Strain identifier

BacDive ID: 10764

Type strain: Yes

Species: Nocardia ignorata

Strain history: CIP <- 2002, DSMZ <- A.F. Yassin, IMMIB <- Microbial Quality Control Lab

NCBI tax ID(s): 1210075 (strain), 145285 (species)

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General

@ref: 11820

BacDive-ID: 10764

DSM-Number: 44496

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

description: Nocardia ignorata DSM 44496 is an aerobe, spore-forming, mesophilic bacterium that builds an aerial mycelium and was isolated from Unknown,MQCL-specimen.

NCBI tax id

NCBI tax idMatching level
1210075strain
145285species

strain history

@refhistory
11820<- A. F. Yassin; IMMIB R-1434 <- Microbial Quality Control Lab. (Mycobacterium sp.)
67770DSM 44496 <-- A. F. Yassin IMMIB R-1434 <-- Microb. Qual. Control Lab. (Mycobacterium sp.).
120045CIP <- 2002, DSMZ <- A.F. Yassin, IMMIB <- Microbial Quality Control Lab

doi: 10.13145/bacdive10764.20230509.8.1

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 ignorata
  • full scientific name: Nocardia ignorata Yassin et al. 2001

@ref: 11820

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardiaceae

genus: Nocardia

species: Nocardia ignorata

full scientific name: Nocardia ignorata Yassin et al. 2001

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no93.91
69480100positive
120045nopositiverod-shaped

colony morphology

@refcolony colorincubation periodmedium used
19672Pale orange10-14 daysISP 2
19672Beige10-14 daysISP 3
19672Beige10-14 daysISP 4
19672Beige10-14 daysISP 5
19672Beige10-14 daysISP 6
19672Beige10-14 daysISP 7
120045

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
19672yesAerial MyceliumWhiteISP 2
19672yesAerial MyceliumWhiteISP 3
19672yesAerial MyceliumWhiteISP 4
19672noISP 5
19672noISP 6
19672noISP 7

multimedia

  • @ref: 11820
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_44496.jpg
  • caption: Medium 535 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11820TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
11820GYM 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
19672ISP 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
19672ISP 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:
19672ISP 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
19672ISP 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
19672ISP 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
19672ISP 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
38226MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
120045CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
19672positiveoptimum28mesophilic
11820positivegrowth28mesophilic
38226positivegrowth30mesophilic
58073positivegrowth30-37mesophilic
67770positivegrowth28mesophilic
120045positivegrowth25-45
120045nogrowth10psychrophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
58073aerobe
120045obligate aerobe

spore formation

@refspore formationconfidence
69481yes92
69480no99.395

halophily

@refsaltgrowthtested relationconcentration
120045NaClpositivegrowth0-6 %
120045NaClnogrowth8 %
120045NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: MK-8(H6), 2,3-epoxy-MK-8(H6)

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371sucrose-builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose-builds acid from17306
68371salicin-builds acid from17814
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose-builds acid from16024
68371D-fructose-builds acid from15824
68371D-glucose-builds acid from17634
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose-builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
120045citrate-carbon source16947
120045esculin+hydrolysis4853
120045hippurate-hydrolysis606565
120045nitrate+reduction17632
120045nitrite-reduction16301
120045nitrate-respiration17632
68379nitrate-reduction17632
68379esculin-hydrolysis4853
68379urea+hydrolysis16199
68379gelatin-hydrolysis5291
68379D-glucose-fermentation17634
68379D-ribose-fermentation16988
68379D-xylose-fermentation65327
68379D-mannitol-fermentation16899
68379maltose-fermentation17306
68379lactose-fermentation17716
68379sucrose-fermentation17992
68379glycogen-fermentation28087

antibiotic resistance

  • @ref: 120045
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 120045
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12004515688acetoin-
12004517234glucose-

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
120045oxidase-
120045beta-galactosidase-3.2.1.23
120045alcohol dehydrogenase-1.1.1.1
120045gelatinase+/-
120045amylase-
120045DNase-
120045caseinase-3.4.21.50
120045catalase+1.11.1.6
120045gamma-glutamyltransferase+2.3.2.2
120045lecithinase-
120045lipase-
120045lysine decarboxylase-4.1.1.18
120045ornithine decarboxylase-4.1.1.17
120045phenylalanine ammonia-lyase-4.3.1.24
120045tryptophan deaminase-
120045urease+3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
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
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
19672---+--+--+---------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
19672+++-++---++---++---
120045+++++--+-++---+-----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
120045------------------------+/--+/-----------------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
120045++-----------------------------------------------+---------++-------------+----++---+---+-++----+-+

