Strain identifier

BacDive ID: 10627

Type strain: Yes

Species: Nocardia alba

Strain history: CIP <- 2004, DSMZ <- W.J. Li <- CCTCC <- YIM

NCBI tax ID(s): 1210063 (strain), 225051 (species)

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General

@ref: 11999

BacDive-ID: 10627

DSM-Number: 44684

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

description: Nocardia alba DSM 44684 is an obligate aerobe, spore-forming, mesophilic bacterium that builds an aerial mycelium and was isolated from soil.

NCBI tax id

NCBI tax idMatching level
1210063strain
225051species

strain history

@refhistory
11999<- W.-J. Li <- CCTCC <- YIM
67770IFM 10588 <-- DSM 44684 <-- W.-J. Li YIM 30243.
116178CIP <- 2004, DSMZ <- W.J. Li <- CCTCC <- YIM

doi: 10.13145/bacdive10627.20230509.8.1

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 alba
  • full scientific name: Nocardia alba Li et al. 2004

@ref: 11999

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardiaceae

genus: Nocardia

species: Nocardia alba

full scientific name: Nocardia alba Li et al. 2004

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no95.676
69480100positive
116178nopositiverod-shaped

colony morphology

@refcolony colorincubation periodmedium used
19688Deep orange10-14 daysISP 2
19688Ivory10-14 daysISP 3
19688Ivory10-14 daysISP 4
19688Deep orange10-14 daysISP 5
19688Deep orange10-14 daysISP 6
19688Deep orange10-14 daysISP 7
116178

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
19688yesAerial MyceliumIvoryISP 2
19688noISP 3
19688noISP 4
19688noISP 5
19688noISP 6
19688noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11999GYM 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
19688ISP 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
19688ISP 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:
19688ISP 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
19688ISP 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
19688ISP 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
19688ISP 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
36734MEDIUM 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)
116178CIP Medium 57yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=57

culture temp

@refgrowthtypetemperaturerange
19688positiveoptimum28mesophilic
11999positivegrowth28mesophilic
36734positivegrowth30mesophilic
67770positivegrowth28mesophilic
116178positivegrowth10-30
116178nogrowth37mesophilic
116178nogrowth41thermophilic
116178nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 116178
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481yes94
69480no98.807

halophily

@refsaltgrowthtested relationconcentration
116178NaClpositivegrowth0-2 %
116178NaClnogrowth4 %
116178NaClnogrowth6 %
116178NaClnogrowth8 %
116178NaClnogrowth10 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1968817234glucose+
1968822599arabinose-
1968817992sucrose-
1968818222xylose-
1968817268myo-inositol-
1968829864mannitol-
1968828757fructose-
1968826546rhamnose-
1968816634raffinose-
1968862968cellulose-
11617816947citrate-carbon source
1161784853esculin-hydrolysis
116178606565hippurate-hydrolysis
11617817632nitrate+reduction
11617816301nitrite-reduction
11617817632nitrate-respiration
683794853esculin+hydrolysis
6837916199urea+hydrolysis
683795291gelatin-hydrolysis
6837917992sucrose+fermentation

antibiotic resistance

  • @ref: 116178
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 116178
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11617815688acetoin-
11617817234glucose-

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
116178oxidase-
116178beta-galactosidase+3.2.1.23
116178alcohol dehydrogenase-1.1.1.1
116178gelatinase-
116178amylase-
116178DNase-
116178caseinase-3.4.21.50
116178catalase+1.11.1.6
116178tween esterase-
116178gamma-glutamyltransferase+2.3.2.2
116178lecithinase-
116178lipase-
116178lysine decarboxylase-4.1.1.18
116178ornithine decarboxylase-4.1.1.17
116178phenylalanine ammonia-lyase-4.3.1.24
116178tryptophan deaminase-
116178urease+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
68382cystine arylamidase-3.4.11.3
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

@refPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELSAC
19688--+--+-++-+

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
19688+++-+----++-+-++---
116178+++-++-+-++-+-++----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
116178-------------------------------+---------------------------+---------------+--------------------+--

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic location
11999soilChinaCHNAsia
67770SoilChinaCHNAsiaHeKou, Yunnan Province
116178Environment, SoilChinaCHNAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_5207.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_578;97_676;98_3882;99_5207&stattab=map
  • Last taxonomy: Nocardia
  • 16S sequence: GQ376158
  • Sequence Identity:
  • Total samples: 70
  • soil counts: 45
  • aquatic counts: 4
  • animal counts: 16
  • plant counts: 5

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
119991Risk group (German classification)
1161782Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Nocardia alba 16S ribosomal RNA gene, partial sequenceGQ3761581439ena225051
20218Nocardia alba 16S ribosomal RNA gene, partial sequenceAY2223211446ena225051

