Strain identifier

BacDive ID: 10778

Type strain: Yes

Species: Nocardia higoensis

Strain history: Y. Mikami IFM 10084.

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 12050

BacDive-ID: 10778

DSM-Number: 44732

keywords: rod-shaped, Gram-positive, mesophilic, aerobe, Bacteria, 16S sequence, genome sequence, human pathogen

description: Nocardia higoensis DSM 44732 is an aerobe, mesophilic, Gram-positive human pathogen that was isolated from human .

NCBI tax id

NCBI tax idMatching level
228599species
1206730strain

strain history

doi: 10.13145/bacdive10778.20220920.7

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 higoensis
  • full scientific name: Nocardia higoensis Kageyama et al. 2004

@ref: 12050

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardiaceae

genus: Nocardia

species: Nocardia higoensis

full scientific name: Nocardia higoensis Kageyama et al. 2004

type strain: yes

Morphology

cell morphology

  • @ref: 31216
  • gram stain: positive
  • cell length: 1.5 µm
  • cell width: 0.7 µm
  • cell shape: rod-shaped
  • motility: no

colony morphology

@refcolony colorincubation periodmedium used
20107Pastel yellow (1034)10-14 daysISP 2
20107Pastel yellow (1034)10-14 daysISP 3
2010710-14 daysISP 4
20107Pastel yellow (1034)10-14 daysISP 5
2010710-14 daysISP 6
20107Pastel yellow (1034)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
20107noISP 2
20107noISP 3
20107noISP 4
20107noISP 5
20107noISP 6
20107noISP 7

pigmentation

  • @ref: 31216
  • production: no

multimedia

  • @ref: 12050
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_44732.jpg
  • caption: Medium 535 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12050TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://bacmedia.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
20107ISP 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
20107ISP 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:
20107ISP 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
20107ISP 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
20107ISP 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
20107ISP 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
33976MEDIUM 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)

culture temp

@refgrowthtypetemperaturerange
12050positivegrowth28mesophilic
20107positiveoptimum28mesophilic
33976positivegrowth30mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 31216
  • oxygen tolerance: aerobe

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2010717234glucose+
2010722599arabinose+
2010717992sucrose+
2010718222xylose+
2010717268myo-inositol-
2010729864mannitol-
2010728757fructose-
2010726546rhamnose-
2010716634raffinose-
2010762968cellulose-
6837917992sucrose-fermentation
683795291gelatin-hydrolysis
6837916199urea-hydrolysis
683794853esculin+hydrolysis

enzymes

@refvalueactivityec
31216urease+3.5.1.5
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
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-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API coryne

@refPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELSAC
20107-++--+-+---

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
20107+++-++++-++---++---

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
12050human (patient with lung nocardiosis)JapanJPNAsia
67770Patient with pleurisyJapanJPNAsia

isolation source categories

Cat1Cat2Cat3
#Infection#Disease
#Host#Human
#Host Body-Site#Oral cavity and airways#Lung

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
12050yes, in single cases1Risk group (German classification)
201072German classification

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Nocardia higoensis strain DSM 44732 isolate VNS38 16S ribosomal RNA gene, partial sequenceAY903620606ena1206730
20218Nocardia higoensis 16S ribosomal RNA gene, partial sequenceGQ3761691441ena228599
20218Nocardia higoensis strain DSM 44732 16S ribosomal RNA gene, partial sequenceJF7973091414ena1206730
12050Nocardia higoensis gene for 16S rRNA, partial sequence, strain:IFM 10084AB1087781497ena1206730

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardia higoensis NBRC 100133 NBRC 100133GCA_000308595contigncbi1206730
66792Nocardia higoensis NBRC 1001331206730.4wgspatric1206730
66792Nocardia higoensis NBRC 1001332551306154draftimg1206730
67770Nocardia higoensis NBRC 100133, whole genome shotgun sequencing projectBAGA00000000ncbi1206730

GC content

@refGC-contentmethod
1205069
6777069.3genome sequence analysis

External links

@ref: 12050

culture collection no.: DSM 44732, CIP 108597, IFM 10084, JCM 12121, NBRC 100133

straininfo link

@refpassport
20218http://www.straininfo.net/strains/381897
20218http://www.straininfo.net/strains/534434
20218http://www.straininfo.net/strains/301447
20218http://www.straininfo.net/strains/381898
20218http://www.straininfo.net/strains/381899

literature

  • topic: Phylogeny
  • Pubmed-ID: 15545412
  • title: Nocardia shimofusensis sp. nov., isolated from soil, and Nocardia higoensis sp. nov., isolated from a patient with lung nocardiosis in Japan.
  • authors: Kageyama A, Yazawa K, Mukai A, Kinoshita M, Takata N, Nishimura K, Kroppenstedt RM, Mikami Y
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.63061-0
  • year: 2004
  • mesh: Aged, Antimetabolites/pharmacology, Bacterial Typing Techniques, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Fatty Acids/analysis/isolation & purification, Female, Fluorouracil/pharmacology, Genes, rRNA, Humans, Japan, Lung/*microbiology, Molecular Sequence Data, Nocardia/chemistry/*classification/drug effects/genetics/*isolation & purification/metabolism, Nocardia Infections/*microbiology, Nucleic Acid Hybridization, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology
  • topic2: Enzymology

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
12050Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44732)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44732
20107Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44732.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
2754210.1099/ijs.0.63061-015545412
31216Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604127542
33976Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6244
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