Strain identifier

BacDive ID: 16912

Type strain: Yes

Species: Actinocorallia glomerata

Strain Designation: I-226

Strain history: T. Itoh I-226.

NCBI tax ID(s): 46203 (species)

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

@ref: 11703

BacDive-ID: 16912

DSM-Number: 44360

keywords: 16S sequence, Bacteria, mesophilic

description: Actinocorallia glomerata I-226 is a mesophilic bacterium that builds an aerial mycelium and was isolated from decayed leaf of a deciduous tree from a pond.

NCBI tax id

  • NCBI tax id: 46203
  • Matching level: species

strain history

@refhistory
11703<- JCM <- T. Itoh, Kitasato Inst., Tokyo, I-226
67770T. Itoh I-226.

doi: 10.13145/bacdive16912.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Streptosporangiales
  • family: Thermomonosporaceae
  • genus: Actinocorallia
  • species: Actinocorallia glomerata
  • full scientific name: Actinocorallia glomerata (Itoh et al. 1996) Zhang et al. 2001
  • synonyms

    • @ref: 20215
    • synonym: Actinomadura glomerata

@ref: 11703

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Thermomonosporaceae

genus: Actinocorallia

species: Actinocorallia glomerata

full scientific name: Actinocorallia glomerata (Itoh et al. 1996) Zhang et al. 2001

strain designation: I-226

type strain: yes

Morphology

colony morphology

@refincubation periodmedium used
1965310-14 daysISP 2
1965310-14 daysISP 3
1965310-14 daysISP 4
1965310-14 daysISP 5
1965310-14 daysISP 6
1965310-14 daysISP 7

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
19653yesAerial MyceliumOyster whiteISP 2
19653yesAerial MyceliumOyster whiteISP 3
19653noISP 4
19653noISP 5
19653noISP 6
19653noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11703N-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
11703GYM 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
19653ISP 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
19653ISP 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:
19653ISP 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
19653ISP 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
19653ISP 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
19653ISP 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

@refgrowthtypetemperaturerange
11703positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

halophily

  • @ref: 19653
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1965317234glucose+
1965322599arabinose+
1965317992sucrose+
1965318222xylose+
1965317268myo-inositol+
1965329864mannitol+
1965328757fructose+
1965326546rhamnose+
1965316634raffinose+
1965362968cellulose+
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate+assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin-
6836835581indole-

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
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
19653++++++++++++---+++-

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19653----+-+---+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
11703decayed leaf of a deciduous tree from a pondSaitamoJapanJPNAsia
67770Decayed leaf of deciduous treeSaitama Pref.JapanJPNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Pond (small)
#Host#Plants#Decomposing plant
#Host#Plants#Tree
#Host Body-Site#Plant#Leaf (Phyllosphere)

taxonmaps

  • @ref: 69479
  • File name: preview.99_67782.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_239;96_29278;97_36909;98_47765;99_67782&stattab=map
  • Last taxonomy: Actinocorallia glomerata
  • 16S sequence: AF134068
  • Sequence Identity:
  • Total samples: 221
  • soil counts: 132
  • aquatic counts: 3
  • animal counts: 3
  • plant counts: 83

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
117031Risk group (German classification)
196531Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Actinomadura glomerata partial 16S rRNA gene, strain IMSNU 22179TAJ2937041509ena46203
20218Actinomadura glomerata 16S ribosomal RNA gene, partial sequenceAF1340681454ena46203
20218Actinomadura glomerata 16S-23S ribosomal RNA intergenic spacer region, partial sequenceAF134098381ena46203
20218Actinocorallia glomerata gene for 16S rRNA, partial sequenceD506601350ena46203
20218Actinocorallia glomerata gene for 16S rRNA, partial sequence, strain: NBRC 15960AB3645911464ena46203

GC content

@refGC-contentmethod
1170371.7
6777070.9high performance liquid chromatography (HPLC)

External links

@ref: 11703

culture collection no.: DSM 44360, IFO 15960, JCM 9376, NBRC 15960, IMSNU 22179

straininfo link

  • @ref: 85917
  • straininfo: 50589

literature

  • topic: Phylogeny
  • Pubmed-ID: 26944933
  • title: Actinocorallia lasiicapitis sp. nov., an actinomycete isolated from the head of an ant (Lasius fuliginosus L.).
  • authors: Liu C, Li Y, Ye L, Zhao J, Piao C, Li Z, Li J, Xiang W, Wang X
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001005
  • year: 2016
  • mesh: Actinomycetales/*classification/genetics/isolation & purification, Animals, Ants/*microbiology, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry
  • topic2: Transcriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11703Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44360)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44360
19653Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44360.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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68368Automatically annotated from API 20E
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
85917Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID50589.1StrainInfo: A central database for resolving microbial strain identifiers