Strain identifier

BacDive ID: 8044

Type strain: Yes

Species: Hamadaea tsunoensis

Strain Designation: 6420-P, 6420P

Strain history: CIP <- 2001, JCM <- K. Asano: strain 6420P

NCBI tax ID(s): 1121946 (strain), 53368 (species)

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General

@ref: 11397

BacDive-ID: 8044

DSM-Number: 44101

keywords: genome sequence, 16S sequence, Bacteria, spore-forming, mesophilic

description: Hamadaea tsunoensis 6420-P is a spore-forming, mesophilic bacterium that builds an aerial mycelium and was isolated from soil, woodland.

NCBI tax id

NCBI tax idMatching level
53368species
1121946strain

strain history

@refhistory
11397<- IFO <- K. Asano, Kyowa Hakko Co., 6420-P
67770IFO 14552 <-- K. Asano 6420-P.
123597CIP <- 2001, JCM <- K. Asano: strain 6420P

doi: 10.13145/bacdive8044.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micromonosporales
  • family: Micromonosporaceae
  • genus: Hamadaea
  • species: Hamadaea tsunoensis
  • full scientific name: Hamadaea tsunoensis (Asano et al. 1989) Ara et al. 2008

  • synonyms

    @refsynonym
    20215Catellatospora tsunoensis
    20215Catellatospora tsunoense

@ref: 11397

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micromonosporaceae

genus: Hamadaea

species: Hamadaea tsunoensis

full scientific name: Hamadaea tsunoensis (Asano et al. 1989) Ara et al. 2008

strain designation: 6420-P, 6420P

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no92.769
69480100positive
123597nococcus-shaped

colony morphology

@refcolony colorincubation periodmedium used
19997Yellow10-14 daysISP 2
19997Rapeseed yellow (1021)10-14 daysISP 3
19997Bright orange10-14 daysISP 4
19997Deep orange (2011)10-14 daysISP 5
19997Yellow10-14 daysISP 6
19997Rapeseed yellow (1021)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium namecomplex namecomplex color
19997noISP 2
19997noISP 3
19997noISP 4
19997yesISP 5Aerial MyceliumWhite
19997noISP 6
19997noISP 7

multimedia

@refmultimedia contentintellectual property rightscaption
11397https://www.dsmz.de/microorganisms/photos/DSM_44101-1.jpg© Leibniz-Institut DSMZ
11397https://www.dsmz.de/microorganisms/photos/DSM_44101.jpg© Leibniz-Institut DSMZMedium 65 28°C
66793EM_DSM_44101_1.jpg© HZI/Manfred Rohdeelectron microscopic image
66793EM_DSM_44101_2.jpg© HZI/Manfred Rohdeelectron microscopic image
66793EM_DSM_44101_3.jpg© HZI/Manfred Rohdeelectron microscopic image
66793EM_DSM_44101_4.jpg© HZI/Manfred Rohdeelectron microscopic image
66793EM_DSM_44101_5.jpg© HZI/Manfred Rohdeelectron microscopic image

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11397GYM 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
19997ISP 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
19997ISP 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:
19997ISP 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
19997ISP 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
19997ISP 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
19997ISP 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
39636MEDIUM 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)
11397N-Z-AMINE-MEDIUM (DSMZ Medium 554)yeshttps://mediadive.dsmz.de/medium/554Name: N-Z-AMINE-MEDIUM (DSMZ Medium 554) Composition: Starch 20.0 g/l Agar 20.0 g/l Glucose 10.0 g/l N-Z amine 5.0 g/l Yeast extract 5.0 g/l CaCO3 1.0 g/l Distilled water
11397ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84)yeshttps://mediadive.dsmz.de/medium/84Name: ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84) Composition: Agar 20.0 g/l Rolled oats 20.0 g/l ZnSO4 x 7 H2O 0.001 g/l MnCl2 x 4 H2O 0.001 g/l FeSO4 x 7 H2O 0.001 g/l Distilled water
123597CIP Medium 57yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=57

culture temp

@refgrowthtypetemperaturerange
19997positiveoptimum28mesophilic
11397positivegrowth28mesophilic
39636positivegrowth30mesophilic
67770positivegrowth28mesophilic
123597positivegrowth25-30mesophilic
123597nogrowth10psychrophilic
123597nogrowth37mesophilic
123597nogrowth41thermophilic
123597nogrowth45thermophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481yes96
69480yes100

halophily

@refsaltgrowthtested relationconcentration
19997NaClpositivegrowth0 %
123597NaClpositivegrowth0 %
123597NaClnogrowth2 %
123597NaClnogrowth4 %
123597NaClnogrowth6 %
123597NaClnogrowth8 %
123597NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: MK-9(H4), MK-9(H6), MK-10(H4), MK-9(H6), MK-9(H4), MK-9(H8)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1999717234glucose+
1999722599arabinose+
1999717992sucrose+
1999718222xylose-
1999717268myo-inositol-
1999729864mannitol+
1999728757fructose+
1999726546rhamnose-
1999716634raffinose-
1999762968cellulose+
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose-builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837128017starch-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose-builds acid from
6837117992sucrose-builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
683714853esculin+builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
6837159640N-acetylglucosamine-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose-builds acid from
6837115824D-fructose-builds acid from
6837117634D-glucose-builds acid from
6837112936D-galactose-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837116988D-ribose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine+hydrolysis
12359716947citrate-carbon source
1235974853esculin+hydrolysis
123597606565hippurate+hydrolysis
12359717632nitrate-reduction
12359716301nitrite-reduction
12359717632nitrate-respiration

