Strain identifier

BacDive ID: 10814

Type strain: Yes

Species: Nocardia terpenica

Strain history: CIP <- 2007, NBRC <- Y. Hoshino, Chiba Univ., Chiba, Japan: strain IFM 0706

NCBI tax ID(s): 1206738 (strain), 455432 (species)

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General

@ref: 12104

BacDive-ID: 10814

DSM-Number: 44935

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

description: Nocardia terpenica DSM 44935 is an aerobe, mesophilic, Gram-positive bacterium that builds an aerial mycelium and was isolated from human.

NCBI tax id

NCBI tax idMatching level
455432species
1206738strain

strain history

@refhistory
12104<- Y. Mikami <- K. Yazawa, IFM
67770Y. Mikami IFM 0706.
123447CIP <- 2007, NBRC <- Y. Hoshino, Chiba Univ., Chiba, Japan: strain IFM 0706

doi: 10.13145/bacdive10814.20230509.8.1

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 terpenica
  • full scientific name: Nocardia terpenica Hoshino et al. 2007

@ref: 12104

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardiaceae

genus: Nocardia

species: Nocardia terpenica

full scientific name: Nocardia terpenica Hoshino et al. 2007

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
31946positive1 µm0.35 µmrod-shapedno
123447positiverod-shapedno

colony morphology

@refcolony colorincubation periodmedium used
20142Ivory (1014)10-14 daysISP 2
20142Cream (9001)10-14 daysISP 3
2014210-14 daysISP 4
20142Cream (9001)10-14 daysISP 5
20142Cream (9001)10-14 daysISP 6
20142Cream (9001)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium namecomplex namecomplex color
20142noISP 2
20142noISP 3
20142noISP 5
20142yesISP 6Aerial MyceliumCream
20142yesISP 7Aerial MyceliumOlive grey

multimedia

  • @ref: 12104
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_44935.jpg
  • caption: Medium 65 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12104GYM 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
20142ISP 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
20142ISP 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:
20142ISP 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
20142ISP 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
20142ISP 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
20142ISP 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
37799MEDIUM 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)
123447CIP Medium 57yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=57

culture temp

@refgrowthtypetemperaturerange
12104positivegrowth28mesophilic
31946positivegrowth37mesophilic
37799positivegrowth30mesophilic
67770positivegrowth35mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
12104aerobe
31946aerobe
123447obligate aerobe

observation

  • @ref: 67770
  • observation: quinones: MK-8(H4, ω-cycl), MK-8(H4), MK-9(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2014217234glucose+
2014222599arabinose-
2014217992sucrose-
2014218222xylose-
2014217268myo-inositol+
2014229864mannitol+
2014228757fructose-
2014226546rhamnose-
2014216634raffinose-
2014262968cellulose-
3194615963ribitol+carbon source
3194616947citrate+carbon source
3194628260galactose+carbon source
3194630911sorbitol+carbon source
12344717632nitrate-reduction
12344716301nitrite-reduction

metabolite production

  • @ref: 123447
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
31946urease+3.5.1.5
123447oxidase-
123447catalase+1.11.1.6
123447urease+3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
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
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
20142+++-+----++---++++-
123447++--+----++----++---

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic location
12104humanJapanJPNAsia
67770Patient with lung nocardiosisJapanJPNAsiaOkayama
123447Human, SputumJapanJPNAsia

isolation source categories

  • Cat1: #Host
  • Cat2: #Human

taxonmaps

  • @ref: 69479
  • File name: preview.99_349.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_243;97_265;98_294;99_349&stattab=map
  • Last taxonomy: Nocardia terpenica subclade
  • 16S sequence: JF797318
  • Sequence Identity:
  • Total samples: 152
  • soil counts: 120
  • aquatic counts: 1
  • animal counts: 18
  • plant counts: 13

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
121042Risk group (German classification)
201422German classification
1234472Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Nocardia terpenica 16S ribosomal RNA gene, partial sequenceGQ3761831441ena455432
20218Nocardia terpenica strain DSM 44935 16S ribosomal RNA gene, partial sequenceJF7973181414ena455432
12104Nocardia terpenica gene for 16S ribosomal RNA, complete sequence, strain: IFM 0706AB2012981485ena455432

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardia terpenica NBRC 1008881206738.4wgspatric1206738
66792Nocardia terpenica strain IFM 0706455432.12wgspatric455432
66792Nocardia terpenica NBRC 1008882551306167draftimg1206738
67770Nocardia terpenica NBRC 100888GCA_000320925contigncbi1206738
67770Nocardia terpenica IFM 0706GCA_013186535contigncbi455432

GC content

@refGC-contentmethod
1210465.4
6777068.5genome sequence analysis
6777065.4high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno90.887no
gram-positiveyes88.533yes
anaerobicno98.887no
aerobicyes89.721no
halophileno92.606no
spore-formingyes78.751no
thermophileno98.42yes
glucose-utilyes90.285no
flagellatedno98.027yes
glucose-fermentno89.916no

External links

@ref: 12104

culture collection no.: DSM 44935, DSM 44897, IFM 0706, JCM 13033, NBRC 100888, CIP 109636

straininfo link

  • @ref: 80076
  • straininfo: 297455

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17625175Nocardia terpenica sp. nov., isolated from Japanese patients with nocardiosis.Hoshino Y, Watanabe K, Iida S, Suzuki SI, Kudo T, Kogure T, Yazawa K, Ishikawa J, Kroppenstedt RM, Mikami YInt J Syst Evol Microbiol10.1099/ijs.0.64695-02007Bacterial Typing Techniques, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Genes, rRNA, Hospitals, Japan, Microscopy, Electron, Scanning, Molecular Sequence Data, Nocardia/chemistry/*classification/genetics/*isolation & purification, Nocardia Infections/*microbiology, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Vitamin K 2/analysisGenetics
Phylogeny19684327Nocardia callitridis sp. nov., an endophytic actinobacterium isolated from a surface-sterilized root of an Australian native pine tree.Kaewkla O, Franco CMMInt J Syst Evol Microbiol10.1099/ijs.0.016337-02009Australia, Base Sequence, Fatty Acids/analysis, Molecular Sequence Data, Nocardia/*classification/genetics/isolation & purification/physiology, Pinus/*microbiology, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, SterilizationGenetics
Genetics32816977Improved De Novo Draft Genome Sequence of the Nocavionin-Producing Type Strain Nocardia terpenica IFM 0706 and Comparative Genomics with the Closely Related Strain Nocardia terpenica IFM 0406.Buchmann A, Gross HMicrobiol Resour Announc10.1128/MRA.00689-202020

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
12104Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44935)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44935
20142Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44935.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
31946Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604128202
37799Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7401
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/
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
80076Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID297455.1StrainInfo: A central database for resolving microbial strain identifiers
123447Curators of the CIPCollection of Institut Pasteur (CIP 109636)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109636