Isolation, sampling and environmental information

isolation

@refsample type
58073Unknown,MQCL-specimen
120045Quality control test

isolation source categories

  • Cat1: #Infection
  • Cat2: #Patient
  • Cat3: #Specimen

taxonmaps

  • @ref: 69479
  • File name: preview.99_1009.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_578;97_676;98_786;99_1009&stattab=map
  • Last taxonomy: Nocardia
  • 16S sequence: AY191254
  • Sequence Identity:
  • Total samples: 189
  • soil counts: 102
  • aquatic counts: 14
  • animal counts: 59
  • plant counts: 14

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
118202Risk group (German classification)
196722Risk group (German classification)
1200452Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Nocardia ignorata partial 16S rRNA gene, strain IMMIB R-1434TAJ3030081489ena145285
20218Nocardia ignorata strain DSM 44496T 16S ribosomal RNA gene, partial sequenceAY1912541398ena145285
20218Nocardia ignorata strain DSM 44496 16S ribosomal RNA gene, partial sequenceAY756554606ena145285
20218Nocardia ignorata strain DSM 44496 16S ribosomal RNA gene, partial sequenceDQ6599071429ena145285
20218Nocardia ignorata 16S ribosomal RNA gene, partial sequenceGQ3761721441ena145285
20218Nocardia ignorata strain DSM 44496 16S ribosomal RNA gene, partial sequenceJN041454462ena145285

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardia ignorata NBRC 1082301210075.4wgspatric1210075
66792Nocardia ignorata strain DSM 44496145285.4wgspatric145285
66792Nocardia ignorata NBRC 1082302731957734draftimg1210075
66792Nocardia ignorata DSM 444962770939491draftimg145285
67770Nocardia ignorata NBRC 108230GCA_001612905contigncbi1210075
67770Nocardia ignorata DSM 44496GCA_004362495scaffoldncbi145285

GC content

  • @ref: 67770
  • GC-content: 68.08
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes92no
motileno92.118no
gram-positiveyes90.053no
anaerobicno99.526yes
halophileno88.601no
spore-formingyes80.597no
thermophileno99.162no
glucose-utilyes90.8no
flagellatedno97.478no
aerobicyes93.548yes
glucose-fermentno92.747yes

External links

@ref: 11820

culture collection no.: DSM 44496, CIP 107670, JCM 11764, NRRL B-24141, CCUG 48296, IMMIB R-1434, CGMCC 4.1830, KCTC 19935, NBRC 108230

straininfo link

  • @ref: 80032
  • straininfo: 50656

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny11760956Nocardia ignorata sp. nov.Yassin AF, Rainey FA, Steiner UInt J Syst Evol Microbiol10.1099/00207713-51-6-21272001DNA, Ribosomal/genetics, Genes, rRNA, Humans, Molecular Sequence Data, Mycobacterium/classification, Mycolic Acids/analysis, Nocardia/chemistry/*classification/genetics/physiology, Nucleic Acid Hybridization, Phylogeny, Quality Control, RNA, Ribosomal, 16S/*genetics, Sequence Analysis, DNAPathogenicity
26644870Molecular, chemical and biological screening of soil actinomycete isolates in seeking bioactive peptide metabolites.Hamedi J, Imanparast S, Mohammadipanah FIran J Microbiol2015
Phylogeny27510998Nocardia lasii sp. nov., a novel actinomycete isolated from the cuticle of an ant (Lasius fuliginosus L).Liu C, Bai L, Ye L, Zhao J, Yan K, Xiang W, Wang XAntonie Van Leeuwenhoek10.1007/s10482-016-0753-y2016Animals, Ants/*microbiology, DNA, Bacterial, Molecular Typing, Nocardia/classification/*isolation & purification, Phylogeny, RNA, Ribosomal, 16S/geneticsEnzymology
Phylogeny35687660Nocardia rosealba sp. nov., a novel ligninase-producing Actinobacterium isolated from soil.Huang Z, He C, Wang Z, Luo X, Sun X, Zhao J, Gao X, Xiang W, Song J, Wang XInt J Syst Evol Microbiol10.1099/ijsem.0.0054162022*Actinobacteria/genetics, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Nocardia, Oxygenases, Phospholipids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil, Soil MicrobiologyTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11820Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44496)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44496
19672Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44496.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
38226Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5131
58073Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 48296)https://www.ccug.se/strain?id=48296
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
80032Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID50656.1StrainInfo: A central database for resolving microbial strain identifiers
120045Curators of the CIPCollection of Institut Pasteur (CIP 107670)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107670