Strain identifier

BacDive ID: 10780

Type strain: Yes

Species: Nocardia takedensis

Strain Designation: MS1-3

Strain history: CIP <- 2005, DSMZ <- M. Hayakawa, Yamanashi Univ., Kofu, Japan: strain MS1-3

NCBI tax ID(s): 1206735 (strain), 259390 (species)

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General

@ref: 11988

BacDive-ID: 10780

DSM-Number: 44801

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

description: Nocardia takedensis MS1-3 is an aerobe, spore-forming, mesophilic human pathogen that was isolated from sediments of moat.

NCBI tax id

NCBI tax idMatching level
1206735strain
259390species

strain history

@refhistory
11988<- M. Hayakawa, Yamanashi Univ.; MS1-3 <- H. Yamamura
67770NBRC 100417 <-- M. Hayakawa MS1-3.
123425CIP <- 2005, DSMZ <- M. Hayakawa, Yamanashi Univ., Kofu, Japan: strain MS1-3

doi: 10.13145/bacdive10780.20230509.8.1

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 takedensis
  • full scientific name: Nocardia takedensis Yamamura et al. 2005

@ref: 11988

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardiaceae

genus: Nocardia

species: Nocardia takedensis

full scientific name: Nocardia takedensis Yamamura et al. 2005

strain designation: MS1-3

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
31274positiverod-shapedno
69480no94.844
69480positive100
123425positiverod-shapedno

colony morphology

@refcolony colorincubation periodmedium used
19706Yellow orange10-14 daysISP 2
1970610-14 daysISP 3
1970610-14 daysISP 4
19706Yellow orange10-14 daysISP 5
19706Yellow orange10-14 daysISP 6
19706Yellow orange10-14 daysISP 7
123425

multicellular morphology

@refforms multicellular complexmedium name
19706noISP 2
19706noISP 3
19706noISP 4
19706noISP 5
19706noISP 6
19706noISP 7

pigmentation

  • @ref: 31274
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11988GYM 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
11988BHI 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
11988TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.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
19706ISP 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
19706ISP 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:
19706ISP 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
19706ISP 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
19706ISP 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
19706ISP 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
36765MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
123425CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
123425CIP Medium 57yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=57

culture temp

@refgrowthtypetemperaturerange
11988positivegrowth28mesophilic
19706positiveoptimum28mesophilic
36765positivegrowth30mesophilic
67770positivegrowth28mesophilic
123425positivegrowth25-41
123425nogrowth10psychrophilic
123425nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31274aerobe
123425obligate aerobe

spore formation

@refspore formationconfidence
69481yes100
69480no96.097

halophily

@refsaltgrowthtested relationconcentration
123425NaClpositivegrowth0-2 %
123425NaClnogrowth4 %
123425NaClnogrowth6 %
123425NaClnogrowth8 %
123425NaClnogrowth10 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3127430089acetate+carbon source
3127428260galactose+carbon source
3127417234glucose+carbon source
3127437684mannose+carbon source
3127417992sucrose+carbon source
312744853esculin+hydrolysis
3127417632nitrate+reduction
12342516947citrate-carbon source
1234254853esculin-hydrolysis
123425606565hippurate+hydrolysis
12342517632nitrate+reduction
12342516301nitrite-reduction
12342517632nitrate-respiration
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

antibiotic resistance

  • @ref: 123425
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 123425
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12342515688acetoin-
12342517234glucose-

enzymes

@refvalueactivityec
31274urease+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
68379pyrazinamidase-3.5.1.B15
123425oxidase-
123425beta-galactosidase-3.2.1.23
123425alcohol dehydrogenase+1.1.1.1
123425gelatinase+/-
123425amylase-
123425DNase-
123425caseinase-3.4.21.50
123425catalase+1.11.1.6
123425tween esterase-
123425gamma-glutamyltransferase-2.3.2.2
123425lecithinase-
123425lipase-
123425lysine decarboxylase-4.1.1.18
123425ornithine decarboxylase-4.1.1.17
123425phenylalanine ammonia-lyase-4.3.1.24
123425tryptophan deaminase-
123425urease+3.5.1.5
68382leucine arylamidase+3.4.11.1
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382alpha-galactosidase-3.2.1.22
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 NAGESCUREGELSACNITControlGLURIBXYLMANMALLACGLYG
19706-++--+-+---
11988--+--+-+---+/---------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
19706+++-+----++---++---
11988--+/--+---------++----
123425++++++---++-+-++----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
123425+---------------------+--------+-+------------------------------------+----+--+----------++-----+--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
11988sediments of moatYamanashi prefectureJapanJPNAsia
67770Sediment from the moat surrounding Takeda ShrineYamanashi Pref.JapanJPNAsia
123425Environment, Moat sedimentTakeda Shrine, YamanashiJapanJPNAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_7203.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_243;97_907;98_1064;99_7203&stattab=map
  • Last taxonomy: Nocardia takedensis
  • 16S sequence: JF797317
  • Sequence Identity:
  • Total samples: 38
  • soil counts: 6
  • aquatic counts: 9
  • animal counts: 23

