We are hiring!

Strain identifier

BacDive ID: 10725

Type strain: Yes

Species: Nocardia seriolae

Strain history: K. Hatai NA 8191.

For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 7.1 (current version):
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 7.1 (current version)

General

@ref: 11488

BacDive-ID: 10725

DSM-Number: 44129

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, animal pathogen

description: Nocardia seriolae DSM 44129 is an aerobe, mesophilic animal pathogen that was isolated from spleen of yellowtail .

NCBI tax id

NCBI tax idMatching level
37332species
1210095strain

strain history

doi: 10.13145/bacdive10725.20221219.7.1

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 seriolae
  • full scientific name: Nocardia seriolae Kudo et al. 1988

@ref: 11488

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardiaceae

genus: Nocardia

species: Nocardia seriolae

full scientific name: Nocardia seriolae Kudo et al. 1988

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: positive
  • confidence: 95.56

colony morphology

@refcolony colorincubation periodmedium used
20002Ochre brown (8001)10-14 daysISP 2
20002Colorless10-14 daysISP 3
20002Colorless10-14 daysISP 4
20002Colorless10-14 daysISP 5
20002Ochre brown (8001)10-14 daysISP 6
20002Ochre brown (8001)10-14 daysISP 7
573615 days

multicellular morphology

@refforms multicellular complexmedium name
20002noISP 2
20002noISP 3
20002noISP 4
20002noISP 5
20002noISP 6
20002noISP 7

multimedia

@refmultimedia contentintellectual property rightscaption
11488https://www.dsmz.de/microorganisms/photos/DSM_44129-1.jpg© Leibniz-Institut DSMZ
11488https://www.dsmz.de/microorganisms/photos/DSM_44129.jpg© Leibniz-Institut DSMZMedium 535 28°C

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11488TRYPTICASE 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
11488GYM 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
20002ISP 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
20002ISP 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:
20002ISP 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
20002ISP 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
20002ISP 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
20002ISP 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
34627MEDIUM 129 - for Pseudonocardia, Nocardia, Skermania and Streptomyces seoulensis, Streptomyces stramineusyesDistilled water make up to (1000.000 ml);Agar (20.000 g);Glucose (10.000g);Yeast extract (1.000 g);Beef extract (1.000 g);Casamino acids (2.000 g)

culture temp

@refgrowthtypetemperaturerange
11488positivegrowth28mesophilic
34627positivegrowth30mesophilic
57361positivegrowth30mesophilic
67770positivegrowth26mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 57361
  • oxygen tolerance: aerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 71.397

halophily

@refsaltgrowthtested relationconcentrationhalophily levelconfidence
20002NaClpositivegrowth0 %
69480non-halophilic96.108

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate+assimilation
6836818257ornithine+degradation
6836825094lysine+degradation
6836829016arginine+hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin-
6836835581indole-

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase+3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)-
68382alkaline phosphatase+3.1.3.1
68368gelatinase-
68368tryptophan deaminase-4.1.99.1
68368urease+3.5.1.5
68368ornithine decarboxylase+4.1.1.17
68368lysine decarboxylase+4.1.1.18
68368arginine dihydrolase+3.5.3.6
68368beta-galactosidase-3.2.1.23

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
20002+-+-++---++---++---

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
20002-++++-+----

Isolation, sampling and environmental information

isolation

@refsample typehost speciescountryorigin.countrycontinentgeographic location
11488spleen of yellowtail (Seriola quinqueradiata)Seriola quinqueradiataJapanJPNAsia
57361Spleen of yellowtail (Seriola quinqueradiata)JapanJPNAsia
67770Spleen of cultured yellowtail (Seriola quinqueradiata)Seriola quinqueradiataJapanJPNAsiaNagasaki Pref.

isolation source categories

Cat1Cat2Cat3
#Host#Fishes
#Host Body-Site#Organ#Spleen

taxonmaps

  • @ref: 69479
  • File name: preview.99_1837.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_243;97_448;98_1452;99_1837&stattab=map
  • Last taxonomy: Nocardia
  • 16S sequence: X80592
  • Sequence Identity:
  • Total samples: 831
  • soil counts: 541
  • aquatic counts: 38
  • animal counts: 141
  • plant counts: 111

Safety information

risk assessment

@refpathogenicity animalbiosafety levelbiosafety level comment
11488yes1Risk group (German classification)
200022German classification

