Strain identifier

BacDive ID: 11121

Type strain: Yes

Species: Nocardioides furvisabuli

Strain Designation: SBS-26

Strain history: CIP <- 2007, JCM <- 2006, S.D. Lee, Cheju Nat. Univ., Jeju, Korea: strain SBS-26

NCBI tax ID(s): 375542 (species)

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General

@ref: 7474

BacDive-ID: 11121

DSM-Number: 18445

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

description: Nocardioides furvisabuli SBS-26 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from beach, black sand.

NCBI tax id

  • NCBI tax id: 375542
  • Matching level: species

strain history

@refhistory
7474<- S. D. Lee; SBS-26
67770S. D. Lee SBS-26.
119498CIP <- 2007, JCM <- 2006, S.D. Lee, Cheju Nat. Univ., Jeju, Korea: strain SBS-26

doi: 10.13145/bacdive11121.20250331.9.3

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 furvisabuli
  • full scientific name: Nocardioides furvisabuli Lee 2007

@ref: 7474

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardioidaceae

genus: Nocardioides

species: Nocardioides furvisabuli

full scientific name: Nocardioides furvisabuli Lee 2007

strain designation: SBS-26

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
31829positive0.9 µm0.45 µmrod-shapedyes
119498positiverod-shapedno

pigmentation

  • @ref: 31829
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7474R2A 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
37750MEDIUM 112 - for JanibacteryesDistilled water make up to (1000.000 ml);Magnesium sulphate heptahydrate (1.000 g);Agar (20.000 g);Yeast extract (5.000 g);Peptone (10.000 g);Tween 80 (50.000 mg);Glycerol (2.000 g);Malt extract (5.000 g);Beef extract (2.000 g);Casamino acids (5.000 g);Ca
119498CIP Medium 112yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=112

culture temp

@refgrowthtypetemperature
7474positivegrowth28
31829positivegrowth4-37
31829positiveoptimum30
37750positivegrowth30
67770positivegrowth28

culture pH

@refabilitytypepHPH range
31829positivegrowth5.1-10.1alkaliphile
31829positiveoptimum7.1

Physiology and metabolism

oxygen tolerance

  • @ref: 31829
  • oxygen tolerance: aerobe

spore formation

  • @ref: 31829
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
31829NaClpositivegrowth0-6 %
31829NaClpositiveoptimum3 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3182930089acetate+carbon source
3182915963ribitol+carbon source
3182922599arabinose+carbon source
3182917057cellobiose+carbon source
3182916947citrate+carbon source
3182915740formate+carbon source
3182928757fructose+carbon source
3182928260galactose+carbon source
3182917234glucose+carbon source
3182917754glycerol+carbon source
3182917716lactose+carbon source
3182925115malate+carbon source
3182917306maltose+carbon source
3182929864mannitol+carbon source
3182937684mannose+carbon source
3182917268myo-inositol+carbon source
3182916634raffinose+carbon source
3182930911sorbitol+carbon source
3182930031succinate+carbon source
3182927082trehalose+carbon source
3182918222xylose+carbon source
3182917632nitrate+reduction
11949817632nitrate+reduction
11949816301nitrite-reduction
68371Potassium 5-ketogluconate-builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837117754glycerol-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose-builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose-builds acid from
6837117992sucrose-builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117306maltose-builds acid from
6837117057cellobiose-builds acid from
6837117814salicin-builds acid from
683714853esculin+builds acid from
6837159640N-acetylglucosamine-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose-builds acid from
6837115824D-fructose-builds acid from
6837117634D-glucose-builds acid from
6837112936D-galactose-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837116988D-ribose-builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from

metabolite production

  • @ref: 119498
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
31829alkaline phosphatase+3.1.3.1
31829alpha-galactosidase+3.2.1.22
31829catalase+1.11.1.6
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382beta-glucosidase+3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382alpha-galactosidase+3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
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
68382valine arylamidase+
68382lipase (C 14)-
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
119498oxidase-
119498catalase+1.11.1.6
119498urease-3.5.1.5
68382beta-galactosidase+3.2.1.23
68382esterase lipase (C 8)+

