Strain identifier

BacDive ID: 11176

Type strain: Yes

Species: Nocardiopsis alborubida

Strain history: CIP <- 2000, DSMZ <- E.B. Shirling, ISP, Streptomyces alborubidus <- G.F. Gauze, INA

NCBI tax ID(s): 1223496 (strain), 146802 (species)

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General

@ref: 9561

BacDive-ID: 11176

DSM-Number: 40465

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, spore-forming, Gram-positive

description: Nocardiopsis alborubida DSM 40465 is an obligate aerobe, spore-forming, Gram-positive bacterium of the family Nocardiopsidaceae.

NCBI tax id

NCBI tax idMatching level
1223496strain
146802species

strain history

@refhistory
9561<- E.B. Shirling, ISP (Streptomyces alborubidus) <- G.F. Gauze, INA
67770KCC S-0717 <-- IFO 13392 <-- SAJ <-- ISP 5465 <-- INA 6476/62.
118858CIP <- 2000, DSMZ <- E.B. Shirling, ISP, Streptomyces alborubidus <- G.F. Gauze, INA

doi: 10.13145/bacdive11176.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Streptosporangiales
  • family: Nocardiopsidaceae
  • genus: Nocardiopsis
  • species: Nocardiopsis alborubida
  • full scientific name: Nocardiopsis alborubida corrig. Grund and Kroppenstedt 1990

  • synonyms

    @refsynonym
    20215Nocardiopsis dassonvillei subsp. albirubida
    20215Nocardiopsis albidorubidus
    20215Nocardiopsis alborubidus

@ref: 9561

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardiopsaceae

genus: Nocardiopsis

species: Nocardiopsis alborubida

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
118858positiverod-shapedno
69480positive92.128
69480no93

colony morphology

  • @ref: 118858

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
9561GYM 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
39725MEDIUM 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)
118858CIP Medium 57yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=57

culture temp

@refgrowthtypetemperature
18595positiveoptimum28
9561positivegrowth28
39725positivegrowth30
67770positivegrowth28
118858positivegrowth10-41
118858nogrowth45

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
118858obligate aerobe
69480aerobe90.56

spore formation

  • @ref: 69481
  • spore formation: yes
  • confidence: 100

halophily

@refsaltgrowthtested relationconcentration
18595NaClpositivemaximum2.5 %
118858NaClpositivegrowth0-10 %

observation

  • @ref: 67770
  • observation: quinones: MK-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1859517234glucose-
1859522599arabinose-
1859517992sucrose+
1859518222xylose-
1859517268myo-inositol-
1859529864mannitol+
1859528757fructose+
1859526546rhamnose-
1859516634raffinose-
1859562968cellulose-
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-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
6837117057cellobiose-builds acid from
6837117814salicin-builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
6837159640N-acetylglucosamine-builds acid from
68371320061methyl alpha-D-glucopyranoside-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
6837117754glycerol+builds acid from
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate+assimilation
6836818257ornithine+degradation
6836825094lysine+degradation
6836829016arginine+hydrolysis
11885816947citrate+carbon source
1188584853esculin-hydrolysis
118858606565hippurate-hydrolysis
11885817632nitrate+reduction
11885816301nitrite-reduction
11885817632nitrate-respiration

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno
11885835581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin+
6836835581indole-
11885815688acetoin-
11885817234glucose-

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
118858oxidase+
118858beta-galactosidase+3.2.1.23
118858alcohol dehydrogenase-1.1.1.1
118858gelatinase+
118858amylase+
118858DNase-
118858caseinase+3.4.21.50
118858catalase+1.11.1.6
118858tween esterase+
118858gamma-glutamyltransferase-2.3.2.2
118858lecithinase-
118858lipase-
118858lysine decarboxylase-4.1.1.18
118858ornithine decarboxylase-4.1.1.17
118858protease+
118858tryptophan deaminase-
118858urease-3.5.1.5
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 zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
118858-+++------++--------

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
18595+++++-+--++

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
118858+---++---+----+---------+/---+/-----------------+/-----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
118858+++-+--+-++----+--++++-+--+----+-+------------+++++--+------++-------------+--+++-------+-++-+-+-+-

Isolation, sampling and environmental information

taxonmaps

  • @ref: 69479
  • File name: preview.99_4184.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_152;96_659;97_762;98_2623;99_4184&stattab=map
  • Last taxonomy: Nocardiopsis
  • 16S sequence: X97882
  • Sequence Identity:
  • Total samples: 98
  • soil counts: 18
  • aquatic counts: 7
  • animal counts: 51
  • plant counts: 22

