Strain identifier

BacDive ID: 10749

Type strain: Yes

Species: Nocardia salmonicida subsp. cummidelens

Strain Designation: W30

Strain history: CIP <- 2001, NCIMB <- M. Goodfellow, Newcastle Univ, UK, strain: W30 <- L. Maldonado

NCBI tax ID(s): 2800120 (subspecies)

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General

@ref: 11814

BacDive-ID: 10749

DSM-Number: 44488

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

description: Nocardia salmonicida subsp. cummidelens W30 is an obligate aerobe, spore-forming, mesophilic bacterium that builds an aerial mycelium and was isolated from soil from river.

NCBI tax id

  • NCBI tax id: 2800120
  • Matching level: subspecies

strain history

@refhistory
11814<- M. Goodfellow; W30
67770NCIMB 13760 <-- M. Goodfellow W30.
122660CIP <- 2001, NCIMB <- M. Goodfellow, Newcastle Univ, UK, strain: W30 <- L. Maldonado

doi: 10.13145/bacdive10749.20250331.9.3

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 cummidelens
    20215Nocardia soli

@ref: 11814

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: W30

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
122660positiverod-shapedno
125439positive98.5
125438positive92.205

colony morphology

@refcolony colorincubation periodmedium used
20063Saffron yellow (1017)10-14 daysISP 2
20063Beige (1001)10-14 daysISP 3
20063Beige (1001)10-14 daysISP 4
20063Saffron yellow (1017)10-14 daysISP 5
20063Saffron yellow (1017)10-14 daysISP 6
20063Saffron yellow (1017)10-14 daysISP 7
122660

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
20063yesAerial MyceliumWhiteISP 2
20063noISP 3
20063yesAerial MyceliumISP 4
20063yesAerial MyceliumWhiteISP 5
20063noISP 6
20063yesAerial MyceliumWhiteISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11814GYM 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
20063ISP 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
20063ISP 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:
20063ISP 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
20063ISP 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
20063ISP 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
20063ISP 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
33702MEDIUM 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)
122660CIP Medium 57yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=57

culture temp

@refgrowthtypetemperature
20063positiveoptimum28
11814positivegrowth28
33702positivegrowth30
67770positivegrowth28
122660positivegrowth25-30
122660nogrowth10
122660nogrowth37
122660nogrowth41
122660nogrowth45

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
122660obligate aerobe
125438aerobe90.368
125439obligate aerobe97.9

halophily

@refsaltgrowthtested relationconcentration
122660NaClpositivegrowth0-2 %
122660NaClnogrowth4 %
122660NaClnogrowth6 %
122660NaClnogrowth8 %
122660NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6837928087glycogen-fermentation
6837917992sucrose-fermentation
6837917306maltose-fermentation
6837916899D-mannitol-fermentation
6837916988D-ribose-fermentation
6837917634D-glucose+fermentation
683795291gelatin+hydrolysis
6837916199urea+hydrolysis
683794853esculin+hydrolysis
6837917632nitrate-reduction
1226604853esculin+hydrolysis
122660606565hippurate-hydrolysis
12266017632nitrate+reduction
12266016301nitrite-reduction
12266017632nitrate-respiration
6837917716lactose-fermentation
6837965327D-xylose-fermentation

antibiotic resistance

  • @ref: 122660
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 122660
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12266015688acetoin-
12266017234glucose-

enzymes

@refvalueactivityec
68382alpha-mannosidase-3.2.1.24
68382beta-glucosidase+3.2.1.21
68382alpha-galactosidase-3.2.1.22
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382leucine arylamidase+3.4.11.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
122660oxidase-
122660beta-galactosidase+3.2.1.23
122660alcohol dehydrogenase-1.1.1.1
122660gelatinase-
122660amylase-
122660DNase-
122660caseinase-3.4.21.50
122660catalase+1.11.1.6
122660tween esterase-
122660gamma-glutamyltransferase+2.3.2.2
122660lecithinase-
122660lipase-
122660lysine decarboxylase-4.1.1.18
122660ornithine decarboxylase-4.1.1.17
122660phenylalanine ammonia-lyase-4.3.1.24
122660tryptophan deaminase-
122660urease+3.5.1.5
68379beta-glucosidase+3.2.1.21
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase+3.1.3.1
68382alpha-fucosidase-3.2.1.51
68382beta-glucuronidase-3.2.1.31
68379gelatinase+
68379urease+3.5.1.5
68379N-acetyl-beta-glucosaminidase+3.2.1.52
68379alpha-glucosidase+3.2.1.20
68379beta-galactosidase+3.2.1.23
68379pyrrolidonyl arylamidase-3.4.19.3
68379pyrazinamidase-3.5.1.B15

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
20063---+-+++++++-------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
20063++++++---++-+-+++--
122660-++-+----+-----+----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
122660------------------+-------------------------------------------+--+--------------------+------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcontinentcountryorigin.country
11814soil from riverMedmenhamEurope
67770Untreated River Thames waterMedmenhamEuropeUnited KingdomGBR
122660Environment, Soil from riverMedmenhamEuropeUnited KingdomGBR

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#River (Creek)
#Environmental#Terrestrial#Soil

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: AF430051
  • 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
118141Risk group (German classification)
200631German classification
1226602Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Nocardia salmonicida strain DSM 44488 16S ribosomal RNA gene, complete sequenceAF4300511494nuccore134962
20218Nocardia soli strain DSM 44488 16S ribosomal RNA gene, partial sequenceAY756562606nuccore134962
11814Nocardia soli 16S ribosomal RNA gene, partial sequenceAF2772231466nuccore53431

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardia soli NBRC 1003761210097.4wgspatric1210097
66792Nocardia salmonicida NBRC 1003762731957749draftimg1210097
67770Nocardia salmonicida NBRC 100376GCA_001613285contigncbi1210097

GC content

  • @ref: 67770
  • GC-content: 67
  • method: genome sequence analysis

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes92.205no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no97.42yes
125438spore-formingspore-formingAbility to form endo- or exosporesyes60.748no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes90.368yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno97.4yes
125438motile2+flagellatedAbility to perform flagellated movementno88.5no
125439BacteriaNetspore_formationAbility to form endo- or exosporesyes72.1
125439BacteriaNetmotilityAbility to perform movementno86.1
125439BacteriaNetgram_stainReaction to gram-stainingpositive98.5
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe97.9

External links

@ref: 11814

culture collection no.: DSM 44488, NBRC 100376, NCIMB 13760, JCM 11441, CCUG 46119, CCUG 46433, CIP 107223, IFM 10177

straininfo link

  • @ref: 80017
  • straininfo: 50650

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
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
11814Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44488)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44488
20063Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44488.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
33702Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/4635
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
80017Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID50650.1StrainInfo: A central database for resolving microbial strain identifiers
122660Curators of the CIPCollection of Institut Pasteur (CIP 107223)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107223
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1