Strain identifier

BacDive ID: 131076

Type strain: Yes

Species: Gordonia didemni

Strain Designation: B204

Strain history: <- F. Fantinatti-Garboggini, CPQBA,Brazil; B204 <- C. B. Afonso de Menezes

NCBI tax ID(s): 1934933 (species)

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General

@ref: 22368

BacDive-ID: 131076

DSM-Number: 46679

keywords: 16S sequence, Bacteria, mesophilic

description: Gordonia didemni B204 is a mesophilic bacterium that was isolated from marine ascidium Didemnum sp..

NCBI tax id

  • NCBI tax id: 1934933
  • Matching level: species

strain history

  • @ref: 22368
  • history: <- F. Fantinatti-Garboggini, CPQBA,Brazil; B204 <- C. B. Afonso de Menezes

doi: 10.13145/bacdive131076.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Mycobacteriales
  • family: Gordoniaceae
  • genus: Gordonia
  • species: Gordonia didemni
  • full scientific name: Gordonia didemni de Menezes et al. 2016

@ref: 22368

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Gordoniaceae

genus: Gordonia

species: Gordonia didemni

full scientific name: Gordonia didemni de Menezes et al. 2016

strain designation: B204

type strain: yes

Morphology

colony morphology

@refcolony colormedium used
69463Beige red (3012)ISP 3
69463Beige red (3012)ISP 4
69463Pastel yellow (1034)ISP 2
69463Pastel yellow (1034)ISP 6
69463Salmon orange (2012)ISP 7
69463Salmon pink (3022)ISP 5
69463Salmon pink (3022)suter without tyrosine
69463Signal orange (2010)suter with tyrosine

multicellular morphology

@refforms multicellular complexcomplex namemedium name
69463noAerial myceliumISP 2
69463noAerial myceliumISP 3
69463noAerial myceliumISP 4
69463noAerial myceliumISP 5
69463noAerial myceliumISP 6
69463noAerial myceliumISP 7
69463noAerial myceliumsuter with tyrosine
69463noAerial myceliumsuter without tyrosine

pigmentation

@refproductionname
69463noMelanin
69463nosoluble pigment

multimedia

  • @ref: 22368
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_46679.jpg
  • caption: Medium 65 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
22368GPHF-MEDIUM (DSMZ Medium 553)yeshttps://mediadive.dsmz.de/medium/553Name: GPHF-MEDIUM (DSMZ Medium 553) Composition: Agar 20.0 g/l Glucose 10.0 g/l Beef extract 5.0 g/l Yeast extract 5.0 g/l Casein peptone 5.0 g/l CaCl2 x 2 H2O 0.74 g/l Distilled water
22368GYM 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

culture temp

  • @ref: 22368
  • growth: positive
  • type: growth
  • temperature: 28
  • range: mesophilic

Physiology and metabolism

halophily

  • @ref: 69463
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6946322599arabinose-growth
6946362968cellulose-growth
6946328757fructose+growth
6946317234glucose+growth
6946317268inositol-growth
6946337684mannose+growth
6946316634raffinose-growth
6946326546rhamnose+growth
6946317992sucrose+growth
6946318222xylose-growth
6837917632nitrate+reduction
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

enzymes

@refvalueactivityec
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
68379pyrrolidonyl arylamidase-3.4.19.3
68379pyrazinamidase-3.5.1.B15
68382alkaline phosphatase+3.1.3.1
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
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 coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
69463+-----+------------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
69463++/-+-++/-+/---++/----++---

Isolation, sampling and environmental information

isolation

  • @ref: 22368
  • sample type: marine ascidium Didemnum sp.
  • host species: Didemnum
  • geographic location: Sao Paulo, Sao Sebastiao
  • country: Brazil
  • origin.country: BRA
  • continent: Middle and South America

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Host#Invertebrates (Other)#Tunicata

taxonmaps

  • @ref: 69479
  • File name: preview.99_2867.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_85;97_90;98_2221;99_2867&stattab=map
  • Last taxonomy: Gordonia
  • 16S sequence: JN615417
  • Sequence Identity:
  • Total samples: 979
  • soil counts: 171
  • aquatic counts: 234
  • animal counts: 526
  • plant counts: 48

Safety information

risk assessment

  • @ref: 22368
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 22368
  • description: Gordonia didemni strain B204 16S ribosomal RNA gene, partial sequence
  • accession: JN615417
  • length: 1386
  • database: ena
  • NCBI tax ID: 1934933

GC content

  • @ref: 22368
  • GC-content: 70.5
  • method: fluorimetric

External links

@ref: 22368

culture collection no.: DSM 46679, CBMAI 1069

straininfo link

  • @ref: 89539
  • straininfo: 399536

literature

  • topic: Phylogeny
  • Pubmed-ID: 26678782
  • title: Gordonia didemni sp. nov. an actinomycete isolated from the marine ascidium Didemnum sp.
  • authors: de Menezes CB, Afonso RS, de Souza WR, Parma M, de Melo IS, Zucchi TD, Fantinatti-Garboggini F
  • journal: Antonie Van Leeuwenhoek
  • DOI: 10.1007/s10482-015-0632-y
  • year: 2015
  • mesh: Actinobacteria/classification/genetics/*isolation & purification, Animals, Brazil, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Urochordata/*microbiology
  • topic2: Genetics

Reference

@idauthorstitledoi/urlcatalogue
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
22368Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-46679Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 46679)
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
69463Wink, J.Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweighttps://cdn.dsmz.de/wink/DSM%2046679.pdf
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
89539Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID399536.1