Strain identifier

BacDive ID: 10816

Type strain: Yes

Species: Nocardia amamiensis

Strain Designation: TT 00-78

Strain history: IFM 10867 <-- DSM 45066 <-- NBRC 102102 <-- T. Tamura TT 00-78.

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@ref: 12311

BacDive-ID: 10816

DSM-Number: 45066

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

description: Nocardia amamiensis TT 00-78 is an aerobe, spore-forming, Gram-positive bacterium that builds an aerial mycelium and was isolated from sugarcane field soil.

NCBI tax id

NCBI tax idMatching level

strain history

12311<- NBRC <- T. Tamura; TT 00-78
67770IFM 10867 <-- DSM 45066 <-- NBRC 102102 <-- T. Tamura TT 00-78.

doi: 10.13145/bacdive10816.20240510.9

Name and taxonomic classification


  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Mycobacteriales
  • family: Nocardiaceae
  • genus: Nocardia
  • species: Nocardia amamiensis
  • full scientific name: Nocardia amamiensis Yamamura et al. 2007

@ref: 12311

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardiaceae

genus: Nocardia

species: Nocardia amamiensis

full scientific name: Nocardia amamiensis Yamamura et al. 2007

strain designation: TT 00-78

type strain: yes


cell morphology

@refgram staincell shapemotilityconfidence

colony morphology

@refcolony colorincubation periodmedium used
20162Cream (9001)10-14 daysISP 2
20162Cream (9001)10-14 daysISP 3
20162Beige (1001)10-14 daysISP 4
20162Beige (1001)10-14 daysISP 5
20162Beige (1001)10-14 daysISP 6
20162Beige (1001)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
20162yesAerial MyceliumCreamISP 2
20162yesAerial MyceliumCreamISP 3
20162yesAerial MyceliumCreamISP 4
20162noISP 5
20162noISP 6
20162noISP 7


  • @ref: 12311
  • multimedia content:
  • caption: Medium 65 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

12311GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)yes 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
20162ISP 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
20162ISP 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:
20162ISP 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
20162ISP 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
20162ISP 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
20162ISP 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

culture temp


Physiology and metabolism

oxygen tolerance

  • @ref: 32025
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence


  • @ref: 32025
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0.0-3.0 %


  • @ref: 67770
  • observation: quinones: MK-8(H4, ω-cycl), MK-8(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3202529987glutamate+carbon source
3202517306maltose+carbon source
3202537684mannose+carbon source
3202530031succinate+carbon source
3202527082trehalose+carbon source


68382alkaline phosphatase+
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+
68382valine arylamidase-
68382cystine arylamidase-
68382acid phosphatase+

API zym

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

Isolation, sampling and environmental information


@refsample typecountryorigin.countrycontinentgeographic location
12311sugarcane field soilJapanJPNAsia
67770Soil in a sugar-cane fieldJapanJPNAsiaAmami Island

isolation source categories

#Host#Plants#Herbaceous plants (Grass,Crops)


  • @ref: 69479
  • File name: preview.99_8137.png
  • url:;96_243;97_907;98_5793;99_8137&stattab=map
  • Last taxonomy: Nocardia amamiensis
  • 16S sequence: GQ217492
  • Sequence Identity:
  • Total samples: 240
  • soil counts: 135
  • aquatic counts: 26
  • animal counts: 56
  • plant counts: 23

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
123112Risk group (German classification)
201621German classification

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Nocardia amamiensis culture-collection CDC:W9691 16S ribosomal RNA gene, partial sequenceGQ2174921441nuccore404578
20218Nocardia amamiensis strain DSM 45066 16S ribosomal RNA gene, partial sequenceJN041463462nuccore404578
12311Nocardia amamiensis gene for 16S ribosomal RNA, partial sequenceAB2751641474nuccore404578

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardia amamiensis NBRC 1021021210066.4wgspatric1210066
66792Nocardia amamiensis NBRC 1021022731957726draftimg1210066
67770Nocardia amamiensis NBRC 102102GCA_001612745contigncbi1210066

GC content

6777067.4high performance liquid chromatography (HPLC)

Genome-based predictions



External links

@ref: 12311

culture collection no.: DSM 45066, KCTC 19208, NBRC 102102, JCM 14877, IFM 10867

straininfo link

  • @ref: 80078
  • straininfo: 297518


Phylogeny17625201Nocardia amamiensis sp. nov., isolated from a sugar-cane field in Japan.Yamamura H, Tamura T, Sakiyama Y, Harayama SInt J Syst Evol Microbiol10.1099/ijs.0.64829-02007Bacterial Typing Techniques, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA, Japan, Microscopy, Electron, Scanning, Molecular Sequence Data, Nocardia/chemistry/*classification/genetics/*isolation & purification, Nucleic Acid Hybridization, Phylogeny, Quinones/analysis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Saccharum/microbiology, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, *Soil MicrobiologyGenetics
Phylogeny20348315Nocardia niwae sp. nov., isolated from human pulmonary sources.Moser BD, Klenk HP, Schumann P, Potter G, Lasker BA, Steigerwalt AG, Hinrikson HP, Brown JMInt J Syst Evol Microbiol10.1099/ijs.0.020370-02010Adult, Aged, Aged, 80 and over, Anti-Bacterial Agents/pharmacology, Bacterial Typing Techniques, DNA Gyrase/genetics, DNA, Bacterial/genetics, Fatty Acids/analysis, Female, Florida, Humans, Lung/*microbiology, Male, Microbial Sensitivity Tests, Middle Aged, Molecular Sequence Data, Nocardia/*classification/drug effects/genetics/isolation & purification, Nocardia Infections/*microbiology, Phenotype, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAPathogenicity


12311Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45066)
20162Wink, J. 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
32025Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604128277
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770Curators of the JCM
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. 1.0 beta
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann 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/ based on the model GenomeNet Sporulation v. 1
80078Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID297518.1StrainInfo: A central database for resolving microbial strain identifiers