Strain identifier

BacDive ID: 10752

Type strain: Yes

Species: Nocardia salmonicida subsp. cummidelens

Strain Designation: 44691, R89

Strain history: CIP <- 2001, NCIMB <- M. Goodfellow, Newcastle Univ, UK, strain: R89

NCBI tax ID(s): 53431 (species)

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General

@ref: 11816

BacDive-ID: 10752

DSM-Number: 44490

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

description: Nocardia salmonicida subsp. cummidelens 44691 is an aerobe, spore-forming, mesophilic bacterium that builds an aerial mycelium and was isolated from natural rubber.

NCBI tax id

  • NCBI tax id: 53431
  • Matching level: species

strain history

@refhistory
11816<- M. Goodfellow; R89
67770NCIMB 13758 <-- M. Goodfellow R89.
118812CIP <- 2001, NCIMB <- M. Goodfellow, Newcastle Univ, UK, strain: R89

doi: 10.13145/bacdive10752.20230509.8.1

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 subsp. cummidelens
  • full scientific name: Nocardia salmonicida subsp. cummidelens (Maldonado et al. 2001) Nouioui et al. 2018

  • synonyms

    @refsynonym
    20215Nocardia soli
    20215Nocardia cummidelens

@ref: 11816

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Mycobacteriales

family: Nocardiaceae

genus: Nocardia

species: Nocardia salmonicida subsp. cummidelens

full scientific name: Nocardia salmonicida subsp. cummidelens (Maldonado et al. 2001) Nouioui et al. 2018

strain designation: 44691, R89

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480positive100
118812positiverod-shapedno

colony morphology

@refcolony colorincubation periodmedium usedhemolysis ability
19671Yellow orange10-14 daysISP 2
19671Yellow orange10-14 daysISP 3
19671Yellow orange10-14 daysISP 4
19671Yellow orange10-14 daysISP 5
19671Yellow orange10-14 daysISP 6
19671Yellow orange10-14 daysISP 7
571412 days
1188121

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
19671yesAerial MyceliumWhiteISP 2
19671yesAerial MyceliumWhiteISP 3
19671noISP 4
19671noISP 5
19671noISP 6
19671noISP 7

multimedia

  • @ref: 11816
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_44490.jpg
  • caption: Medium 535 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11816GPHF-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
11816TRYPTICASE 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
11816GYM 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
19671ISP 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
19671ISP 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:
19671ISP 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
19671ISP 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
19671ISP 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
19671ISP 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
33703MEDIUM 57 - for Streptomyces, Nocardioides, Lentzea albidocapillata and Streptoverticillium reticulumyesDistilled water make up to (1000.000 ml);Agar (15.000 g);Glucose (4.000g);Yeast extract (4.000 g);Malt extract (10.000 g);Calcium carbonate (2.000 g)
118812CIP Medium 57yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=57

culture temp

@refgrowthtypetemperaturerange
19671positiveoptimum28mesophilic
11816positivegrowth28mesophilic
33703positivegrowth30mesophilic
57070positivegrowth30mesophilic
57141positivegrowth30mesophilic
67770positivegrowth28mesophilic
118812positivegrowth25-30mesophilic
118812nogrowth10psychrophilic
118812nogrowth37mesophilic
118812nogrowth41thermophilic
118812nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
57070aerobe
57141aerobe
118812obligate aerobe

spore formation

@refspore formationconfidence
69481yes94
69480no91.752

halophily

@refsaltgrowthtested relationconcentration
118812NaClpositivegrowth0-4 %
118812NaClnogrowth6 %
118812NaClnogrowth8 %
118812NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1188124853esculin-hydrolysis
118812606565hippurate+hydrolysis
11881217632nitrate+reduction
11881216301nitrite-reduction
11881217632nitrate-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

antibiotic resistance

  • @ref: 118812
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 118812
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11881215688acetoin-
11881217234glucose-

