Strain identifier

BacDive ID: 11144

Type strain: Yes

Species: Nocardioides sediminis

Strain history: <- CJ Kim, KRIBB

NCBI tax ID(s): 433648 (species)

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General

@ref: 7912

BacDive-ID: 11144

DSM-Number: 19263

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

description: Nocardioides sediminis DSM 19263 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from sediment.

NCBI tax id

  • NCBI tax id: 433648
  • Matching level: species

strain history

@refhistory
7912<- C.-J. Kim <- S. G. Dastager <- Y. J. Ju, Korea Res. Inst. Biosci. & Biotechnol. (KRIBB), Taejon, South Korea; MSL 01
67770DSM 19263 <-- C.-J. Kim <-- S. G. Dastager <-- Y. J. Ju MSL-01.
67771<- CJ Kim, KRIBB

doi: 10.13145/bacdive11144.20230509.8.1

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 sediminis
  • full scientific name: Nocardioides sediminis Dastager et al. 2009

@ref: 7912

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardioidaceae

genus: Nocardioides

species: Nocardioides sediminis

full scientific name: Nocardioides sediminis Dastager et al. 2009

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
28939positive0.9-1.4 µm0.3-0.8 µmrod-shapedyes
67771positive
69480no92.754
69480positive100

Culture and growth conditions

culture medium

  • @ref: 7912
  • name: R2A MEDIUM (DSMZ Medium 830)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/830
  • composition: Name: 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

culture temp

@refgrowthtypetemperaturerange
7912positivegrowth28mesophilic
18614positiveoptimum28mesophilic
28939positivegrowth20-37
28939positiveoptimum28mesophilic
67770positivegrowth28mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepH
28939positivegrowth7.0-7.5
28939positiveoptimum7.25

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
28939aerobe
67771aerobe

spore formation

@refspore formationconfidence
28939no
69481no100
69480no98.807

observation

@refobservation
28939aggregates in clumps
67770quinones: MK-8(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2893917057cellobiose+carbon source
2893928757fructose+carbon source
2893928260galactose+carbon source
2893917234glucose+carbon source
2893917716lactose+carbon source
2893917306maltose+carbon source
2893929864mannitol+carbon source
2893928053melibiose+carbon source
2893917268myo-inositol+carbon source
2893926546rhamnose+carbon source
2893917992sucrose+carbon source
2893927082trehalose+carbon source
2893918222xylose+carbon source
2893917632nitrate+reduction
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
28939alkaline phosphatase+3.1.3.1
28939catalase+1.11.1.6
28939gelatinase+
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
18614---+--+---+------+-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
18614+++-+++--+--+-++---

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7912sedimentBigeum IslandRepublic of KoreaKORAsia
67770Sediment from Bigeum IslandRepublic of KoreaKORAsia
67771From farming fieldBikeum islandRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Sediment
#Environmental#Terrestrial#Sediment

Safety information

risk assessment

  • @ref: 7912
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 7912
  • description: Nocardioides sediminis strain MSL-01 16S ribosomal RNA gene, partial sequence
  • accession: EF466110
  • length: 1437
  • database: ena
  • NCBI tax ID: 433648

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardioides sediminis strain KCTC 19271433648.4wgspatric433648
66792Nocardioides sediminis KCTC 192712866221110draftimg433648
67770Nocardioides sediminis KCTC 19271GCA_003047295contigncbi433648

GC content

@refGC-contentmethod
791271.5high performance liquid chromatography (HPLC)
2893971.5

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveyes89.971yes
anaerobicno98.758no
halophileno86.546no
spore-formingno87.706yes
glucose-utilyes89.46yes
aerobicyes92.419yes
flagellatedno98.497no
motileno94.69yes
thermophileno95.832yes
glucose-fermentno92.62yes

External links

@ref: 7912

culture collection no.: DSM 19263, JCM 19559, KCTC 19271, MSL 01

straininfo link

  • @ref: 80393
  • straininfo: 407644

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19196766Nocardioides sediminis sp. nov., isolated from a sediment sample.Dastager SG, Lee JC, Ju YJ, Park DJ, Kim CJInt J Syst Evol Microbiol10.1099/ijs.0.002162-02009Actinomycetales/*classification/genetics/isolation & purification/ultrastructure, Geologic Sediments/*microbiology, Korea, Microscopy, Electron, Scanning, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Species SpecificityGenetics
Phylogeny30547859Nocardioides gansuensis sp. nov., isolated from geopark soil.Wu S, Xia X, Zhou Z, Wang D, Wang GInt J Syst Evol Microbiol10.1099/ijsem.0.0031572018Actinobacteria/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7912Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19263)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19263
18614Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM19263.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
28939Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2537828776041
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/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
80393Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID407644.1StrainInfo: A central database for resolving microbial strain identifiers