Strain identifier

BacDive ID: 11056

Type strain: Yes

Species: Nocardioides fastidiosus

Strain Designation: J41

Strain history: NCIMB 12713 <-- M. D. Collins J41.

NCBI tax ID(s): 52699 (species)

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General

@ref: 3972

BacDive-ID: 11056

DSM-Number: 10552

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

description: Nocardioides fastidiosus J41 is an aerobe, mesophilic bacterium that was isolated from herbage.

NCBI tax id

  • NCBI tax id: 52699
  • Matching level: species

strain history

@refhistory
3972<- IFO <- M.D. Collins <- J.M. Grainger, J41
67770NCIMB 12713 <-- M. D. Collins J41.

doi: 10.13145/bacdive11056.20230509.8.1

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 fastidiosus
  • full scientific name: Nocardioides fastidiosus corrig. Collins and Stackebrandt 1989

  • synonyms

    @refsynonym
    20215Nocardioides fastidiosa
    20215Aeromicrobium fastidiosum

@ref: 3972

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardioidaceae

genus: Aeromicrobium

species: Aeromicrobium fastidiosum

full scientific name: Aeromicrobium fastidiosum (Collins and Stackebrandt 1989) Tamura and Yokota 1994

strain designation: J41

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no93.983
69480100positive

colony morphology

@refcolony colorincubation periodmedium used
18356Cream (9001)10-14 days5006
18356Beige (1001)10-14 days5425
18356Cream (9001)10-14 days5428
18356Cream (9001)10-14 days5530
18356Transparent10-14 daysISP 2

multicellular morphology

@refforms multicellular complexmedium name
18356noISP 2
18356no5006
18356no5425
18356no5428
18356no5530

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
18356ISP 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
183565530yes
183565428yes
183565425yesName: Brain Heart Infusion (BHI) Agar; 5425 Composition: Calf brain infusion 200.0 g/l Beef heart infusion 250.0 g/l Casein (meat) peptone 10.0 g/l Glucose 2.0 g/l NaCl 5.0 g/l Na2HPO4 2.5 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.4 Usage: Maintenance and revitalization Organisms: Dermatophilus congolensis, Nocardia brasieliensis, N. asteroides, Rhodococcus equi, R. fascians, R. rhodochrous, Streptomyces thermoviol aceus subsp. apingens, Coryneform species
183565006yesMedium: 5006 Name: Composition (g/l) Sucrose 3,0 Dextrin 15,0 Meat extract 1,0 Yeast extract 2,0 Tryptone soy broth (Oxoid) 5,0 NaCl 0,5 K2HPO4 0,5 MgSO4 x 7 H2O 0,5 FeSO4 x 7 H2O 0,01 Agar 20,0 Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7,3 Usage: Maintenance Organisms: All Actinomycetes
3972TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yesName: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled waterhttps://mediadive.dsmz.de/medium/92
3972CORYNEBACTERIUM AGAR (DSMZ Medium 53)yesName: CORYNEBACTERIUM AGAR (DSMZ Medium 53) Composition: Agar 15.0 g/l Casein peptone 10.0 g/l NaCl 5.0 g/l Glucose 5.0 g/l Yeast extract 5.0 g/l Distilled waterhttps://mediadive.dsmz.de/medium/53
3972R2A MEDIUM (DSMZ Medium 830)yesName: 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 waterhttps://mediadive.dsmz.de/medium/830

culture temp

@refgrowthtypetemperaturerange
18356positiveoptimum28mesophilic
52464positivegrowth30mesophilic
67770positivegrowth28mesophilic
3972positivegrowth28mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 52464
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.991

murein

  • @ref: 3972
  • murein short key: A41.01
  • type: A3gamma LL-Dpm-Gly

observation

  • @ref: 67770
  • observation: quinones: MK-9(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis
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

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

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

enzymes

@refvalueactivityec
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
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

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
18356---+---------------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
18356+++++++++++--------

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
18356-----------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
3972herbageUnited KingdomGBREurope
52464Herbage
67770Herbage

isolation source categories

  • Cat1: #Host
  • Cat2: #Plants
  • Cat3: #Herbaceous plants (Grass,Crops)

taxonmaps

  • @ref: 69479
  • File name: preview.99_87938.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_142;96_1793;97_2145;98_5855;99_87938&stattab=map
  • Last taxonomy: Aeromicrobium
  • 16S sequence: X76862
  • Sequence Identity:
  • Total samples: 1165
  • soil counts: 415
  • aquatic counts: 120
  • animal counts: 581
  • plant counts: 49

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
183561
39721Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218N.fastidiosa 16S rRNA geneX768621460ena52699
3972A.fastidiosum 16S rRNA geneZ782091468ena52699
67770Aeromicrobium fastidiosum 16S ribosomal RNA gene, partial sequenceAF0050221472ena52699
67770Nocardioides fastidiosa 16S rRNA (part.)X531891449ena52699

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Aeromicrobium fastidiosum DSM 10552GCA_017876595contigncbi52699
66792Aeromicrobium fastidiosum strain DSM 1055252699.6wgspatric52699
66792Aeromicrobium fastidiosum DSM 105522918376121draftimg52699
67770Aeromicrobium fastidiosum NRBC 14897GCA_004134885scaffoldncbi52699

GC content

@refGC-contentmethod
397271thermal denaturation, midpoint method (Tm)
6777071-72thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveyes91.09no
anaerobicno99.179no
halophileno92.126no
spore-formingno90.72no
glucose-utilyes88.061no
thermophileno98.791no
motileno94.105no
aerobicyes95.543yes
flagellatedno98.362no
glucose-fermentno88.659yes

External links

@ref: 3972

culture collection no.: DSM 10552, ATCC 49363, IFO 14897, NBRC 14897, NCIMB 12713, CCUG 35026, LMG 16205, JCM 8088, IMSNU 22010, KCCM 41090, KCTC 9576, VKM Ac-1324

straininfo link

  • @ref: 80305
  • straininfo: 8164

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3972Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 10552)https://www.dsmz.de/collection/catalogue/details/culture/DSM-10552
18356Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM10552.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
52464Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 35026)https://www.ccug.se/strain?id=35026
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
68379Automatically annotated from API Coryne
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
80305Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID8164.1StrainInfo: A central database for resolving microbial strain identifiers