Strain identifier

BacDive ID: 10719

Type strain: Yes

Species: Nocardia uniformis

Strain Designation: A-0224

Strain history: CIP <- 1996, JCM, Nocardia uniformis <- KCC: strain A-0224 <- DSM <- L. Ettlinger: strain LBG A-3004 <- R. Hütter: strain ETH 26650 <- I. Szabo

NCBI tax ID(s): 1210100 (strain), 53432 (species)

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General

@ref: 10683

BacDive-ID: 10719

DSM-Number: 43136

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

description: Nocardia uniformis A-0224 is an obligate aerobe, spore-forming, mesophilic bacterium that was isolated from salty soil.

NCBI tax id

NCBI tax idMatching level
53432species
1210100strain

strain history

@refhistory
10683<- L. Ettlinger, LBG <- R. Hütter, ETH <- I. Szabó
67770KCC A-0224 <-- DSM 43136 <-- L. Ettlinger A-3004 <-- ETH 26650 <-- I. Szabó.
123732CIP <- 1996, JCM, Nocardia uniformis <- KCC: strain A-0224 <- DSM <- L. Ettlinger: strain LBG A-3004 <- R. Hütter: strain ETH 26650 <- I. Szabo

doi: 10.13145/bacdive10719.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Mycobacteriales
  • family: Nocardiaceae
  • genus: Nocardia
  • species: Nocardia uniformis
  • full scientific name: Nocardia uniformis (ex Marton and Szabó 1959) Isik et al. 1999

@ref: 10683

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardiaceae

genus: Nocardia

species: Nocardia uniformis

full scientific name: Nocardia uniformis (ex Marton and Szabó 1959) Isik et al. 1999 emend. Nouioui et al. 2018

strain designation: A-0224

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no96.595
69480100positive
123732nonegativerod-shaped

colony morphology

@refcolony colorincubation periodmedium used
19543Beige10-14 daysISP 2
19543Beige10-14 daysISP 3
19543Beige10-14 daysISP 4
19543Beige10-14 daysISP 5
19543Beige10-14 daysISP 6
19543Beige10-14 daysISP 7
123732

multicellular morphology

@refforms multicellular complexmedium name
19543noISP 2
19543noISP 3
19543noISP 4
19543noISP 5
19543noISP 6
19543noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
10683GYM 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
19543ISP 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
19543ISP 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:
19543ISP 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
19543ISP 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
19543ISP 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
19543ISP 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
41321MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
123732CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
19543positiveoptimum28mesophilic
10683positivegrowth28mesophilic
41321positivegrowth30mesophilic
67770positivegrowth28mesophilic
123732positivegrowth25-37mesophilic
123732nogrowth10psychrophilic
123732nogrowth41thermophilic
123732nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 123732
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481yes100
69480yes91.815

halophily

@refsaltgrowthtested relationconcentration
123732NaClpositivegrowth0-6 %
123732NaClnogrowth8 %
123732NaClnogrowth10 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1954317234glucose+
1954322599arabinose-
1954317992sucrose-
1954318222xylose-
1954317268myo-inositol+
1954329864mannitol+
1954328757fructose+
1954326546rhamnose+
1954316634raffinose-
1954362968cellulose-
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-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
6837117306maltose-builds acid from
6837117057cellobiose-builds acid from
6837117814salicin-builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-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
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
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate+assimilation
6836818257ornithine+degradation
6836825094lysine+degradation
6836829016arginine+hydrolysis
12373216947citrate-carbon source
1237324853esculin+hydrolysis
123732606565hippurate+hydrolysis
12373217632nitrate+reduction
12373216301nitrite-reduction
12373217632nitrate-respiration
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

antibiotic resistance

  • @ref: 123732
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno
12373235581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin-
6836835581indole-
12373215688acetoin-
12373217234glucose-

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
123732oxidase-
123732beta-galactosidase+3.2.1.23
123732alcohol dehydrogenase-1.1.1.1
123732gelatinase-
123732amylase-
123732DNase-
123732caseinase-3.4.21.50
123732catalase+1.11.1.6
123732tween esterase-
123732gamma-glutamyltransferase-2.3.2.2
123732lecithinase-
123732lipase-
123732lysine decarboxylase-4.1.1.18
123732ornithine decarboxylase-4.1.1.17
123732phenylalanine ammonia-lyase-4.3.1.24
123732tryptophan deaminase-
123732urease+3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase lipase (C 8)+
68382leucine arylamidase+3.4.11.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
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
19543---+-++-++-------+-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
19543+-+++++++++-+-++---
123732+++-+----++---++----