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
119498-+++-+++--++++-++---

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
119498------------------------+------------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7474beach, black sandJejuRepublic of KoreaKORAsia
67770Black sand around Samyang BeachJeju IslandRepublic of KoreaKORAsia
119498Environment, Black sandSamyang beach, Jeju IslandRepublic of KoreaKORAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_60603.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_142;96_2445;97_2980;98_12269;99_60603&stattab=map
  • Last taxonomy: Nocardioides
  • 16S sequence: DQ411542
  • Sequence Identity:
  • Total samples: 306
  • soil counts: 65
  • aquatic counts: 100
  • animal counts: 125
  • plant counts: 16

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
74741Risk group (German classification)
1194981Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7474
  • description: Nocardioides furvisabuli strain SBS-26 16S ribosomal RNA gene, partial sequence
  • accession: DQ411542
  • length: 1398
  • database: nuccore
  • NCBI tax ID: 375542

Genome sequences

  • @ref: 66792
  • description: Nocardioides furvisabuli JCM 13813
  • accession: GCA_021083185
  • assembly level: contig
  • database: ncbi
  • NCBI tax ID: 375542

GC content

@refGC-contentmethod
747469.1
6777069.1high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes88.505no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no97.273yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes88.925no
125438spore-formingspore-formingAbility to form endo- or exosporesno63.069yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno95.486no
125438motile2+flagellatedAbility to perform flagellated movementno72.6no

External links

@ref: 7474

culture collection no.: DSM 18445, JCM 13813, NRRL B-24465, CIP 109516

straininfo link

  • @ref: 80370
  • straininfo: 297273

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17220437Nocardioides furvisabuli sp. nov., isolated from black sand.Lee SDInt J Syst Evol Microbiol10.1099/ijs.0.64444-02007Actinomycetales/chemistry/*classification/genetics/isolation & purification, Bacterial Typing Techniques, DNA, Bacterial/analysis, Genes, rRNA, Geologic Sediments/*microbiology, Korea, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNAGenetics
Phylogeny18175721Nocardioides hwasunensis sp. nov.Lee SD, Lee DW, Kim JSInt J Syst Evol Microbiol10.1099/ijs.0.65015-02008Actinomycetales/*classification/genetics/isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, DNA Fingerprinting/methods, DNA, Bacterial/analysis, Genes, rRNA, Korea, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S, Seawater/*microbiology, Sequence Analysis, DNA, Species SpecificityGenetics
Phylogeny27654931Nocardioides flavus sp. nov., isolated from marine sediment.Wang S, Zhou Y, Zhang GInt J Syst Evol Microbiol10.1099/ijsem.0.0015072016Actinomycetales/*classification/genetics/isolation & purification, Bacteria, Aerobic/classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Pacific Ocean, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/chemistryEnzymology
Phylogeny27902315Nocardioides cavernae sp. nov., an actinobacterium isolated from a karst cave.Han MX, Fang BZ, Tian Y, Zhang WQ, Jiao JY, Liu L, Zhang ZT, Xiao M, Wei DQ, Li WJInt J Syst Evol Microbiol10.1099/ijsem.0.0016762017Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Caves/*microbiology, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny29372423Nocardioides astragali sp. nov., isolated from a nodule of wild Astragalus chrysopterus in northwestern China.Xu L, Zhang Y, Li C, Wang X, Liu J, Friman VPAntonie Van Leeuwenhoek10.1007/s10482-018-1020-12018Actinobacteria/classification/genetics/*isolation & purification/metabolism, Astragalus Plant/*microbiology, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry/metabolism, China, DNA, Bacterial/genetics, Fatty Acids/chemistry/metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, Root Nodules, Plant/*microbiology, Soil MicrobiologyMetabolism
Phylogeny34846610Nocardioides lacusdianchii sp. nov., an attached bacterium of Microcystis aeruginosa.Xiao Y, Wang L, Wang X, Chen M, Chen J, Tian BY, Zhang BHAntonie Van Leeuwenhoek10.1007/s10482-021-01690-92021DNA, Bacterial/genetics, *Microcystis/genetics, Nocardioides, Phylogeny, RNA, Ribosomal, 16S/genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7474Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18445)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18445
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
31829Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2809528776041
37750Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7268
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/
68371Automatically annotated from API 50CH acid
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
80370Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID297273.1StrainInfo: A central database for resolving microbial strain identifiers
119498Curators of the CIPCollection of Institut Pasteur (CIP 109516)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109516
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