon source
3020517306maltose+carbon source
3020529864mannitol+carbon source
3020537684mannose+carbon source
3020528053melibiose+carbon source
3020518401phenylacetate+carbon source
3020528044phenylalanine+carbon source
3020526271proline+carbon source
3020533942ribose+carbon source
3020517814salicin+carbon source
3020517822serine+carbon source
302059300suberic acid+carbon source
3020517992sucrose+carbon source
3020527082trehalose+carbon source
3020518222xylose+carbon source
6945022599arabinose-growth
6945062968cellulose-growth
6945028757fructose-growth
6945017234glucose+growth
6945017268inositol+/-growth
6945037684mannose-growth
6945016634raffinose-growth
6945026546rhamnose-growth
6945017992sucrose-growth
6945018222xylose-growth
11973717632nitrate+reduction
11973716301nitrite-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

metabolite production

  • @ref: 119737
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
30205urease+3.5.1.5
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
119737catalase+1.11.1.6
119737urease-3.5.1.5
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
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 coryne

@refPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
69450-------+---------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
69450+++-+++/-+/-+/-++----+---
119737-++-+----++----+----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
19134sea sandCaribbean SeaGrenadaGRDMiddle and South America
62507Sea sand,5m depthCaribbean Sea, near Grenada
67770Sand at a depth of 5 m in the Caribbean Sea near Grenada
119737Environment, Soil, sand at a depth of 5 mCarribean SeaGrenadaGRDNorth America

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Terrestrial#Sandy

taxonmaps

  • @ref: 69479
  • File name: preview.99_7757.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_243;97_658;98_761;99_7757&stattab=map
  • Last taxonomy: Nocardia
  • 16S sequence: FR729900
  • Sequence Identity:
  • Total samples: 64
  • soil counts: 49
  • animal counts: 15

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
191341Risk group (German classification)
1197372Risk group (French classification)

Sequence information

16S sequences

  • @ref: 19134
  • description: Nocardia grenadensis NBRC 108939 partial 16S rRNA gene, type strain GW5-5797T
  • accession: FR729900
  • length: 1432
  • database: ena
  • NCBI tax ID: 1223546

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardia grenadensis NBRC 1089391223546.4wgspatric1223546
66792Nocardia grenadensis NBRC 1089392731957754draftimg1223546
67770Nocardia grenadensis NBRC 108939GCA_001613445contigncbi1223546

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno92.094no
gram-positiveyes87.255yes
anaerobicno98.937yes
aerobicyes89.908no
halophileno85.676no
spore-formingyes60.823yes
glucose-utilyes89.323yes
flagellatedno97.857no
thermophileno98.714yes
glucose-fermentno91.045yes

External links

@ref: 19134

culture collection no.: DSM 45869, CCUG 60970, CIP 110294, JCM 19117, NBRC 108939

straininfo link

  • @ref: 87391
  • straininfo: 405986

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny21551327Nocardia grenadensis sp. nov., isolated from sand of the Caribbean Sea.Kampfer P, Lodders N, Grun-Wollny I, Martin K, Busse HJInt J Syst Evol Microbiol10.1099/ijs.0.030684-02011Bacterial Typing Techniques, Benzoquinones/analysis, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Geologic Sediments/*microbiology, Grenada, Molecular Sequence Data, Nocardia/*classification/genetics/*isolation & purification/physiology, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/analysis, Phylogeny, Polyamines/analysis, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Silicon DioxideGenetics
Phylogeny26547854Nocardia zapadnayensis sp. nov., isolated from soil.Ozdemir-Kocak F, Saygin H, Saricaoglu S, Cetin D, Potter G, Sproer C, Guven K, Isik K, Klenk HP, Sahin NAntonie Van Leeuwenhoek10.1007/s10482-015-0612-22015Bacterial Typing Techniques, Base Sequence, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Diaminopimelic Acid/analysis/chemistry, Fatty Acids/analysis, Microscopy, Electron, Scanning, Molecular Sequence Data, Nocardia/chemistry/cytology/genetics/*isolation & purification, Nucleic Acid Hybridization, Phospholipids/analysis/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil, *Soil MicrobiologyGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
19134Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45869)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45869
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
30205Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2655028776041
62507Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 60970)https://www.ccug.se/strain?id=60970
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
69450Wink, J.https://cdn.dsmz.de/wink/DSM%2045869.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
87391Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID405986.1StrainInfo: A central database for resolving microbial strain identifiers
119737Curators of the CIPCollection of Institut Pasteur (CIP 110294)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110294