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Nocardia seriolae strain ATCC 43993 16S ribosomal RNA gene, partial sequenceGQ3761931440ena37332
20218Nocardia seriolae 16S rRNA gene, strain ATCC 43993TX805921396ena37332
20218Nocardia seriolae strain DSM 44129 16S ribosomal RNA gene, complete sequenceAF4300391492ena37332
20218Nocardia seriolae strain DSM 44129 note copy 1 16S-23S ribosomal RNA intergenic spacer, complete sequenceAF536474322ena37332
20218Nocardia seriolae strain DSM 44129 note copy 2 16S-23S ribosomal RNA intergenic spacer, complete sequenceAF536475326ena37332
20218Nocardia seriolae strain DSM 44129 16S ribosomal RNA gene, partial sequenceAY756561606ena37332
20218Nocardia seriolae strain JCM 3360 16S ribosomal RNA gene, partial sequenceDQ6599151417ena37332
20218N.seriolae gene for 16S ribosomal RNAZ369251472ena37332

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardia seriolae NBRC 155571210095.3wgspatric1210095
67770Nocardia seriolae NBRC 15557 NBRC 15557GCA_007990715contigncbi1210095
66792Clostridia bacterium AS05jafATM_84GCA_012842035contigpatric2044939

GC content

  • @ref: 11488
  • GC-content: 67.3
  • method: high performance liquid chromatography (HPLC)

External links

@ref: 11488

culture collection no.: DSM 44129, ATCC 43993, CCUG 46828, CIP 104778, IFO 15557, JCM 3360, NBRC 15557, NCIMB 13256, VKM Ac-1967, BCRC 13745, IFM 0286, IMSNU 21188

straininfo link

@refpassport
20218http://www.straininfo.net/strains/153430
20218http://www.straininfo.net/strains/113414
20218http://www.straininfo.net/strains/331397
20218http://www.straininfo.net/strains/153429
20218http://www.straininfo.net/strains/153431
20218http://www.straininfo.net/strains/113415
20218http://www.straininfo.net/strains/333775
20218http://www.straininfo.net/strains/153432
20218http://www.straininfo.net/strains/227470

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15960657Nocardiosis in large yellow croaker, Larimichthys crocea (Richardson).Wang GL, Yuan SP, Jin SJ Fish Dis10.1111/j.1365-2761.2005.00637.x2005Animals, Aquaculture, Base Sequence, China/epidemiology, Cluster Analysis, DNA Primers, Disease Outbreaks/*veterinary, Fish Diseases/*epidemiology/*microbiology/pathology, Kidney/ultrastructure, Microscopy, Electron/veterinary, Molecular Sequence Data, Myocardium/pathology, Nocardia/genetics/*ultrastructure, Nocardia Infections/epidemiology/pathology/*veterinary, *Perciformes, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA/veterinary, Spleen/pathologyGenetics
Phylogeny18482385Genetic and phenotypic comparison of Nocardia seriolae isolated from fish in Japan.Shimahara Y, Nakamura A, Nomoto R, Itami T, Chen SC, Yoshida TJ Fish Dis10.1111/j.1365-2761.2008.00920.x2008Animals, Fish Diseases/*microbiology, Fishes/*microbiology, Japan, Molecular Sequence Data, Nocardia/*enzymology/*genetics/isolation & purification, Nocardia Infections/microbiology/*veterinary, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, alpha-Glucosidases/metabolismGenetics
Phylogeny19335609Nocardia seriolae infection in the three striped tigerfish, Terapon jarbua (Forsskal).Wang PC, Chen SD, Tsai MA, Weng YJ, Chu SY, Chern RS, Chen SCJ Fish Dis10.1111/j.1365-2761.2008.00991.x2009Animals, Fish Diseases/*microbiology/mortality/pathology, Heat-Shock Proteins/genetics, Molecular Sequence Data, Nocardia/classification/genetics/isolation & purification/*physiology, Nocardia Infections/mortality/pathology/*veterinary, Perciformes/*microbiology, Phylogeny, RNA Polymerase II/genetics, RNA, Ribosomal, 16S/geneticsGenetics
Pathogenicity29166272In vitro activity of some essential oils alone and in combination against the fish pathogen Nocardia seriolae.Ismail TF, Yoshida TPol J Vet Sci10.1515/pjvs-2017-00682017Animals, Bacteriological Techniques, Fishes/*microbiology, Microbial Sensitivity Tests, Nocardia/*drug effects, Oils, Volatile/*pharmacology, Oxazines, Plant Oils/*pharmacology, Xanthenes
Phylogeny33146799Nocardia terrae sp. nov., an actinomycete isolated from soil in Thailand.Kanchanasin P, Yuki M, Kudo T, Ohkuma M, Phongsopitanun W, Tanasupawat SArch Microbiol10.1007/s00203-020-02107-32020Base Composition, Fatty Acids/chemistry, Nocardia/*classification/genetics/isolation & purification, Phospholipids/chemistry, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Species Specificity, ThailandEnzymology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11488Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44129)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44129
20002Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44129.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
34627Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16724
57361Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 46828)https://www.ccug.se/strain?id=46828
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68368Automatically annotated from API 20E
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)