Strain identifier

BacDive ID: 11090

Type strain: Yes

Species: Nocardioides albus

Strain Designation: 652-48

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

NCBI tax ID(s): 1841 (species)

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General

@ref: 10772

BacDive-ID: 11090

DSM-Number: 43109

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

description: Nocardioides albus 652-48 is an aerobe, mesophilic bacterium that builds an aerial mycelium and was isolated from soil, lavender field.

NCBI tax id

  • NCBI tax id: 1841
  • Matching level: species

strain history

@refhistory
10772<- IMET <- H. Prauser, 652-48
67770KCC A-0185 <-- IMET 7807 <-- H. Prauser 652-48.
116200CIP <- 1986, NCIMB <- H. Prauser, IMET

doi: 10.13145/bacdive11090.20230509.8.1

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 albus
  • full scientific name: Nocardioides albus Prauser 1976 (Approved Lists 1980)

@ref: 10772

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardioidaceae

genus: Nocardioides

species: Nocardioides albus

full scientific name: Nocardioides albus Prauser 1976

strain designation: 652-48

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no93.938
69480100positive

colony morphology

@refcolony colorincubation periodmedium used
19541Beige10-14 daysISP 2
19541Beige10-14 daysISP 3
19541Beige10-14 daysISP 4
19541Beige10-14 daysISP 5
19541Beige10-14 daysISP 6
19541Beige10-14 daysISP 7
54001>3 days

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
19541yesAerial MyceliumWhiteISP 2
19541yesAerial MyceliumWhiteISP 3
19541yesAerial MyceliumWhiteISP 4
19541noISP 5
19541noISP 6
19541noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
10772GYM 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
19541ISP 2yesName: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
19541ISP 3yesName: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
19541ISP 4yesName: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
19541ISP 5yesName: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
19541ISP 6yesName: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
19541ISP 7yesName: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes
34267MEDIUM 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)
10772R2A 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
116200CIP Medium 236yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=236
116200CIP Medium 57yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=57

culture temp

@refgrowthtypetemperaturerange
19541positiveoptimum30mesophilic
10772positivegrowth28mesophilic
34267positivegrowth25mesophilic
54001positivegrowth37mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 54001
  • oxygen tolerance: aerobe

compound production

@refcompound
10772xanthine dehydrogenase
20216xanthine dehydrogenase (Jpn. Pat. 61,170,386)

halophily

  • @ref: 19541
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 5 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1954117234glucose+
1954122599arabinose+
1954117992sucrose+
1954118222xylose-
1954117268myo-inositol+
1954129864mannitol+
1954128757fructose+
1954126546rhamnose+
1954116634raffinose-
1954162968cellulose-
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
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

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    54001C14:00.314
    54001C15:0115
    54001C16:04.716
    54001C17:03.417
    54001C18:01.418
    54001C12:0 ISO0.211.608
    54001C14:0 ISO1.413.618
    54001C15:0 ANTEISO0.214.711
    54001C15:0 ISO1.414.621
    54001C16:0 10-methyl0.816.433
    54001C16:0 iso42.215.626
    54001C16:1 ISO H0.415.461
    54001C16:1 ω7c3.515.819
    54001C17:0 10-methyl1.117.41
    54001C17:0 anteiso1.316.722
    54001C17:0 iso1.216.629
    54001C17:1 ω5c ISO0.416.461
    54001C17:1 ω6c4.916.862
    54001C17:1 ω8c8.416.792
    54001C18:0 ISO0.617.632
    54001C18:1 ISO H0.317.46
    54001C18:1 ω7c /12t/9t117.824
    54001C18:1 ω9c11.517.769
    54001C19:1 ω11c/19:1 ω9c0.318.762
    54001TBSA 10Me18:01.618.392
    54001Unidentified3.715.935
    54001Unidentified1.616.105
    54001Unidentified0.516.3
    54001Unidentified0.417.12
    54001Unidentified0.418.095
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
19541++-+++++-++-+-++---

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19541++--+----++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
10772soil, lavender fieldpeninsula TihanyHungaryHUNEurope
54001Soil (lavender field)TihanyHungaryHUNEurope
67770SoilTihanyHungaryHUNEurope
116200Environment, Soil, lavender fieldTihanyHungaryHUNEurope

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture#Field
#Environmental#Terrestrial#Soil
#Host#Plants#Herbaceous plants (Grass,Crops)

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: AF004988
  • 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
107721Risk group (German classification)
195411Hazard group
1162001Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Nocardioides albus partial 16S rRNAX532111450ena1841
20218Nocardioides albus strain KCTC 9186 16S ribosomal RNA gene, partial sequenceAF0049881470ena1841
20218Nocardioides albus strain KCTC 9186 16S-23S internal transcribed spacer, complete sequenceAF017470514ena1841

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardioides albus JCM 3185GCA_014648255scaffoldncbi1841
66792Nocardioides albus CECT 3302GCA_014191915scaffoldncbi1841
66792Nocardioides albus strain CECT 33021841.3wgspatric1841
66792Nocardioides albus strain JCM 31851841.4wgspatric1841
66792Nocardioides albus CECT 33022824326936draftimg1841

GC content

  • @ref: 67770
  • GC-content: 68.6
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno77no
flagellatedno97.755no
gram-positiveyes89.451no
anaerobicno98.607no
aerobicyes91.655yes
halophileno89.228no
spore-formingno64.414no
thermophileno99.279yes
glucose-utilyes90.46no
motileno96.846no
glucose-fermentno89.87no

External links

@ref: 10772

culture collection no.: DSM 43109, ATCC 27980, CCM 2712, IMET 7807, JCM 3185, NCIB 11454, CCUG 37987, CIP 103451, BCRC 12442, CECT 3302, CGMCC 4.1230, CGMCC 4.1334, IFO 13917, IMSNU 20105, KACC 20014, KCTC 9186, LMG 16326, NBRC 13917, NCIMB 11454, NRRL B-5389, VKM Ac-682, VKM Ac-805

straininfo link

  • @ref: 80339
  • straininfo: 9323

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Genetics10611537A teichoic acid of Nocardioides albus VKM Ac-805T cell walls.Shashkov AS, Tul'skaya EM, Evtushenko LI, Naumova IBBiochemistry (Mosc)BCM641115441999Actinomycetales/*chemistry, Carbohydrate Sequence, Cell Wall/*chemistry, Magnetic Resonance Spectroscopy, Molecular Sequence Data, Teichoic Acids/*chemistry
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
10772Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 43109)https://www.dsmz.de/collection/catalogue/details/culture/DSM-43109
19541Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM43109.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
20216Curators of the HKIhttp://www.leibniz-hki.de/de/Collection Description Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie e. V. Hans-Knöll-Institut (HKI)
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
34267Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15250
54001Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 37987)https://www.ccug.se/strain?id=37987
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
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)
80339Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID9323.1StrainInfo: A central database for resolving microbial strain identifiers
116200Curators of the CIPCollection of Institut Pasteur (CIP 103451)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103451