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardia alba NBRC 1082341210063.4wgspatric1210063
66792Nocardia alba strain DSM 44684225051.3wgspatric225051
66792Nocardia alba NBRC 1082342731957724draftimg1210063
66792Nocardia alba DSM 446842770939659draftimg225051
67770Nocardia alba NBRC 108234GCA_001612665contigncbi1210063
67770Nocardia alba DSM 44684GCA_004339125scaffoldncbi225051

GC content

  • @ref: 67770
  • GC-content: 74
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes94no
motileno93.511no
gram-positiveyes87.418no
anaerobicno99.346no
aerobicyes91.603no
halophileno90.996no
spore-formingyes73.461no
glucose-utilyes88.504yes
flagellatedno97.967no
thermophileno99.727yes
glucose-fermentno92.375no

External links

@ref: 11999

culture collection no.: DSM 44684, CCTCC AA 001030, CIP 108434, YIM 30243, JCM 13373, IFM 10588, NBRC 108234

straininfo link

  • @ref: 79899
  • straininfo: 134244

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15214636Nocardia alba sp.nov., a novel actinomycete strain isolated from soil in China.Li WJ, Jiang Y, Kroppenstedt RM, Xu LH, Jiang CLSyst Appl Microbiol10.1078/0723-2020-002702004Bacterial Typing Techniques, Base Composition, Carbohydrate Metabolism, Carbohydrates/analysis/isolation & purification, China, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Genes, rRNA/genetics, Lipids/analysis/isolation & purification, Molecular Sequence Data, Nocardia/*classification/cytology/*isolation & purification/physiology, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, *Soil Microbiology, Vitamin K 2/analysis/isolation & purificationEnzymology
Phylogeny17392183Nocardia ninae sp. nov., isolated from a bronchial aspirate.Laurent F, Rodriguez-Nava V, Noussair L, Couble A, Nicolas-Chanoine MH, Boiron PInt J Syst Evol Microbiol10.1099/ijs.0.64476-02007Asthma, Bronchi/*microbiology, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Humans, Middle Aged, Molecular Sequence Data, Nocardia/*classification/cytology/*isolation & purification/physiology, Phylogeny, RNA, Ribosomal, 16S/geneticsPathogenicity
Enzymology19165845(1)H and (13)C NMR assignments of eight nitrogen containing compounds from Nocardia alba sp.nov (YIM 30243(T)).Ding ZG, Zhao JY, Yang PW, Li MG, Huang R, Cui XL, Wen MLMagn Reson Chem10.1002/mrc.23932009Carbon Isotopes, Flavins/*chemistry/isolation & purification, Magnetic Resonance Spectroscopy, Molecular Structure, Nocardia/*chemistry, Peptides, Cyclic/*chemistry/isolation & purification, Piperazines/*chemistry/isolation & purification, Protons, Uracil/*analogs & derivatives/*chemistry/isolation & purificationPhylogeny
Phylogeny24510973Nocardia sungurluensis sp. nov., isolated from soil.Camas M, Veyisoglu A, Sahin NInt J Syst Evol Microbiol10.1099/ijs.0.051334-02014Bacterial Typing Techniques, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Molecular Sequence Data, Nocardia/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Turkey, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny26297293Nocardia halotolerans sp. nov., a halotolerant actinomycete isolated from saline soil.Moshtaghi Nikou M, Ramezani M, Ali Amoozegar M, Rasooli M, Harirchi S, Shahzadeh Fazeli SA, Schumann P, Sproer C, Ventosa AInt J Syst Evol Microbiol10.1099/ijsem.0.0003942015Actinobacteria/genetics, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Molecular Sequence Data, *Nocardia/classification, Phospholipids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride, Soil, Soil Microbiology, WetlandsGenetics
Phylogeny28820104Nocardia cavernae sp. nov., a novel actinobacterium isolated from a karst cave sample.Li QQ, Han MX, Fang BZ, Jiao JY, Liu L, Yang ZW, Zhang WQ, Wei DQ, Li WJInt J Syst Evol Microbiol10.1099/ijsem.0.0020722017Bacterial Typing Techniques, Base Composition, Caves/*microbiology, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Mycolic Acids/chemistry, Nocardia/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny32375925Nocardia colli sp. nov., a new pathogen isolated from a patient with primary cutaneous nocardiosis.Zhou T, Wang XY, Deng DQ, Xu LH, Li XL, Guo Y, Li WH, Xie H, Zhang PL, Zhou XHInt J Syst Evol Microbiol10.1099/ijsem.0.0038562020Adult, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Female, Humans, Mycolic Acids/chemistry, Neck, Nocardia/*classification/isolation & purification, Nocardia Infections/*microbiology, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryPathogenicity

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11999Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44684)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44684
19688Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44684.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
36734Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6056
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/
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
79899Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID134244.1StrainInfo: A central database for resolving microbial strain identifiers
116178Curators of the CIPCollection of Institut Pasteur (CIP 108434)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108434