Strain identifier

BacDive ID: 10728

Type strain: Yes

Species: Nocardia paucivorans

Strain history: CIP <- 2000, JCM <- DSMZ <- A.F. Yassin: strain IMMIB D-1632 <- Inst. Microbiol., Immunol. and Med. Lab., Berlin, Germany

NCBI tax ID(s): 1206734 (strain), 114259 (species)

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General

@ref: 11507

BacDive-ID: 10728

DSM-Number: 44386

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

description: Nocardia paucivorans DSM 44386 is an aerobe, spore-forming, mesophilic bacterium that builds an aerial mycelium and was isolated from sputum.

NCBI tax id

NCBI tax idMatching level
1206734strain
114259species

strain history

@refhistory
11507<- A. F. Yassin; IMMIB D-1632 <- Inst. of Microbiology, Immunology and Medical Lab., Berlin
67770DSM 44386 <-- A. F. Yassin IMMIB D-1632 <-- Inst. Microbiol., Immunol. Med. Lab., Berlin.
121636CIP <- 2000, JCM <- DSMZ <- A.F. Yassin: strain IMMIB D-1632 <- Inst. Microbiol., Immunol. and Med. Lab., Berlin, Germany

doi: 10.13145/bacdive10728.20230509.8.1

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 paucivorans
  • full scientific name: Nocardia paucivorans Yassin et al. 2000

@ref: 11507

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardiaceae

genus: Nocardia

species: Nocardia paucivorans

full scientific name: Nocardia paucivorans Yassin et al. 2000

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480positive100
121636positiverod-shapedno

colony morphology

@refcolony colorincubation periodmedium used
20053Pastel yellow (1034)10-14 daysISP 2
20053Pastel yellow (1034)10-14 daysISP 3
20053Colorless10-14 daysISP 4
20053Colorless10-14 daysISP 5
20053Colorless10-14 daysISP 6
20053Colorless10-14 daysISP 7
121636

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
20053yesAerial MyceliumWhiteISP 2
20053noISP 3
20053noISP 4
20053noISP 5
20053noISP 6
20053noISP 7

multimedia

  • @ref: 11507
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_44386.jpg
  • caption: Medium 693 37°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11507BHI MEDIUM (DSMZ Medium 215)yeshttps://mediadive.dsmz.de/medium/215Name: BHI MEDIUM (DSMZ Medium 215) Composition: Brain heart infusion 37.0 g/l Distilled water
11507COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://mediadive.dsmz.de/medium/693Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
20053ISP 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
20053ISP 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:
20053ISP 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
20053ISP 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
20053ISP 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
20053ISP 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
39584MEDIUM 111 - for ClavibacteryesDistilled water make up to (1000.000 ml);Sodium chloride (5.000 g);Agar(15.000 g);Glucose (5.000 g);Yeast extract (5.000 g);Trypticase peptone (10.000 g)
121636CIP Medium 111yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=111

culture temp

@refgrowthtypetemperaturerange
20053positiveoptimum37mesophilic
11507positivegrowth37mesophilic
39584positivegrowth37mesophilic
57068positivegrowth30-37mesophilic
67770positivegrowth37mesophilic
121636positivegrowth25-45
121636nogrowth10psychrophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
57068aerobe
121636obligate aerobe

spore formation

@refspore formationconfidence
69481yes100
69480no98.919

halophily

@refsaltgrowthtested relationconcentration
121636NaClpositivegrowth0-6 %
121636NaClnogrowth8 %
121636NaClnogrowth10 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12163616947citrate-carbon source
1216364853esculin-hydrolysis
121636606565hippurate-hydrolysis
12163617632nitrate+reduction
12163616301nitrite-reduction
12163617632nitrate-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

metabolite production

  • @ref: 121636
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12163615688acetoin+
12163617234glucose-

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
121636oxidase-
121636beta-galactosidase-3.2.1.23
121636alcohol dehydrogenase-1.1.1.1
121636gelatinase-
121636amylase-
121636DNase-
121636caseinase-3.4.21.50
121636catalase+1.11.1.6
121636tween esterase+
121636gamma-glutamyltransferase-2.3.2.2
121636lecithinase-
121636lipase-
121636lysine decarboxylase-4.1.1.18
121636ornithine decarboxylase-4.1.1.17
121636protease-
121636tryptophan deaminase-
121636urease-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
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