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno
12359735581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin+
6836835581indole-
12359715688acetoin-
12359717234glucose-

enzymes

@refvalueactivityec
68368gelatinase-
68368tryptophan deaminase-4.1.99.1
68368urease-3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368lysine decarboxylase-4.1.1.18
68368arginine dihydrolase+3.5.3.6
68368beta-galactosidase+3.2.1.23
123597oxidase-
123597beta-galactosidase+3.2.1.23
123597alcohol dehydrogenase-1.1.1.1
123597gelatinase-
123597catalase+1.11.1.6
123597gamma-glutamyltransferase+2.3.2.2
123597lysine decarboxylase-4.1.1.18
123597ornithine decarboxylase-4.1.1.17
123597phenylalanine ammonia-lyase-4.3.1.24
123597tryptophan deaminase-
123597urease+3.5.1.5
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

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
123597--++-+----++-+-++---

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19997++-------+-

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
123597--+/-+/---------------------++/-+/-+/---------+/-------+/------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
11397soil, woodlandYamaguchi, Tsuno-GunJapanJPNAsia
67770Woodland soilTsuno-gun, Yamaguchi Pref.JapanJPNAsia
123597Environment, Woodland soilJapanJPNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Forest
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_8120.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_94;96_3745;97_4605;98_5913;99_8120&stattab=map
  • Last taxonomy: Hamadaea tsunoensis subclade
  • 16S sequence: X93200
  • Sequence Identity:
  • Total samples: 5386
  • soil counts: 3787
  • aquatic counts: 105
  • animal counts: 144
  • plant counts: 1350

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
113971Risk group (German classification)
199971German classification
1235971Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218C.tsuoense 16S rRNA geneX932001452ena1121946
11397Hamadaea tsunoensis strain IMSNU 22005 16S ribosomal RNA gene, partial sequenceAF1521101509ena1121946

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Hamadaea tsunoensis DSM 441011121946.6wgspatric1121946
66792Hamadaea tsunoensis DSM 441012523533533draftimg1121946
67770Hamadaea tsunoensis DSM 44101GCA_000428945scaffoldncbi1121946

GC content

@refGC-contentmethod
1139770.3
6777070.6thermal denaturation, midpoint method (Tm)
6777070.3high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes96no
motileno93.874no
flagellatedno97.718no
gram-positiveyes87.822no
anaerobicno99.161no
halophileno95.089yes
spore-formingyes94.453no
thermophileno99.47yes
glucose-utilyes88.01yes
aerobicyes91.747no
glucose-fermentno90.051no

External links

@ref: 11397

culture collection no.: DSM 44101, ATCC 49365, CIP 107014, FERM BP-1195, IFO 14552, JCM 9105, NBRC 14552, NRRL B-16491, VKM Ac-2010, IMSNU 22005, CGMCC 4.1403, CGMCC 4.1506, CGMCC 4.5568, KCTC 9355

straininfo link

  • @ref: 77472
  • straininfo: 88632

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18676486Transfer of Catellatospora koreensis Lee et al. 2000 as Catelliglobosispora koreensis gen. nov., comb. nov. and Catellatospora tsunoense Asano et al. 1989 as Hamadaea tsunoensis gen. nov., comb. nov., and emended description of the genus Catellatospora Asano and Kawamoto 1986 emend. Lee and Hah 2002.Ara I, Bakir MA, Kudo TInt J Syst Evol Microbiol10.1099/ijs.0.65548-02008Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Japan, Korea, Micromonosporaceae/chemistry/*classification/genetics/physiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Species SpecificityGenetics
Phylogeny20207801Allocatelliglobosispora scoriae gen. nov., sp. nov., isolated from volcanic ash.Lee DW, Lee SDInt J Syst Evol Microbiol10.1099/ijs.0.020313-02010Bacterial Typing Techniques, Carbohydrates/analysis, DNA, Bacterial/genetics, Lipids/analysis, Micromonosporaceae/*classification/genetics/isolation & purification, Molecular Sequence Data, *Phylogeny, Pigments, Biological/analysis, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analysis, *Volcanic EruptionsGenetics
Phylogeny26842996Hamadaea flava sp. nov., isolated from a soil sample and emended description of the genus Hamadaea.Chu X, Li S, Chen W, Devi Asem M, Duan YQ, Nie GX, Hozzein WN, Zhi XY, Li WJInt J Syst Evol Microbiol10.1099/ijsem.0.0009492016Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Micromonosporaceae/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny30444473Allorhizocola rhizosphaerae gen. nov., sp. nov., a new member of Micromonosporaceae isolated from rhizosphere soil of the plant Calligonum mongolicum.Sun Y, Jiang ZM, Zhao LL, Su J, Yu LY, Tian YQ, Zhang YQInt J Syst Evol Microbiol10.1099/ijsem.0.0031142018Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Micromonosporaceae/*classification/isolation & purification, Peptidoglycan/chemistry, *Phylogeny, Polygonaceae/*microbiology, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11397Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44101)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44101
19997Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44101.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
39636Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/19208
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)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life 35: 676-683 201728604660
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68368Automatically annotated from API 20E
68371Automatically annotated from API 50CH acid
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
77472Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID88632.1StrainInfo: A central database for resolving microbial strain identifiers
123597Curators of the CIPCollection of Institut Pasteur (CIP 107014)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107014