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19543+++++-+----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
123732+/-----------+/----------+/---+/---------------+/----------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
123732++----------------++---+-------+++---------------+---------+------------------+++---+---+-++----+-+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
10683salty soilHortobagy SteppeHungaryHUNEurope
67770Salty soil
123732Environment, Salty soil

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Condition#Saline

taxonmaps

  • @ref: 69479
  • File name: preview.99_2685.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_243;97_448;98_2082;99_2685&stattab=map
  • Last taxonomy: Nocardia uniformis
  • 16S sequence: Z46752
  • Sequence Identity:
  • Total samples: 145
  • soil counts: 137
  • aquatic counts: 4
  • animal counts: 3
  • plant counts: 1

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
106831Risk group (German classification)
1237322Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Nocardia uniformis strain DSM 43136 16S ribosomal RNA gene, complete sequenceAF4300441492ena53432
20218Nocardia uniformis strain DSM 43136 note copy 1 16S-23S ribosomal RNA intergenic spacer, complete sequenceAF536487330ena53432
20218Nocardia uniformis strain DSM 43136 note copy 2 16S-23S ribosomal RNA intergenic spacer, complete sequenceAF536488336ena53432
20218Nocardia uniformis strain JCM 3224 16S ribosomal RNA gene, partial sequenceAY756564606ena53432
20218Nocardia uniformis strain W9869 16S ribosomal RNA gene, partial sequenceGQ8530691439ena53432
20218N.uniformis gene for 16S ribosomal RNAZ467521472ena53432

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardia uniformis NBRC 137021210100.4wgspatric1210100
66792Nocardia uniformis strain JCM 322453432.3wgspatric53432
66792Nocardia uniformis NBRC 137022731957751draftimg1210100
67770Nocardia uniformis NBRC 13702GCA_001613345contigncbi1210100
67770Nocardia uniformis JCM 3224GCA_013004475contigncbi53432

GC content

  • @ref: 67770
  • GC-content: 66
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno93.081no
gram-positiveyes88.261no
anaerobicno99.567no
aerobicyes89.792no
halophileno90.623no
spore-formingyes85.98no
thermophileno99.211yes
glucose-utilyes88.625no
flagellatedno97.951no
glucose-fermentno89.569no

External links

@ref: 10683

culture collection no.: DSM 43136, CBS 224.60, CCRC 13368, CIP 104824, IFO 13702, JCM 3224, KCC A-0224, LBG A 3004, NBRC 13702, NCIB 963, ETH 26650, BCRC 13368, CGMCC 4.1137, CIP 106796, IFM 0856, IMSNU 21186, LBG A-3004

straininfo link

  • @ref: 79988
  • straininfo: 50187

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Genetics10425784Nocardia uniformis nom. rev.Isik K, Chun J, Hah YC, Goodfellow MInt J Syst Bacteriol10.1099/00207713-49-3-12271999Algorithms, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Genotype, Molecular Sequence Data, Nocardia/chemistry/*classification/cytology/physiology, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil MicrobiologyPhylogeny
Metabolism35792521Two Bioactive Compounds, Uniformides A and B, Isolated from a Culture of Nocardia uniformis IFM0856(T) in the Presence of Animal Cells.Hara Y, Watanabe K, Takaya A, Manome T, Yaguchi T, Ishibashi MOrg Lett10.1021/acs.orglett.2c020922022Animals, Cell Line, Lipopolysaccharides/pharmacology, Mice, NF-kappa B/metabolism, Nitric Oxide, Nitric Oxide Synthase Type II/metabolism, *Nocardia/metabolismPhylogeny

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
10683Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 43136)https://www.dsmz.de/collection/catalogue/details/culture/DSM-43136
19543Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM43136.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
41321Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16775
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
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
79988Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID50187.1StrainInfo: A central database for resolving microbial strain identifiers
123732Curators of the CIPCollection of Institut Pasteur (CIP 104824)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104824