Strain identifier

BacDive ID: 132635

Type strain: Yes

Species: Nocardioides baekrokdamisoli

Strain Designation: B2-12

Strain history: <- Jung-Sook Lee, KRIBB

NCBI tax ID(s): 1804624 (species)

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General

@ref: 24424

BacDive-ID: 132635

DSM-Number: 100725

keywords: genome sequence, 16S sequence, Bacteria, aerobe, psychrophilic, Gram-positive, coccus-shaped, colony-forming

description: Nocardioides baekrokdamisoli B2-12 is an aerobe, psychrophilic, Gram-positive bacterium that forms circular colonies and was isolated from sediment soil of a crater lake.

NCBI tax id

  • NCBI tax id: 1804624
  • Matching level: species

strain history

@refhistory
24424<- J. S. Lee, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Republik of Korea; B2-12
67771<- Jung-Sook Lee, KRIBB

doi: 10.13145/bacdive132635.20230509.8.1

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 baekrokdamisoli
  • full scientific name: Nocardioides baekrokdamisoli Lee et al. 2016

@ref: 24424

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardioidaceae

genus: Nocardioides

species: Nocardioides baekrokdamisoli

full scientific name: Nocardioides baekrokdamisoli Lee et al. 2016

strain designation: B2-12

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
24903positive0.5-0.6 µm0.4-0.5 µmcoccus-shapedno
24903rod-shaped
69480positive100
69480no94.237

colony morphology

  • @ref: 24903
  • colony color: creamy white
  • colony shape: circular
  • medium used: R2A agar (Reasoner's 2A agar)

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
244241/10 R2A MEDIUM (DSMZ Medium 1578)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium1578.pdf
24903Reasoner's 2A agar (R2A)yes
24424HETEROTROPHIC MEDIUM H3P (DSMZ Medium 428)yeshttps://mediadive.dsmz.de/medium/428Name: HETEROTROPHIC MEDIUM H3P (DSMZ Medium 428) Composition: Agar 19.802 g/l Na2HPO4 x 2 H2O 2.87129 g/l KH2PO4 2.27723 g/l D-Glucose 1.9802 g/l Na-lactate 0.990099 g/l Na-pyruvate 0.990099 g/l D-Mannitol 0.990099 g/l DL-Malate 0.990098 g/l Na-acetate 0.990098 g/l Yeast extract 0.990098 g/l NH4Cl 0.990098 g/l Disodium succinate 0.990098 g/l MgSO4 x 7 H2O 0.495049 g/l Ferric ammonium citrate 0.049505 g/l CaCl2 x 2 H2O 0.00990098 g/l NaVO3 x H2O 0.00495049 g/l Thiamine-HCl x 2 H2O 0.00247525 g/l Nicotinic acid 0.00247525 g/l Pyridoxine hydrochloride 0.00247525 g/l Calcium pantothenate 0.00247525 g/l H3BO3 0.00148515 g/l CoCl2 x 6 H2O 0.000990099 g/l Riboflavin 0.00049505 g/l ZnSO4 x 7 H2O 0.00049505 g/l MnCl2 x 4 H2O 0.000148515 g/l Na2MoO4 x 2 H2O 0.000148515 g/l NiCl2 x 6 H2O 9.90099e-05 g/l CuCl2 x 2 H2O 4.95049e-05 g/l Vitamin B12 4.95049e-05 g/l Folic acid 9.90099e-06 g/l Biotin 4.9505e-06 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
24903positivegrowth15psychrophilic
24903positivegrowth15.0-30.0
24903positiveoptimum25mesophilic
67771positivegrowth25mesophilic
24424positivegrowth25mesophilic

culture pH

@refabilitytypepH
24903positivegrowth6.0-8.0
24903positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
24903aerobe
67771aerobe

spore formation

@refspore formationconfidence
24903no
69481no100
69480no99.891

halophily

@refsalttested relationconcentrationgrowth
24903NaCloptimum0 %
24903NaClgrowth<1.0 %(w/v)positive