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
118812oxidase-
118812beta-galactosidase+3.2.1.23
118812alcohol dehydrogenase-1.1.1.1
118812gelatinase-
118812amylase-
118812DNase-
118812caseinase-3.4.21.50
118812catalase+1.11.1.6
118812tween esterase-
118812gamma-glutamyltransferase+2.3.2.2
118812lecithinase-
118812lipase-
118812lysine decarboxylase-4.1.1.18
118812ornithine decarboxylase-4.1.1.17
118812phenylalanine ammonia-lyase-4.3.1.24
118812tryptophan deaminase-
118812urease+3.5.1.5
68382esterase (C 4)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
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

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    57141C16:022.216
    57141C17:01.317
    57141C18:05.618
    57141C16:1 ω7c/C15:0 ISO 2OH23.515.85
    57141C18:1 ω9c18.817.769
    57141C18:2 ω6,9c/C18:0 ANTE17.517.724
    57141C20:2 ω6,9c1.819.735
    57141TBSA 10Me18:0818.392
    57141Unidentified1.318.56
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
19671--++--+-++-------+-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
19671+++-++++-++---++---
118812-+--+----+----++----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
118812+++++-++++++++++++++++++++-----+-+++-----+-------+---------++-+--+-------------++-+---+-+--+----+-+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcontinentcountryorigin.country
11816natural rubberMedmenhamEurope
67770Vulcanized natural rubber pipe rings, River Thames waterMedmenhamEuropeUnited KingdomGBR
118812Vulcanised rubberMedmenhamEuropeUnited KingdomGBR

isolation source categories

  • Cat1: #Host Body Product
  • Cat2: #Plant
  • Cat3: #Plant sap (Flux)

taxonmaps

  • @ref: 69479
  • File name: preview.99_2052.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_578;97_676;98_786;99_2052&stattab=map
  • Last taxonomy: Nocardia
  • 16S sequence: AF277202
  • Sequence Identity:
  • Total samples: 1826
  • soil counts: 648
  • aquatic counts: 183
  • animal counts: 707
  • plant counts: 288

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
118161Risk group (German classification)
196711Risk group (German classification)
1188122Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Nocardia cummidelens strain DSM 44490 16S ribosomal RNA gene, complete sequenceAF4300521494ena165807
20218Nocardia cummidelens strain DSM 44490 16S ribosomal RNA gene, partial sequenceAY756549606ena165807
11816Nocardia cummidelens strain R89 16S ribosomal RNA gene, partial sequenceAF2772021458ena53431

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardia cummidelens NBRC 1003781210073.4wgspatric1210073
66792Nocardia salmonicida NBRC 1003782731957732draftimg1210073
67770Nocardia salmonicida subsp. cummidelens NBRC 100378GCA_001612865contigncbi1210073

GC content

  • @ref: 67770
  • GC-content: 67.1
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes94no
motileno93.652no
gram-positiveyes86.712no
anaerobicno99.254yes
aerobicyes87.179no
halophileno89.416no
spore-formingyes81.257no
thermophileno99.408yes
glucose-utilyes89.244no
flagellatedno98.01no
glucose-fermentno88.884no

External links

@ref: 11816

culture collection no.: DSM 44490, CIP 107225, JCM 11439, NBRC 100378, NCIMB 13758, CCUG 46121, CCUG 46295, IFM 10176

straininfo link

  • @ref: 80020
  • straininfo: 50652

literature

  • topic: Phylogeny
  • Pubmed-ID: 26868112
  • title: Nocardia camponoti sp. nov., an actinomycete isolated from the head of an ant (Camponotus japonicas Mayr).
  • authors: Liu C, Guan X, Li Y, Li W, Ye L, Kong X, Song J, Wang X, Xiang W
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.000963
  • year: 2016
  • mesh: Animals, 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/chemistry
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11816Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44490)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44490
19671Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44490.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
33703Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/4637
57070Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 46121)https://www.ccug.se/strain?id=46121
57141Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 46295)https://www.ccug.se/strain?id=46295
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
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
80020Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID50652.1StrainInfo: A central database for resolving microbial strain identifiers
118812Curators of the CIPCollection of Institut Pasteur (CIP 107225)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107225