Strain identifier

BacDive ID: 10765

Type strain: Yes

Species: Nocardia crassostreae

Strain Designation: NB4H

Strain history: CIP <- 1999, R.P. Hedrick, Bodega Marine Lab., California Univ., Davis, California, USA: strain NB4H

NCBI tax ID(s): 53428 (species)

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General

@ref: 11912

BacDive-ID: 10765

DSM-Number: 44597

keywords: genome sequence, 16S sequence, Bacteria, spore-forming, mesophilic, animal pathogen

description: Nocardia crassostreae NB4H is a spore-forming, mesophilic animal pathogen that was isolated from diseased Pacific oyster.

NCBI tax id

  • NCBI tax id: 53428
  • Matching level: species

strain history

@refhistory
11912<- ATCC <- C. S. Friedman; NB4H
402711999, R.P. Hedrick, Bodega Marine Lab., CA Univ. USA: strain NB4H
67770C. S. Friedman NB4H.
118778CIP <- 1999, R.P. Hedrick, Bodega Marine Lab., California Univ., Davis, California, USA: strain NB4H

doi: 10.13145/bacdive10765.20230509.8.1

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 crassostreae
  • full scientific name: Nocardia crassostreae Friedman et al. 1998

@ref: 11912

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardiaceae

genus: Nocardia

species: Nocardia crassostreae

full scientific name: Nocardia crassostreae Friedman et al. 1998 emend. Nouioui et al. 2018

strain designation: NB4H

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no95.943
69480100positive
118778nopositiverod-shaped

colony morphology

@refcolony colorincubation periodmedium used
20078Beige (1001)10-14 daysISP 2
20078Beige (1001)10-14 daysISP 3
20078Beige (1001)10-14 daysISP 4
20078Beige (1001)10-14 daysISP 5
20078Beige (1001)10-14 daysISP 6
20078Beige (1001)10-14 daysISP 7
118778

multicellular morphology

@refforms multicellular complexmedium name
20078noISP 2
20078noISP 3
20078noISP 4
20078noISP 5
20078noISP 6
20078noISP 7

multimedia

  • @ref: 11912
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_44597.jpg
  • caption: Medium 553 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11912GPHF-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
11912BHI 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
20078ISP 2yesName: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
20078ISP 3yesName: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
20078ISP 4yesName: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
20078ISP 5yesName: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
20078ISP 6yesName: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
20078ISP 7yesName: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes
40271MEDIUM 9 - Brain heart infusion BHIyesDistilled water make up to (1000.000 ml);Brain heart infusion (37.000 g)
118778CIP Medium 9yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=9

culture temp

@refgrowthtypetemperaturerange
11912positivegrowth28mesophilic
20078positiveoptimum28mesophilic
40271positivegrowth22psychrophilic
67770positivegrowth25mesophilic
118778positivegrowth10-30
118778nogrowth37mesophilic
118778nogrowth41thermophilic
118778nogrowth45thermophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481yes100
69480yes92.762

halophily

@refsaltgrowthtested relationconcentration
118778NaClpositivegrowth0-4 %
118778NaClnogrowth6 %
118778NaClnogrowth8 %
118778NaClnogrowth10 %

observation

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

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose+builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen+builds acid from28087
68371starch+builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose+builds acid from27082
68371sucrose-builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose+builds acid from17306
68371salicin+builds acid from17814
68371esculin+builds acid from4853
68371arbutin+builds acid from18305
68371N-acetylglucosamine+builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose+builds acid from16024
68371D-fructose+builds acid from15824
68371D-glucose+builds acid from17634
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose+builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
118778esculin-hydrolysis4853
118778hippurate-hydrolysis606565
68379nitrate-reduction17632
68379esculin-hydrolysis4853
68379urea+hydrolysis16199
68379gelatin+hydrolysis5291
68379D-glucose-fermentation17634
68379D-ribose-fermentation16988
68379D-xylose-fermentation65327
68379D-mannitol-fermentation16899
68379maltose-fermentation17306
68379lactose-fermentation17716
68379sucrose-fermentation17992
68379glycogen-fermentation28087

metabolite production

  • @ref: 118778
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11877815688acetoin-
11877817234glucose-

