Strain identifier

BacDive ID: 11131

Type strain: Yes

Species: Nocardioides daphniae

Strain Designation: D287

Strain history: CCM 7403 <-- DSM 18664 <-- E. M. Tóth D287.

NCBI tax ID(s): 402297 (species)

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General

@ref: 7645

BacDive-ID: 11131

DSM-Number: 18664

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

description: Nocardioides daphniae D287 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from Daphnia cucullata.

NCBI tax id

  • NCBI tax id: 402297
  • Matching level: species

strain history

@refhistory
7645<- E.M. Toth; strain D287
67770CCM 7403 <-- DSM 18664 <-- E. M. Tóth D287.

doi: 10.13145/bacdive11131.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Propionibacteriales
  • family: Nocardioidaceae
  • genus: Nocardioides
  • species: Nocardioides daphniae
  • full scientific name: Nocardioides daphniae Tóth et al. 2008

@ref: 7645

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardioidaceae

genus: Nocardioides

species: Nocardioides daphniae

full scientific name: Nocardioides daphniae Tóth et al. 2008

strain designation: D287

type strain: yes

Morphology

cell morphology

  • @ref: 32319
  • gram stain: positive
  • cell length: 1.7 µm
  • cell width: 0.9 µm
  • cell shape: rod-shaped
  • motility: no

colony morphology

@refcolony colorincubation periodmedium used
19770Zinc yellow (1018)10-14 daysISP 2
19770Zinc yellow (1018)10-14 daysISP 3
19770Zinc yellow (1018)10-14 daysISP 4
19770Zinc yellow (1018)10-14 daysISP 5
19770Zinc yellow (1018)10-14 daysISP 6
19770Zinc yellow (1018)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
19770noISP 2
19770noISP 3
19770noISP 4
19770noISP 5
19770noISP 6
19770noISP 7

pigmentation

  • @ref: 32319
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7645TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
19770ISP 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
19770ISP 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:
19770ISP 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
19770ISP 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
19770ISP 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
19770ISP 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

culture temp

@refgrowthtypetemperaturerange
7645positivegrowth28mesophilic
19770positiveoptimum28mesophilic
32319positivegrowth04-38
32319positiveoptimum28mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
32319positivegrowth5.5-10.5alkaliphile
32319positiveoptimum8

Physiology and metabolism

oxygen tolerance

  • @ref: 32319
  • oxygen tolerance: aerobe

spore formation

  • @ref: 32319
  • spore formation: no

halophily

  • @ref: 32319
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-5 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
32319620642,3-butanediol+carbon source
3231930089acetate+carbon source
32319286442-oxopentanoate+carbon source
3231928757fructose+carbon source
3231917234glucose+carbon source
3231917596inosine+carbon source
3231924996lactate+carbon source
3231925115malate+carbon source
3231937684mannose+carbon source
3231937657methyl D-glucoside+carbon source
3231951850methyl pyruvate+carbon source
3231915361pyruvate+carbon source
3231933942ribose+carbon source
3231930911sorbitol+carbon source
3231917748thymidine+carbon source
3231927082trehalose+carbon source
3231916704uridine+carbon source
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

enzymes

@refvalueactivityec
32319catalase+1.11.1.6
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
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)+
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin+3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase-
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
19770-+++--+--++------+-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
19770+++++--+-+----+----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinenthost species
7645Daphnia cucullataLake BalatonHungaryHUNEurope
67770Water flea Daphnia cucullata originating from Lake BalatonHungaryHUNEuropeDaphnia cucullata

isolation source categories

  • Cat1: #Host
  • Cat2: #Arthropoda
  • Cat3: #Crustacea

taxonmaps

  • @ref: 69479
  • File name: preview.99_123066.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_142;96_37073;97_47122;98_82778;99_123066&stattab=map
  • Last taxonomy: Nocardioides daphniae subclade
  • 16S sequence: AM398438
  • Sequence Identity:
  • Total samples: 1087
  • soil counts: 571
  • aquatic counts: 150
  • animal counts: 280
  • plant counts: 86

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
76451Risk group (German classification)
197701Risk group (German classification)

Sequence information

16S sequences

  • @ref: 7645
  • description: Nocardioides daphniae partial 16S RNA gene, type strain D287T
  • accession: AM398438
  • length: 1371
  • database: ena
  • NCBI tax ID: 402297

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardioides daphniae CCM 7403GCA_014635145scaffoldncbi402297
66792Nocardioides daphniae JCM 16608GCA_004777465completencbi402297
66792Nocardioides daphniae strain CCM 7403402297.4wgspatric402297
66792Nocardioides daphniae strain JCM 16608402297.3completepatric402297
66792Nocardioides daphniae JCM 166082841404167completeimg402297

GC content

@refGC-contentmethod
764569.9high performance liquid chromatography (HPLC)
3231969.9

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno93.913yes
gram-positiveyes88.715yes
anaerobicno98.36yes
aerobicyes92.432yes
halophileno93.951no
spore-formingno88.322yes
glucose-utilyes84.926yes
thermophileno98.039no
motileno81.977yes
glucose-fermentno88.748yes

External links

@ref: 7645

culture collection no.: DSM 18664, CCM 7403, JCM 16608

straininfo link

  • @ref: 80380
  • straininfo: 408088

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18175687Nocardioides daphniae sp. nov., isolated from Daphnia cucullata (Crustacea: Cladocera).Toth EM, Keki Z, Homonnay ZG, Borsodi AK, Marialigeti K, Schumann PInt J Syst Evol Microbiol10.1099/ijs.0.65305-02008Actinomycetales/*classification/genetics/*isolation & purification/physiology, Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, Daphnia/*microbiology, Genes, rRNA, Hungary, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species SpecificityGenetics
Phylogeny25893957Nocardioides solisilvae sp. nov., isolated from a forest soil.Sultanpuram VR, Mothe T, Mohammed FAntonie Van Leeuwenhoek10.1007/s10482-015-0455-x2015Actinobacteria/*classification/genetics/*isolation & purification/physiology, Aerobiosis, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Forests, India, Molecular Sequence Data, Peptidoglycan/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analysisGenetics
Phylogeny31511125Nocardioides yefusunii sp. nov., isolated from Equus kiang (Tibetan wild ass) faeces.Huang Y, Wang X, Yang J, Lu S, Lai XH, Jin D, Pu J, Huang Y, Ren Z, Zhu W, Meng J, Dong K, Ge Y, Zhou J, Zhang G, Zhang S, Lei W, Liang H, Xu JInt J Syst Evol Microbiol10.1099/ijsem.0.0036742019Actinobacteria/*classification/isolation & purification, Animals, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Equidae/*microbiology, Fatty Acids/chemistry, Feces/*microbiology, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Tibet, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
7645Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18664)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18664
19770Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM18664.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
32319Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2855528776041
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 updates33211880Nucleic Acids Res. 49: D498-D508 2020
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
80380Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID408088.1StrainInfo: A central database for resolving microbial strain identifiers