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
11988yes, in single cases1Risk group (German classification)
1234252Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Nocardia takedensis strain DSM 44801 16S ribosomal RNA gene, partial sequenceJF7973171414ena259390
11988Nocardia takedensis gene for 16S rRNA, partial sequence, strain:MS1-3AB1582771448ena259390
67770Nocardia takedensis 16S ribosomal RNA gene, partial sequenceGQ3761851441ena259390

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardia takedensis NBRC 1004171206735.3wgspatric1206735
66792Nocardia takedensis NBRC 1004172551306172draftimg1206735
67770Nocardia takedensis NBRC 100417GCA_000308695contigncbi1206735

GC content

@refGC-contentmethod
1198868.6
6777068.6high performance liquid chromatography (HPLC)
6777069.5genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno94.905yes
gram-positiveyes89.502no
anaerobicno98.992no
aerobicyes88.708yes
halophileno95.446no
spore-formingyes84.606no
thermophileno99.424yes
glucose-utilyes87.502yes
flagellatedno98.24yes
glucose-fermentno92.939yes

External links

@ref: 11988

culture collection no.: DSM 44801, CIP 108681, NBRC 100417, JCM 13313, IFM 10572

straininfo link

  • @ref: 80046
  • straininfo: 135133

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15653914Nocardia takedensis sp. nov., isolated from moat sediment and scumming activated sludge.Yamamura H, Hayakawa M, Nakagawa Y, Tamura T, Kohno T, Komatsu F, Iimura YInt J Syst Evol Microbiol10.1099/ijs.0.63189-02005Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fresh Water/*microbiology, Genes, rRNA, Genotype, Geologic Sediments/*microbiology, Molecular Sequence Data, Nocardia/*classification/genetics/isolation & purification/physiology, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiologyGenetics
Metabolism17259606Bacterial degradation of poly(trans-1,4-isoprene) (gutta percha).Warneke S, Arenskotter M, Tenberge KB, Steinbuchel AMicrobiology (Reading)10.1099/mic.0.2006/000109-02007Carbon Dioxide/metabolism, Culture Media, DNA, Bacterial/analysis, Gutta-Percha/*metabolism, Microscopy, Electron, Scanning, Molecular Sequence Data, Nocardia/*classification/genetics/growth & development/isolation & purification/*metabolism, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAPhylogeny
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
Phylogeny32815801Nocardia macrotermitis sp. nov. and Nocardia aurantia sp. nov., isolated from the gut of the fungus-growing termite Macrotermes natalensis.Benndorf R, Schwitalla JW, Martin K, de Beer ZW, Vollmers J, Kaster AK, Poulsen M, Beemelmanns CInt J Syst Evol Microbiol10.1099/ijsem.0.0043982020Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Gastrointestinal Microbiome, Isoptera/*microbiology, Nocardia/*classification/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, South Africa, Vitamin K 2/analogs & derivatives/chemistryEnzymology
Phylogeny33560199Nocardia bovistercoris sp. nov., an actinobacterium isolated from cow dung.Zhang X, Zhang L, Yu X, Zhang J, Jiao Y, Ju H, Wang X, Zhao J, Xiang WInt J Syst Evol Microbiol10.1099/ijsem.0.0046992021

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
11988Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44801)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44801
19706Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44801.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
31274Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604127594
36765Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6336
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
80046Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID135133.1StrainInfo: A central database for resolving microbial strain identifiers
123425Curators of the CIPCollection of Institut Pasteur (CIP 108681)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108681