Strain identifier

BacDive ID: 10818

Type strain: Yes

Species: Nocardia acidivorans

Strain Designation: GW4-1778

Strain history: CIP <- 2006, P. Kämpfer, J. Liebig Univ., Giessen, Germany: strain GW4-1778

NCBI tax ID(s): 1210062 (strain), 404580 (species)

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General

@ref: 12298

BacDive-ID: 10818

DSM-Number: 45049

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

description: Nocardia acidivorans GW4-1778 is an aerobe, spore-forming, mesophilic bacterium that builds an aerial mycelium and was isolated from soil.

NCBI tax id

NCBI tax idMatching level
404580species
1210062strain

strain history

@refhistory
12298<- P. Kämpfer; GW4-1778 <- I. Grün-Wollny
67770IFM 10820 <-- DSM 45049 <-- P. Kämpfer GW4-1778 <-- I. Grün-Wollny.
116025CIP <- 2006, P. Kämpfer, J. Liebig Univ., Giessen, Germany: strain GW4-1778

doi: 10.13145/bacdive10818.20230509.8.1

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 acidivorans
  • full scientific name: Nocardia acidivorans Kämpfer et al. 2007

@ref: 12298

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardiaceae

genus: Nocardia

species: Nocardia acidivorans

full scientific name: Nocardia acidivorans Kämpfer et al. 2007

strain designation: GW4-1778

type strain: yes

Morphology

cell morphology

@refgram stainmotilityconfidencecell shape
32014positive
69480no96.742
69480positive100
116025positivenorod-shaped

colony morphology

@refcolony colorincubation periodmedium used
19905Pale brown10-14 daysISP 2
19905Cream10-14 daysISP 3
19905Light ivory10-14 daysISP 5
19905Light ivory10-14 daysISP 6
19905Light ivory10-14 daysISP 7
598933 days

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
19905yesAerial MyceliumCreamISP 2
19905noISP 3
19905
19905noISP 5
19905noISP 6
19905noISP 7

pigmentation

  • @ref: 32014
  • production: yes

multimedia

  • @ref: 12298
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_45049.jpg
  • caption: Medium 553 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12298GPHF-MEDIUM (DSMZ Medium 553)yeshttps://mediadive.dsmz.de/medium/553Name: GPHF-MEDIUM (DSMZ Medium 553) Composition: Agar 20.0 g/l Glucose 10.0 g/l Beef extract 5.0 g/l Yeast extract 5.0 g/l Casein peptone 5.0 g/l CaCl2 x 2 H2O 0.74 g/l Distilled water
12298GYM 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
19905ISP 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
19905ISP 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:
19905ISP 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
19905ISP 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
19905ISP 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
37508MEDIUM 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)
116025CIP Medium 57yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=57

culture temp

@refgrowthtypetemperaturerange
12298positivegrowth28mesophilic
32014positivegrowth25-30mesophilic
32014positiveoptimum27.5mesophilic
37508positivegrowth30mesophilic
59893positivegrowth30mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
59893aerobe
116025obligate aerobe

spore formation

@refspore formationconfidence
32014yes
69481yes100
69480no96.488

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1990517234glucose+
1990522599arabinose-
1990517992sucrose-
1990518222xylose-
1990517268myo-inositol+/-
1990529864mannitol+/-
1990528757fructose+/-
1990526546rhamnose-
1990516634raffinose-
1990562968cellulose-
3201430089acetate+carbon source
3201416449alanine+carbon source
3201422599arabinose+carbon source
3201416947citrate+carbon source
3201428260galactose+carbon source
320145417glucosamine+carbon source
3201427570histidine+carbon source
3201429864mannitol+carbon source
3201437684mannose+carbon source
3201417272propionate+carbon source
3201417148putrescine+carbon source
3201415361pyruvate+carbon source
3201417822serine+carbon source
11602517632nitrate-reduction
11602516301nitrite-reduction

metabolite production

  • @ref: 116025
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
32014cytochrome oxidase+1.9.3.1
116025oxidase-
116025catalase+1.11.1.6
116025urease+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-fucosidase-3.2.1.51

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
19905+++++++++++-+-++-+-
116025+++++++++++-+-++----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
12298soilisland StromboliItalyITAEurope
59893SoilStromboliItalyITAEurope
67770SoilStromboliItalyITAEurope
116025Environment, SoilStromboliItalyITAEurope

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_5558.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_243;97_448;98_4146;99_5558&stattab=map
  • Last taxonomy: Nocardia
  • 16S sequence: AM402972
  • Sequence Identity:
  • Total samples: 57
  • soil counts: 44
  • aquatic counts: 4
  • animal counts: 4
  • plant counts: 5

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
122981Risk group (German classification)
199051Risk group (German classification)
1160252Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Nocardia acidivorans 16S ribosomal RNA gene, partial sequenceGQ3761561440ena404580
12298Nocardia acidivorans partial 16S rRNA gene, type strain GW4-1778TAM4029721493ena404580

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardia acidivorans NBRC 1082471210062.4wgspatric1210062
66792Nocardia acidivorans NBRC 1082472731957723draftimg1210062
67770Nocardia acidivorans NBRC 108247GCA_001625085contigncbi1210062

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno95.239no
gram-positiveyes89.848yes
anaerobicno99.634yes
aerobicyes92.646yes
halophileno94.64no
spore-formingyes84.321yes
glucose-utilyes88.647yes
flagellatedno98.05no
thermophileno99.46yes
glucose-fermentno90.744no

External links

@ref: 12298

culture collection no.: DSM 45049, CCUG 53410, CIP 109315, JCM 14671, IFM 10820, NBRC 108247

straininfo link

  • @ref: 80080
  • straininfo: 297508

literature

  • topic: Phylogeny
  • Pubmed-ID: 17551026
  • title: Nocardia acidivorans sp. nov., isolated from soil of the island of Stromboli.
  • authors: Kampfer P, Huber B, Buczolits S, Thummes K, Grun-Wollny I, Busse HJ
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.64813-0
  • year: 2007
  • mesh: Bacterial Typing Techniques, Genes, rRNA, Italy, Lipids/analysis, Molecular Sequence Data, Nocardia/chemistry/*classification/genetics/*isolation & purification, Nucleic Acid Hybridization, Phylogeny, Quinones/analysis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, *Soil Microbiology, Spores, Bacterial
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
12298Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45049)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45049
19905Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM45049.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
32014Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604128267
37508Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7043
59893Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 53410)https://www.ccug.se/strain?id=53410
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/
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
80080Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID297508.1StrainInfo: A central database for resolving microbial strain identifiers
116025Curators of the CIPCollection of Institut Pasteur (CIP 109315)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109315