Strain identifier

BacDive ID: 10727

Type strain: Yes

Species: Nocardia salmonicida

Strain Designation: A-7604, Rucker

Strain history: CIP <- 1995, IFO <- E.B. Shirling: strain ISP 5472 <- Lederle Lab.: strain A-7604, Streptomyces salmonicida

NCBI tax ID(s): 53431 (species)

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General

@ref: 9566

BacDive-ID: 10727

DSM-Number: 40472

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, spore-forming, mesophilic, Gram-positive, animal pathogen

description: Nocardia salmonicida A-7604 is an obligate aerobe, spore-forming, mesophilic animal pathogen that was isolated from blueback salmon.

NCBI tax id

  • NCBI tax id: 53431
  • Matching level: species

strain history

@refhistory
9566<- E.B. Shirling, ISP, (Streptomyces salmonicida) <- H.D. Tresner, A-7604, strain Rucker
67770KCC S-0826 <-- IFO 13393 <-- SAJ <-- ISP 5472 <-- Lederle Labs.; A-7604 <-- R. Rucker.
122398CIP <- 1995, IFO <- E.B. Shirling: strain ISP 5472 <- Lederle Lab.: strain A-7604, Streptomyces salmonicida

doi: 10.13145/bacdive10727.20230509.8.1

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 salmonicida
  • full scientific name: Nocardia salmonicida (ex Rucker 1949) Isik et al. 1999

@ref: 9566

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardiaceae

genus: Nocardia

species: Nocardia salmonicida subsp. salmonicida

full scientific name: Nocardia salmonicida subsp. salmonicida (Isik et al. 1999) Nouioui et al. 2018

strain designation: A-7604, Rucker

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shape
69480positive100
122398positiverod-shaped

multimedia

  • @ref: 9566
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_40472.jpg
  • caption: Medium 65 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
9566GYM 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
35686MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
122398CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
18597positiveoptimum28mesophilic
9566positivegrowth28mesophilic
35686positivegrowth30mesophilic
67770positivegrowth28mesophilic
122398positivegrowth10-30
122398nogrowth37mesophilic
122398nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 122398
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481yes97
69480no99.909

halophily

@refsaltgrowthtested relationconcentration
122398NaClpositivegrowth0-4 %
122398NaClnogrowth6 %
122398NaClnogrowth8 %
122398NaClnogrowth10 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1859717234glucose+
1859722599arabinose-
1859717992sucrose-
1859718222xylose-
1859717268myo-inositol-
1859729864mannitol-
1859728757fructose+
1859726546rhamnose-
1859716634raffinose-
1859762968cellulose-
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate+assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis
1223984853esculin+hydrolysis
122398606565hippurate-hydrolysis
12239817632nitrate-reduction
12239816301nitrite-reduction
122398132112sodium thiosulfate+builds gas from
12239817632nitrate-respiration
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

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno
12239835581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin-
6836835581indole-
12239815688acetoin-

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
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
122398oxidase-
122398beta-galactosidase+/-3.2.1.23
122398alcohol dehydrogenase-1.1.1.1
122398gelatinase-
122398amylase-
122398DNase-
122398caseinase-3.4.21.50
122398catalase+1.11.1.6
122398tween esterase-
122398lecithinase-
122398lysine decarboxylase-4.1.1.18
122398ornithine decarboxylase-4.1.1.17
122398urease+3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase lipase (C 8)+
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
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
18597---+--+-+----------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
18597+-++---+-+---+++---
122398+++-+----++---++----

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
18597----+------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
122398++----------------+------------+------------------+--+----++---------------+--+---------+--+----+-+

Isolation, sampling and environmental information

isolation

@refsample typehost species
9566blueback salmon
67770Blueback salmon (Oncorhynchus nerka)Oncorhynchus nerka

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Host#Fishes#Salmonidae

taxonmaps

  • @ref: 69479
  • File name: preview.99_1437.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_578;97_676;98_786;99_1437&stattab=map
  • Last taxonomy: Nocardia
  • 16S sequence: Z46750
  • Sequence Identity:
  • Total samples: 545
  • soil counts: 106
  • aquatic counts: 144
  • animal counts: 225
  • plant counts: 70