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    57068C14:05.114
    57068C16:032.116
    57068C18:04.818
    57068C16:0 10-methyl1.316.433
    57068C16:1 ω11c1.715.757
    57068C16:1 ω7c215.819
    57068C16:1 ω7c/C15:0 ISO 2OH3.115.85
    57068C18:1 ω9c15.317.769
    57068C18:2 ω6,9c/C18:0 ANTE13.717.724
    57068C20:2 ω6,9c1.219.735
    57068TBSA 10Me18:018.218.392
    57068Unidentified1.515.609
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
20053---+---------------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
20053++++++-+-++----+---
121636+++-+----++----+----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121636------------+--------------------------------------------------------------+--+-----------+--------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
11507sputumBerlinGermanyDEUEurope
57068Human sputum,chronic lung diseaseBerlinGermanyDEUEurope
67770Sputa of a patient with chronic lung disease
121636Human, Sputum

isolation source categories

  • Cat1: #Host Body Product
  • Cat2: #Fluids
  • Cat3: #Sputum

taxonmaps

  • @ref: 69479
  • File name: preview.99_5286.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_243;97_3135;98_3937;99_5286&stattab=map
  • Last taxonomy: Nocardia
  • 16S sequence: GQ376188
  • Sequence Identity:
  • Total samples: 1410
  • soil counts: 1068
  • aquatic counts: 52
  • animal counts: 144
  • plant counts: 146

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
115072Risk group (German classification)
200532German classification
1216362Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Nocardia paucivorans 16S ribosomal RNA gene, complete sequenceAF1798651459ena114259
20218Nocardia paucivorans clone A4 16S ribosomal RNA gene, partial sequenceAY262324502ena114259
20218Nocardia paucivorans strain ATCC BAA-278 16S ribosomal RNA gene, partial sequenceDQ6599131393ena114259
20218Nocardia paucivorans strain ATCC BAA-278 16S ribosomal RNA gene, partial sequenceFJ172128608ena114259
20218Nocardia paucivorans strain ATCC BAA-278 16S ribosomal RNA gene, partial sequenceGQ3761881443ena114259
20218Nocardia paucivorans strain ATCC BAA-278 clone 1 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceGU236432646ena114259
20218Nocardia paucivorans strain ATCC BAA-278 clone 2 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceGU236433646ena114259
20218Nocardia paucivorans strain ATCC BAA-278 clone 3 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceGU236434646ena114259
20218Nocardia paucivorans strain ATCC BAA-278 clone 4 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceGU236435646ena114259
20218Nocardia paucivorans strain ATCC BAA-278 clone 5 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceGU236436646ena114259
20218Nocardia paucivorans strain DSM 44386 16S ribosomal RNA gene, complete sequenceAF4300411494ena114259
20218Nocardia paucivorans strain DSM 44386 16S ribosomal RNA gene, partial sequenceAY756557606ena114259
20218Nocardia paucivorans strain DSM 44386 16S ribosomal RNA gene, partial sequenceJN041587464ena114259

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardia paucivorans NBRC 1003731206734.4wgspatric1206734
66792Nocardia paucivorans NBRC 1003732551306169draftimg1206734
67770Nocardia paucivorans NBRC 100373GCA_000308675contigncbi1206734

GC content

@refGC-contentmethod
6777065.9high performance liquid chromatography (HPLC)
6777066.6genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno92.453no
gram-positiveyes89.593no
anaerobicno98.728no
aerobicyes87.211no
halophileno87.845no
spore-formingyes61.799no
glucose-utilyes86.493no
flagellatedno97.927no
thermophileno95.984no
glucose-fermentno90.436yes

External links

@ref: 11507

culture collection no.: DSM 44386, ATCC BAA 278, JCM 10919, NBRC 100373, CCUG 46117, IMMIB D-1632, CGMCC 4.1722, CIP 106798, IFM 10001

straininfo link

  • @ref: 79996
  • straininfo: 50604

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny10758891Nocardia paucivorans sp. nov.Yassin AF, Rainey FA, Burghardt J, Brzezinka H, Mauch M, Schaal KPInt J Syst Evol Microbiol10.1099/00207713-50-2-8032000Bacterial Typing Techniques, Base Composition, Bronchi/microbiology, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Genes, rRNA, Humans, Lipids/analysis, Lung Diseases/*microbiology, Middle Aged, Molecular Sequence Data, Nocardia/chemistry/*classification/isolation & purification/physiology, Nocardia Infections/*microbiology, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sputum/microbiologyPathogenicity
Phylogeny10939654Nocardia abscessus sp. nov.Yassin AF, Rainey FA, Mendrock U, Brzezinka H, Schaal KPInt J Syst Evol Microbiol10.1099/00207713-50-4-14872000Adult, Cloning, Molecular, DNA, Bacterial/genetics, Genes, Bacterial, Humans, Male, Middle Aged, Molecular Sequence Data, Nocardia/chemistry/*classification/genetics, Nucleic Acid Hybridization, Phylogeny, RNA, Bacterial/analysis, RNA, Ribosomal, 16S/analysisEnzymology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11507Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44386)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44386
20053Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44386.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
39584Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18968
57068Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 46117)https://www.ccug.se/strain?id=46117
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
79996Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID50604.1StrainInfo: A central database for resolving microbial strain identifiers
121636Curators of the CIPCollection of Institut Pasteur (CIP 106798)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106798