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.

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

@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
1210066strain
404578species

strain history

@refhistory
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

LPSN

  • @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

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
32025positiverod-shapedno
69480no93.148

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

multimedia

  • @ref: 12311
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_45066.jpg
  • caption: Medium 65 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12311GYM 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
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

@refgrowthtypetemperature
12311positivegrowth28
20162positiveoptimum28
67770positivegrowth28

Physiology and metabolism

oxygen tolerance

  • @ref: 32025
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
32025yes
69480yes90.569
69481yes100

halophily

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

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2016217234glucose+
2016222599arabinose-
2016217992sucrose-
2016218222xylose-
2016217268myo-inositol-
2016229864mannitol-
2016228757fructose-
2016226546rhamnose-
2016216634raffinose-
2016262968cellulose-
3202529987glutamate+carbon source
3202517306maltose+carbon source
3202537684mannose+carbon source
3202530031succinate+carbon source
3202527082trehalose+carbon source
320254853esculin+hydrolysis
3202517632nitrate+reduction

enzymes

@refvalueactivityec
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 zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
20162+++-+--+-++-+-++---

Isolation, sampling and environmental information

isolation

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

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture#Field
#Environmental#Terrestrial#Soil
#Host#Plants#Herbaceous plants (Grass,Crops)

taxonmaps

  • @ref: 69479
  • File name: preview.99_8137.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;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

@refGC-contentmethod
3202567.4
6777067.4high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno93.148yes
gram-positiveyes85.781yes
anaerobicno99.002yes
aerobicyes91.371yes
halophileno89.88no
spore-formingyes90.569yes
thermophileno99.03yes
glucose-utilyes88.55yes
flagellatedno97.85yes
glucose-fermentno91.888no

External links

@ref: 12311

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

straininfo link

  • @ref: 80078
  • straininfo: 297518

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
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

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
12311Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45066)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45066
20162Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM45066.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
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 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/
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
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