Safety information

risk assessment

@refpathogenicity animalbiosafety levelbiosafety level comment
9566yes1Risk group (German classification)
185972German classification
1223982Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Nocardia salmonicida strain DSM 40472 16S ribosomal RNA gene, complete sequenceAF4300501494ena53431
20218Nocardia salmonicida strain DSM 40472 note copy 1 16S-23S ribosomal RNA intergenic spacer, complete sequenceAF536472335ena53431
20218Nocardia salmonicida strain DSM 40472 note copy 2 16S-23S ribosomal RNA intergenic spacer, complete sequenceAF536473329ena53431
20218Nocardia salmonicida strain JCM 4826 16S ribosomal RNA gene, partial sequenceAY756560606ena53431
20218Nocardia salmonicida gene for 16S ribosomal RNA, partial sequence, strain: JCM 4826D44392120ena53431
20218N.salmonicida gene for 16S ribosomal RNAZ467501474ena53431

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardia salmonicida NBRC 133931210085.4wgspatric1210085
66792Nocardia salmonicida NBRC 133932731957743draftimg1210085
67770Nocardia salmonicida NBRC 13393GCA_001613085contigncbi1210085

GC content

@refGC-contentmethod
956666.9high performance liquid chromatography (HPLC)
6777066fluorimetric

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes97no
motileno92.956no
gram-positiveyes85.24no
anaerobicno99.33no
aerobicyes88.274no
halophileno89.665no
spore-formingyes80.105no
glucose-utilyes90.998yes
flagellatedno97.656no
thermophileno99.361yes
glucose-fermentno90.696yes

External links

@ref: 9566

culture collection no.: DSM 40472, ATCC 27463, CBS 694.72, IFO 13393, ISP 5472, JCM 4826, NBRC 13393, NRRL B-2778, RIA 1354, BCRC 12441, CGMCC 4.1136, CGMCC 4.1502, CIP 104517, IFM 10710, IMSNU 21183, KCTC 9372, NRRL B-12385

straininfo link

  • @ref: 79995
  • straininfo: 264375

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny10319509Nocardia salmonicida nom. rev., a fish pathogen.Isik K, Chun J, Hah YC, Goodfellow MInt J Syst Bacteriol10.1099/00207713-49-2-8331999Animals, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fish Diseases/*microbiology, Genes, rRNA, Molecular Sequence Data, Nocardia/*classification/genetics/isolation & purification/physiology, Nocardia Infections/microbiology/*veterinary, Oncorhynchus/*microbiology, Phenotype, RNA, Ribosomal, 16S/geneticsGenetics
Phylogeny26868112Nocardia camponoti sp. nov., an actinomycete isolated from the head of an ant (Camponotus japonicas Mayr).Liu C, Guan X, Li Y, Li W, Ye L, Kong X, Song J, Wang X, Xiang WInt J Syst Evol Microbiol10.1099/ijsem.0.0009632016Animals, Ants/*microbiology, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Molecular Sequence Data, Nocardia/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny27510998Nocardia lasii sp. nov., a novel actinomycete isolated from the cuticle of an ant (Lasius fuliginosus L).Liu C, Bai L, Ye L, Zhao J, Yan K, Xiang W, Wang XAntonie Van Leeuwenhoek10.1007/s10482-016-0753-y2016Animals, Ants/*microbiology, DNA, Bacterial, Molecular Typing, Nocardia/classification/*isolation & purification, Phylogeny, RNA, Ribosomal, 16S/geneticsEnzymology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9566Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40472)https://www.dsmz.de/collection/catalogue/details/culture/DSM-40472
18597Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM40472.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
35686Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16435
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/
68368Automatically annotated from API 20E
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
79995Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID264375.1StrainInfo: A central database for resolving microbial strain identifiers
122398Curators of the CIPCollection of Institut Pasteur (CIP 104517)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104517