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
185952German classification
95612Risk group (German classification)
1188581Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218N.alborubida 16S rRNA geneX978821461nuccore146802
20218Nocardiopsis dassonvillei subsp. albirubida gene for 16S ribosomal RNA, partial sequence, strain: JCM 4717D44307119nuccore146802
20218Nocardiopsis dassonvillei subsp. albirubida gene for 16S rRNA, partial sequenceAB3687121458nuccore146802

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardiopsis dassonvillei subsp. albirubida NBRC 133921223496.3wgspatric1223496
66792Nocardiopsis dassonvillei subsp. albirubida strain ATCC 23612146802.3wgspatric146802
66792Nocardiopsis dassonvillei albirubida NBRC 133922731957597draftimg1223496
66792Nocardiopsis dassonvillei albirubida ATCC 236122896009406draftimg146802
67770Nocardiopsis alborubida NBRC 13392GCA_001552695contigncbi1223496
67770Nocardiopsis alborubida ATCC 23612GCA_012396365contigncbi146802

GC content

  • @ref: 67770
  • GC-content: 72
  • method: genome sequence analysis

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesyes100no
69480gram-positivegram-positivePositive reaction to Gram-stainingyes92.128no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no97.837no
69480spore-formingspore-formingAbility to form endo- or exosporesyes85.482no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes90.56no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno92.689yes
69480flagellatedmotile2+Ability to perform flagellated movementno93no

External links

@ref: 9561

culture collection no.: DSM 40465, ATCC 23612, CBS 693.72, CIP 106424, IFO 13392, INA 6476/62, ISP 5465, KCC S-0717, NBRC 13392, PCM 2490, RIA 1353, JCM 4717, BCRC 15175, BCRC 16386, CGMCC 4.2086, IFM 10203, IMSNU 21332, MTCC 1102, VKM Ac-1882, VKM Ac-1885, DSM 40645

straininfo link

  • @ref: 80425
  • straininfo: 37932

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny9336896Description of Nocardiopsis synnemataformans sp. nov., elevation of Nocardiopsis alba subsp. prasina to Nocardiopsis prasina comb. nov., and designation of Nocardiopsis antarctica and Nocardiopsis alborubida as later subjective synonyms of Nocardiopsis dassonvillei.Yassin AF, Rainey FA, Burghardt J, Gierth D, Ungerechts J, Lux I, Seifert P, Bal C, Schaal KPInt J Syst Bacteriol10.1099/00207713-47-4-9831997Base Composition, Culture Media, Conditioned/metabolism, DNA, Bacterial/*analysis, Humans, Microscopy, Electron, Molecular Sequence Data, Propionibacteriaceae/chemistry/*classification/genetics/growth & development/metabolism/ultrastructure, RNA, Ribosomal, 16S/*analysisCultivation
Phylogeny10826789Nocardiopsis tropica sp. nov., Nocardiopsis trehalosi sp. nov., nom. rev. and Nocardiopsis dassonvillei subsp. albirubida subsp. nov., comb. nov.Evtushenko LI, Taran VV, Akimov VN, Kroppenstedt RM, Tiedje JM, Stackebrandt EInt J Syst Evol Microbiol10.1099/00207713-50-1-732000Actinomycetales/chemistry/*classification/cytology/physiology, DNA, Bacterial/analysis/genetics, DNA, Ribosomal/analysis/genetics, Fatty Acids/analysis, Mathematics, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics
Phylogeny33095134Nocardiopsis dassonvillei subsp. crassaminis subsp. nov., isolated from freshwater sediment, and reappraisal of Nocardiopsis alborubida Grund and Kroppenstedt 1990 emend. Nouioui et al. 2018.Camacho Pozo MI, Wieme AD, Perez SR, Llaurado Maury G, Snauwaert C, Lescaylle Veranes Y, Pena Zamora L, Schumann P, Vandamme PInt J Syst Evol Microbiol10.1099/ijsem.0.0045142020Bacterial Typing Techniques, Base Composition, Cuba, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Fresh Water/*microbiology, Geologic Sediments/*microbiology, Nocardiopsis/*classification/isolation & purification, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9561Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40465)https://www.dsmz.de/collection/catalogue/details/culture/DSM-40465
18595Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM40465.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
39725Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18553
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/
68368Automatically annotated from API 20E
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
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
80425Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID37932.1StrainInfo: A central database for resolving microbial strain identifiers
118858Curators of the CIPCollection of Institut Pasteur (CIP 106424)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106424