Strain identifier

BacDive ID: 11125

Type strain: Yes

Species: Nocardioides marinisabuli

Strain Designation: SBS-12

Strain history: <- Soon Dong Lee, SBS-12

NCBI tax ID(s): 419476 (species)

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General

@ref: 7723

BacDive-ID: 11125

DSM-Number: 18965

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

description: Nocardioides marinisabuli SBS-12 is a mesophilic, Gram-positive, rod-shaped bacterium that was isolated from beach sand.

NCBI tax id

  • NCBI tax id: 419476
  • Matching level: species

strain history

  • @ref: 7723
  • history: <- Soon Dong Lee, SBS-12

doi: 10.13145/bacdive11125.20230509.8.1

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 marinisabuli
  • full scientific name: Nocardioides marinisabuli Lee et al. 2007

@ref: 7723

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardioidaceae

genus: Nocardioides

species: Nocardioides marinisabuli

full scientific name: Nocardioides marinisabuli Lee et al. 2007

strain designation: SBS-12

type strain: yes

Morphology

cell morphology

  • @ref: 32206
  • gram stain: positive
  • cell length: 1.75 µm
  • cell width: 0.7 µm
  • cell shape: rod-shaped
  • motility: no

colony morphology

@refcolony colorincubation periodmedium used
19774Beige (1001)10-14 daysISP 3
19774Lemon yellow (1012)10-14 daysISP 4
1977410-14 daysISP 5
1977410-14 daysISP 6
19774Beige (1001)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
19774noISP 3
19774noISP 4
19774noISP 5
19774noISP 6
19774noIPS 7

pigmentation

  • @ref: 32206
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7723R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
19774ISP 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:
19774ISP 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
19774ISP 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
19774ISP 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
19774ISP 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
7723BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
7723positivegrowth28mesophilic
19774positiveoptimum28mesophilic
32206positivegrowth04-40
32206positiveoptimum22psychrophilic

culture pH

@refabilitytypepHPH range
32206positivegrowth5.1-12.1alkaliphile
32206positiveoptimum7.6

Physiology and metabolism

spore formation

  • @ref: 32206
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
32206NaClpositivegrowth0-8 %
32206NaClpositiveoptimum4 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3220616947citrate+carbon source
3220628757fructose+carbon source
3220628260galactose+carbon source
3220624265gluconate+carbon source
3220617306maltose+carbon source
3220629864mannitol+carbon source
3220627082trehalose+carbon source
3220618222xylose+carbon source
322064853esculin+hydrolysis
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
32206alkaline phosphatase+3.1.3.1
32206catalase+1.11.1.6
68379gelatinase+
68379urease-3.5.1.5
68379beta-glucosidase-3.2.1.21
68379N-acetyl-beta-glucosaminidase-3.2.1.52
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
19774--++--+/----+--------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
19774+++-++---++---+----

Isolation, sampling and environmental information

isolation

  • @ref: 7723
  • sample type: beach sand
  • geographic location: Jeju
  • country: Republic of Korea
  • origin.country: KOR
  • continent: Asia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Coast
#Environmental#Terrestrial#Sandy

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
77231Risk group (German classification)
197741Risk group (German classification)

Sequence information

16S sequences

  • @ref: 7723
  • description: Nocardioides marinisabuli partial 16S rRNA gene, strain SBS-12T
  • accession: AM422448
  • length: 1415
  • database: ena
  • NCBI tax ID: 419476

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardioides marinisabuli DSM 18965GCA_013409965contigncbi419476
66792Nocardioides marinisabuli DSM 18965GCA_013466785completencbi419476
66792Nocardioides marinisabuli strain DSM 18965419476.3wgspatric419476
66792Nocardioides marinisabuli strain DSM 18965419476.4completepatric419476
66792Nocardioides marinisabuli DSM 189652844814621draftimg419476

GC content

  • @ref: 7723
  • GC-content: 73.1

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno96.137no
flagellatedno98.382yes
gram-positiveyes92.949no
anaerobicno98.334no
aerobicyes91.764no
halophileno78.7no
spore-formingno87.981no
thermophileno97.374yes
glucose-utilyes90.62no
glucose-fermentno90.643yes

External links

@ref: 7723

culture collection no.: DSM 18965, JBRI 2003, KCCM 42681

straininfo link

  • @ref: 80374
  • straininfo: 402831

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18048757Nocardioides marinisabuli sp. nov., a novel actinobacterium isolated from beach sand.Lee DW, Hyun CG, Lee SDInt J Syst Evol Microbiol10.1099/ijs.0.65127-02007Actinomycetales/chemistry/*classification/genetics/*isolation & purification, Bacterial Typing Techniques, Base Composition, Catalase/analysis, Cell Wall/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Genes, rRNA, Geologic Sediments/*microbiology, Korea, Locomotion/physiology, Molecular Sequence Data, Oxidoreductases/analysis, Peptidoglycan/chemistry, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Silicon Dioxide, Vitamin K 2/analysisEnzymology
Phylogeny18768604Nocardioides salarius sp. nov., isolated from seawater enriched with zooplankton.Kim HM, Choi DH, Hwang CY, Cho BCInt J Syst Evol Microbiol10.1099/ijs.0.65569-02008Actinomycetales/*classification/genetics/*isolation & purification/physiology, Aerobiosis, Animals, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Genes, rRNA, Hydrogen-Ion Concentration, Locomotion, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Quinones/analysis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Sodium Chloride/metabolism, Temperature, Zooplankton/*microbiologyGenetics
Phylogeny18984703Nocardioides dokdonensis sp. nov., an actinomycete isolated from sand sediment.Park SC, Baik KS, Kim MS, Chun J, Seong CNInt J Syst Evol Microbiol10.1099/ijs.0.65835-02008Actinomycetales/*classification/genetics/isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Geologic Sediments/*microbiology, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Silicon Dioxide, Species SpecificityGenetics
Phylogeny19126721Nocardioides basaltis sp. nov., isolated from black beach sand.Kim KH, Roh SW, Chang HW, Nam YD, Yoon JH, Jeon CO, Oh HM, Bae JWInt J Syst Evol Microbiol10.1099/ijs.0.65785-02009Actinomycetales/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Geologic Sediments/*microbiology, Korea, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, *Silicon Dioxide, Species SpecificityPhenotype
Phylogeny22228655Nocardioides lianchengensis sp. nov., an actinomycete isolated from soil.Zhang J, Ma Y, Yu HInt J Syst Evol Microbiol10.1099/ijs.0.036723-02012Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analysisGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7723Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18965)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18965
19774Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM18965.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
32206Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2844828776041
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)
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
80374Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID402831.1StrainInfo: A central database for resolving microbial strain identifiers