murein

  • @ref: 24903
  • murein short key: A41.01
  • type: A3gamma LL-Dpm-Gly

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
24903168082-dehydro-D-gluconate-builds acid from
24903581435-dehydro-D-gluconate-builds acid from
2490317128adipate-assimilation
2490322599arabinose-assimilation
2490315963ribitol-builds acid from
2490317108D-arabinose-builds acid from
2490318333D-arabitol-builds acid from
2490328847D-fucose-builds acid from
2490317634D-glucose-assimilation
2490317716lactose-builds acid from
2490362318D-lyxose-builds acid from
2490316024D-mannose-assimilation
249036731melezitose-builds acid from
2490328053melibiose-builds acid from
2490316634raffinose-builds acid from
2490317924D-sorbitol-builds acid from
2490332528turanose-builds acid from
2490365327D-xylose-builds acid from
2490327689decanoate-assimilation
2490317113erythritol-builds acid from
2490316813galactitol-builds acid from
249035291gelatin-hydrolysis
2490324265gluconate-builds acid from
2490317234glucose-fermentation
2490317268myo-inositol-builds acid from
2490315443inulin-builds acid from
2490318403L-arabitol-builds acid from
2490318287L-fucose-builds acid from
2490362345L-rhamnose-builds acid from
2490317266L-sorbose-builds acid from
2490325115malate-assimilation
2490317306maltose-assimilation
2490329864mannitol-assimilation
24903320061methyl alpha-D-glucopyranoside-builds acid from
2490343943methyl alpha-D-mannoside-builds acid from
2490374863methyl beta-D-xylopyranoside-builds acid from
24903506227N-acetylglucosamine-assimilation
2490317632nitrate-reduction
2490318401phenylacetate-assimilation
2490332032potassium gluconate-assimilation
2490353258sodium citrate-assimilation
2490317151xylitol-builds acid from
2490327613amygdalin+builds acid from
2490318305arbutin+builds acid from
2490317057cellobiose+builds acid from
2490315824D-fructose+builds acid from
2490312936D-galactose+builds acid from
2490317634D-glucose+builds acid from
2490316899D-mannitol+builds acid from
2490316024D-mannose+builds acid from
2490316988D-ribose+builds acid from
2490316443D-tagatose+builds acid from
2490316551D-trehalose+builds acid from
249034853esculin+hydrolysis
24903esculin ferric citrate+builds acid from
2490328066gentiobiose+builds acid from
2490317754glycerol+builds acid from
2490328087glycogen+builds acid from
2490330849L-arabinose+builds acid from
2490365328L-xylose+builds acid from
2490317306maltose+builds acid from
24903506227N-acetylglucosamine+builds acid from
2490317814salicin+builds acid from
2490328017starch+builds acid from
2490317992sucrose+builds acid from

metabolite production

  • @ref: 24903
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
24903acid phosphatase+3.1.3.2
24903alkaline phosphatase-3.1.3.1
24903alpha-chymotrypsin-3.4.21.1
24903alpha-fucosidase-3.2.1.51
24903alpha-galactosidase-3.2.1.22
24903alpha-glucosidase-3.2.1.20
24903alpha-mannosidase-3.2.1.24
24903arginine dihydrolase-3.5.3.6
24903beta-galactosidase-3.2.1.23
24903beta-glucosidase-3.2.1.21
24903beta-glucuronidase-3.2.1.31
24903catalase-1.11.1.6
24903cystine arylamidase-3.4.11.3
24903cytochrome oxidase-1.9.3.1
24903esterase (C 4)+
24903esterase lipase (C 8)+
24903leucine arylamidase+3.4.11.1
24903lipase (C 14)-
24903N-acetyl-beta-glucosaminidase-3.2.1.52
24903naphthol-AS-BI-phosphohydrolase+
24903trypsin-3.4.21.4
24903urease-3.5.1.5
24903valine arylamidase+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentenrichment cultureenrichment culture durationenrichment culture temperature
24424sediment soil of a crater lakeJeju island, Hallasan volcano, Baekrodam lakeRepublic of KoreaKORAsia
24903R2A agar (Reasoner's 2A agar) (BD)28 days25
67771From soilJejuRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Lake (large)
#Environmental#Aquatic#Sediment
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_159105.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_142;96_16080;97_19727;98_24656;99_159105&stattab=map
  • Last taxonomy: Nocardioides baekrokdamisoli
  • 16S sequence: LC127008
  • Sequence Identity:
  • Total samples: 154
  • soil counts: 114
  • aquatic counts: 2
  • animal counts: 20
  • plant counts: 18

Safety information

risk assessment

  • @ref: 24424
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 24424
  • description: Nocardioides baekrokdamisoli gene for 16S rRNA, partial sequence
  • accession: LC127008
  • length: 1437
  • database: ena
  • NCBI tax ID: 1804624

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardioides baekrokdamisoli KCTC 39748GCA_003945325completencbi1804624
66792Nocardioides baekrokdamisoli strain KCTC 397481804624.3completepatric1804624
66792Nocardioides baekrokdamisoli KCTC 397482843215260completeimg1804624

GC content

@refGC-contentmethod
2490367high performance liquid chromatography (HPLC)
2442467.0high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno96.137yes
flagellatedno98.593yes
gram-positiveyes92.977yes
anaerobicno97.652yes
aerobicyes91.21yes
halophileno94.656yes
spore-formingno94.642no
glucose-utilyes59.098yes
thermophileno97.956no
glucose-fermentno89.556no

External links

@ref: 24424

culture collection no.: DSM 100725, KCTC 39748, NRRL B-65313

straininfo link

  • @ref: 90949
  • straininfo: 405510

literature

  • topic: Phylogeny
  • Pubmed-ID: 27470265
  • title: Nocardioides baekrokdamisoli sp. nov., isolated from soil of a crater lake.
  • authors: Lee KC, Kim KK, Kim JS, Kim DS, Ko SH, Yang SH, Shin YK, Lee JS
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001340
  • year: 2016
  • mesh: Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Lakes/*microbiology, Nucleic Acid Hybridization, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
24424Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-100725Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100725)
24903K. C. K. Lee, Kwang Kyu,Kim, Jong-Shik,Kim, Dae-Shin,Ko, Suk-Hyung,Yang, Seung-Hoon,Shin, Yong Kook,Lee, Jung-SookNocardioides baekrokdamisoli sp. nov., isolated from soil of a crater lake10.1099/ijsem.0.001340IJSEM 66: 4231-4235 201627470265
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
90949Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID405510.1