Strain identifier

BacDive ID: 11102

Type strain: Yes

Species: Nocardioides luteus

Strain Designation: 939-9

Strain history: CIP <- 1986, NCIMB <- H. Prauser, IMET

NCBI tax ID(s): 1844 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 10986

BacDive-ID: 11102

DSM-Number: 43366

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic

description: Nocardioides luteus 939-9 is an aerobe, mesophilic bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 1844
  • Matching level: species

strain history

@refhistory
10986<- IMET <- H. Prauser, 939-9
67770IMET 7830 <-- H. Prauser 939-9.
120707CIP <- 1986, NCIMB <- H. Prauser, IMET

doi: 10.13145/bacdive11102.20230509.8.1

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 luteus
  • full scientific name: Nocardioides luteus Prauser 1985

@ref: 10986

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardioidaceae

genus: Nocardioides

species: Nocardioides luteus

full scientific name: Nocardioides luteus Prauser 1985

strain designation: 939-9

type strain: yes

Morphology

colony morphology

  • @ref: 54000
  • incubation period: >3 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
10986GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)yeshttps://mediadive.dsmz.de/medium/65Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water
40646MEDIUM 57 - for Streptomyces, Nocardioides, Lentzea albidocapillata and Streptoverticillium reticulumyesDistilled water make up to (1000.000 ml);Agar (15.000 g);Glucose (4.000g);Yeast extract (4.000 g);Malt extract (10.000 g);Calcium carbonate (2.000 g)
10986R2A MEDIUM (DSMZ Medium 830)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium830.pdf
120707CIP Medium 57yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=57
120707CIP Medium 236yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=236

culture temp

@refgrowthtypetemperaturerange
18488positiveoptimum30mesophilic
10986positivegrowth28mesophilic
40646positivegrowth25mesophilic
54000positivegrowth37mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 54000
  • oxygen tolerance: aerobe

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1848817234glucose+
1848822599arabinose+
1848817992sucrose+
1848818222xylose-
1848817268myo-inositol-
1848829864mannitol+
1848828757fructose+
1848826546rhamnose-
1848816634raffinose-
1848862968cellulose-
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate+assimilation
6836818257ornithine+degradation
6836825094lysine+degradation
6836829016arginine+hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin+
6836835581indole-

enzymes

@refvalueactivityec
68368gelatinase+
68368tryptophan deaminase-4.1.99.1
68368urease+3.5.1.5
68368ornithine decarboxylase+4.1.1.17
68368lysine decarboxylase+4.1.1.18
68368arginine dihydrolase+3.5.3.6
68368beta-galactosidase+3.2.1.23

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
18488+++++-+--++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
10986soilKhartoumSudanSDNAfrica
54000Soil under FicusKhartoumSudanSDNAfrica
67770Soil
120707Environment, Soil under FicusKhartoumSudanSDNAfrica

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_7662.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_142;96_3563;97_4377;98_5605;99_7662&stattab=map
  • Last taxonomy: Nocardioides
  • 16S sequence: AF005007
  • Sequence Identity:
  • Total samples: 15718
  • soil counts: 9755
  • aquatic counts: 920
  • animal counts: 2174
  • plant counts: 2869

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
109861Risk group (German classification)
184881
1207071Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Nocardioides luteus 16S ribosomal RNA gene, partial sequenceAF0050071469ena1844
20218Nocardioides luteus strain KCTC 9575 16S-23S internal transcribed spacer, complete sequenceAF017492473ena1844
20218Nocardioides luteus partial 16S rRNAX532121447ena1844

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardioides luteus JCM 3358GCA_014648595scaffoldncbi1844
66792Nocardioides luteus strain JCM 33581844.5wgspatric1844
66792Nocardioides luteus DSM 433662923421364draftimg1844

GC content

  • @ref: 67770
  • GC-content: 67.5
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno97.633no
gram-positiveyes90.605no
anaerobicno99.167yes
aerobicyes93.978yes
halophileno81.352no
spore-formingno56.782no
thermophileno97.642yes
glucose-utilyes89.14no
motileno97.348no
glucose-fermentno91.807no

External links

@ref: 10986

culture collection no.: DSM 43366, ATCC 43052, DSM 43811, IFO 14491, IMET 7830, JCM 3358, NBRC 14491, NCIB 11455, CCUG 37986, CIP 103450, IMSNU 22020, KCTC 9575, LMG 16209, NCIMB 11455, VKM Ac-1246

straininfo link

  • @ref: 80351
  • straininfo: 13982

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny9542088Inter- and intraspecific phylogenetic analysis of the genus Nocardioides and related taxa based on 16S rDNA sequences.Yoon JH, Lee ST, Park YHInt J Syst Bacteriol10.1099/00207713-48-1-1871998DNA, Bacterial/analysis, Molecular Sequence Data, Nocardiaceae/*classification/*genetics, Phylogeny, RNA, Bacterial/analysis, RNA, Ribosomal, 16S/*analysisGenetics
Genetics10810191Structure of a teichoic acid from Nocardioides luteus VKM Ac-1246T cell wall.Shashkov AS, Tul'skaya EM, Evtushenko LI, Gratchev AA, Naumova IBBiochemistry (Mosc)BCM650405982000Actinomycetales/*chemistry, Carbohydrate Conformation, Carbohydrate Sequence, Cell Wall/*chemistry, Chromatography, Gel, Magnetic Resonance Spectroscopy, Molecular Sequence Data, Pyruvic Acid/chemistry, Teichoic Acids/*chemistry
Phylogeny15545450Nocardioides aestuarii sp. nov., isolated from tidal flat sediment.Yi H, Chun JInt J Syst Evol Microbiol10.1099/ijs.0.63192-02004Actinomycetales/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, Cyanoacrylates/analysis, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Fatty Acids/analysis/isolation & purification, Genes, rRNA, Geologic Sediments/*microbiology, Korea, Molecular Sequence Data, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analysis/isolation & purificationEnzymology
Phylogeny22552630Nocardioides panzhihuaensis sp. nov., a novel endophytic actinomycete isolated from medicinal plant Jatropha curcas L.Qin S, Yuan B, Zhang YJ, Bian GK, Tamura T, Sun BZ, Li WJ, Jiang JHAntonie Van Leeuwenhoek10.1007/s10482-012-9745-82012Actinomycetales/classification/genetics/*isolation & purification/metabolism, Base Composition, Endophytes/classification/genetics/*isolation & purification/metabolism, Fatty Acids/metabolism, Jatropha/*microbiology, Molecular Sequence Data, Phylogeny, Plants, Medicinal/*microbiologyMetabolism
Phylogeny22798645Nocardioides albertanoniae sp. nov., isolated from Roman catacombs.Alias-Villegas C, Jurado V, Laiz L, Miller AZ, Saiz-Jimenez CInt J Syst Evol Microbiol10.1099/ijs.0.043885-02012Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rome, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/analysisGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
10986Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 43366)https://www.dsmz.de/collection/catalogue/details/culture/DSM-43366
18488Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM43366.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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
40646Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15249
54000Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 37986)https://www.ccug.se/strain?id=37986
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 updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68368Automatically annotated from API 20E
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
80351Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID13982.1StrainInfo: A central database for resolving microbial strain identifiers
120707Curators of the CIPCollection of Institut Pasteur (CIP 103450)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103450