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
118778oxidase-
118778beta-galactosidase-3.2.1.23
118778alcohol dehydrogenase-1.1.1.1
118778gelatinase-
118778amylase-
118778DNase-
118778caseinase-3.4.21.50
118778catalase+1.11.1.6
118778tween esterase+
118778gamma-glutamyltransferase-2.3.2.2
118778lecithinase-
118778lipase-
118778lysine decarboxylase-4.1.1.18
118778ornithine decarboxylase-4.1.1.17
118778phenylalanine ammonia-lyase-4.3.1.24
118778protease-
118778tryptophan deaminase-
118778urease-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
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
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

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
20078---+-----++--------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
20078+++-++++-+----+----
118778+++-+--+-++---+-----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
118778----+-----+++--------++/-++++/-+---+---++--+---------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinenthost speciesisolation date
11912diseased Pacific oysterBritish Columbia, Nanoose BayCanadaCANNorth America
67770Pacific oyster (Crassostrea gigas)Nanoose Bay, Vancouver Island, British ColumbiaCanadaCANNorth AmericaCrassostrea gigas
118778Pacific oystersNanoose bay, British ColumbiaCanadaCANNorth America1986

isolation source categories

  • Cat1: #Host
  • Cat2: #Invertebrates (Other)
  • Cat3: #Mollusca

taxonmaps

  • @ref: 69479
  • File name: preview.99_7517.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_243;97_448;98_5509;99_7517&stattab=map
  • Last taxonomy: Nocardia
  • 16S sequence: Z37989
  • Sequence Identity:
  • Total samples: 56
  • soil counts: 21
  • aquatic counts: 25
  • animal counts: 10

Safety information

risk assessment

@refpathogenicity animalbiosafety levelbiosafety level comment
11912yes1Risk group (German classification)
200781German classification
1187782Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Nocardia crassostreae strain ATCC 700418 16S ribosomal RNA gene, partial sequenceAY756548606ena53428
20218N.crassostrae gene for 16S ribosomal RNA (partial)Z379891473ena53428
20218Nocardia crassostreae strain JCM 10500 16S ribosomal RNA gene, complete sequenceAF4300491493ena53428
20218Nocardia crassostreae strain JCM 10500 note copy 1 16S-23S ribosomal RNA intergenic spacer, complete sequenceAF536418297ena53428
20218Nocardia crassostreae strain JCM 10500 note copy 2 16S-23S ribosomal RNA intergenic spacer, complete sequenceAF536419297ena53428

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardia crassostreae strain NBRC 10034253428.4wgspatric53428
66792Nocardia crassostreae NBRC 1003422713896925draftimg53428
67770Nocardia crassostreae NBRC 100342GCA_001613405contigncbi53428

GC content

@refGC-contentmethod
1191268.6-69.3
6777067.7genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
gram-positiveyes88.625no
anaerobicno99.554no
halophileno93.738no
spore-formingyes83.779no
glucose-utilyes89.339no
thermophileno99.132no
flagellatedno97.745no
aerobicyes90.32no
motileno92.363no
glucose-fermentno89.473yes

External links

@ref: 11912

culture collection no.: DSM 44597, ATCC 700418, JCM 10500, CCUG 46826, CIP 105895, IFM 10173, NBRC 100342

straininfo link

  • @ref: 80033
  • straininfo: 43927

literature

  • topic: Phylogeny
  • Pubmed-ID: 9542093
  • title: Nocardia crassostreae sp. nov., the causal agent of nocardiosis in Pacific oysters.
  • authors: Friedman CS, Beaman BL, Chun J, Goodfellow M, Gee A, Hedrick RP
  • journal: Int J Syst Bacteriol
  • DOI: 10.1099/00207713-48-1-237
  • year: 1998
  • mesh: Animals, Culture Media, DNA, Bacterial/analysis, Microscopy, Electron, Molecular Sequence Data, Nocardia/*classification/genetics/ultrastructure, Nocardia Infections/*microbiology, Ostreidae/*microbiology, Pacific Ocean, Phenotype, Phylogeny, RNA, Bacterial/analysis, RNA, Ribosomal, 16S/analysis, Sequence Analysis, RNA
  • topic2: Cultivation

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11912Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44597)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44597
20078Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44597.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
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
40271Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17964
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/
68371Automatically annotated from API 50CH acid
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
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
80033Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID43927.1StrainInfo: A central database for resolving microbial strain identifiers
118778Curators of the CIPCollection of Institut Pasteur (CIP 105895)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105895