Strain identifier

BacDive ID: 10610

Type strain: Yes

Species: Gordonia otitidis

Strain history: Y. Mikami IFM 10032.

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

@ref: 12094

BacDive-ID: 10610

DSM-Number: 44809

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive, coccus-shaped

description: Gordonia otitidis DSM 44809 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from human.

NCBI tax id

NCBI tax idMatching level
249058species
1108044strain

strain history

@refhistory
12094<- Y. Mikami, IFM
67770Y. Mikami IFM 10032.

doi: 10.13145/bacdive10610.20230509.8.1

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 otitidis
  • full scientific name: Gordonia otitidis Iida et al. 2005

@ref: 12094

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Gordoniaceae

genus: Gordonia

species: Gordonia otitidis

full scientific name: Gordonia otitidis Iida et al. 2005

type strain: yes

Morphology

cell morphology

  • @ref: 31314
  • gram stain: positive
  • cell length: 2.5-3.1 µm
  • cell width: 0.6-0.8 µm
  • cell shape: coccus-shaped
  • motility: no

colony morphology

@refcolony colorincubation periodmedium used
20124Pure orange (2004)10-14 daysISP 2
20124Beige (1001)10-14 daysISP 3
2012410-14 daysISP 4
20124Pure orange (2004)10-14 daysISP 5
20124Beige (1001)10-14 daysISP 6
20124Pure orange (2004)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
20124noISP 2
20124noISP 3
20124noISP 4
20124noISP 5
20124noISP 6
20124noISP 7

pigmentation

  • @ref: 31314
  • production: yes

multimedia

  • @ref: 12094
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_44809.jpg
  • caption: Medium 65 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12094GYM 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
12094TRYPTICASE 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
20124ISP 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
20124ISP 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:
20124ISP 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
20124ISP 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
20124ISP 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
20124ISP 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
12094positivegrowth28mesophilic
20124positiveoptimum28mesophilic
59484positivegrowth30-37mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31314aerobe
59484aerobe

observation

@refobservation
31314aggregates in clumps
67770quinones: MK-9(H2), MK-8(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2012417234glucose+
2012422599arabinose-
2012417992sucrose+
2012418222xylose-
2012417268myo-inositol-
2012429864mannitol+
2012428757fructose+
2012426546rhamnose-
2012416634raffinose-
2012462968cellulose-
31314178794-hydroxybenzoate+carbon source
3131416449alanine+carbon source
3131422599arabinose+carbon source
3131418403L-arabitol+carbon source
3131428260galactose+carbon source
3131425017leucine+carbon source
31314506227N-acetylglucosamine+carbon source
3131418401phenylacetate+carbon source
3131426271proline+carbon source
3131417148putrescine+carbon source
3131426490quinate+carbon source
3131417822serine+carbon source
3131417992sucrose+carbon source
683794853esculin-hydrolysis
6837916199urea-hydrolysis
683795291gelatin-hydrolysis
6837917992sucrose+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 (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 coryne

@refPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELSAC
20124-----+----+

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
20124--+++----++---++---

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
12094humanJapanJPNAsia
59484HumanJapanJPNAsia
67770Ear discharge of a Japanese patient with external otitis

isolation source categories

  • Cat1: #Host
  • Cat2: #Human

taxonmaps

  • @ref: 69479
  • File name: preview.99_3430.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_85;97_2147;98_2632;99_3430&stattab=map
  • Last taxonomy: Gordonia
  • 16S sequence: AB122026
  • Sequence Identity:
  • Total samples: 5392
  • soil counts: 169
  • aquatic counts: 1283
  • animal counts: 3862
  • plant counts: 78

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
120942Risk group (German classification)
201242German classification

Sequence information

16S sequences

  • @ref: 31314
  • description: Gordonia otitidis gene for 16S rRNA, partial sequence, strain:IFM 10032
  • accession: AB122026
  • length: 1471
  • database: nuccore
  • NCBI tax ID: 1108044

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Gordonia otitidis NBRC 1004261108044.3wgspatric1108044
66792Gordonia otitidis NBRC 1004262514885045draftimg1108044
67770Gordonia otitidis NBRC 100426GCA_000248075contigncbi1108044

GC content

@refGC-contentmethod
3131464.9
6777064.9high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno92.557yes
flagellatedno98.433yes
gram-positiveyes90.492no
anaerobicno99.224yes
aerobicyes88.696yes
halophileno82.181no
spore-formingno81.697no
thermophileno99.157yes
glucose-utilyes89.026yes
glucose-fermentno88.108no

External links

@ref: 12094

culture collection no.: DSM 44809, IFM 10032, JCM 12355, NBRC 100426, CCUG 52243, CIP 109016

straininfo link

  • @ref: 79883
  • straininfo: 127244

literature

  • topic: Phylogeny
  • Pubmed-ID: 16166681
  • title: Gordonia otitidis sp. nov., isolated from a patient with external otitis.
  • authors: Iida S, Taniguchi H, Kageyama A, Yazawa K, Chibana H, Murata S, Nomura F, Kroppenstedt RM, Mikami Y
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.63282-0
  • year: 2005
  • mesh: Actinomycetales Infections/*microbiology, Adult, Bronchitis/*microbiology, DNA, Bacterial, Female, Genes, rRNA, Genotype, Gordonia Bacterium/chemistry/*classification/genetics/isolation & purification, Humans, Male, Middle Aged, Molecular Sequence Data, Nucleic Acid Hybridization, Otitis Externa/*microbiology, Phenotype, Phylogeny, Pleural Effusion/*microbiology, RNA, Ribosomal, 16S
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
12094Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44809)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44809
20124Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44809.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
31314Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2762928776041
59484Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 52243)https://www.ccug.se/strain?id=52243
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
79883Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID127244.1StrainInfo: A central database for resolving microbial strain identifiers