Strain identifier

BacDive ID: 10611

Type strain: Yes

Species: Gordonia effusa

Strain history: CIP <- 2006, JCM <- 2003, IFM

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

@ref: 12095

BacDive-ID: 10611

DSM-Number: 44810

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

description: Gordonia effusa CCUG 53882 is an aerobe, spore-forming, mesophilic human pathogen that was isolated from human sputum.

NCBI tax id

NCBI tax idMatching level
1077974strain
263908species

strain history

@refhistory
12095<- Y. Mikami, IFM
67770Y. Mikami IFM 10200.
118998CIP <- 2006, JCM <- 2003, IFM

doi: 10.13145/bacdive10611.20230509.8.1

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 effusa
  • full scientific name: Gordonia effusa Kageyama et al. 2006

@ref: 12095

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Gordoniaceae

genus: Gordonia

species: Gordonia effusa

full scientific name: Gordonia effusa Kageyama et al. 2006 emend. Nouioui et al. 2018

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31693positive0.5-2.1 µm0.3-0.6 µmrod-shapedno
69480no95.48
69480positive99.999
118998positiverod-shapedno

colony morphology

@refcolony colorincubation periodmedium used
20125Pastel yellow (1034)10-14 daysISP 2
20125Pastel yellow (1034)10-14 daysISP 3
20125Pastel yellow (1034)10-14 daysISP 4
20125Pastel yellow (1034)10-14 daysISP 5
20125Pastel yellow (1034)10-14 daysISP 6
20125Pastel yellow (1034)10-14 daysISP 7
600512 days

multicellular morphology

@refforms multicellular complexmedium name
20125noISP 2
20125noISP 3
20125noISP 4
20125noISP 5
20125noISP 6
20125noISP 7

pigmentation

  • @ref: 31693
  • production: yes

multimedia

  • @ref: 12095
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_44810.jpg
  • caption: Medium 535 28 °C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12095TRYPTICASE 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
20125ISP 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
20125ISP 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:
20125ISP 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
20125ISP 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
20125ISP 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
20125ISP 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
37519MEDIUM 116 - for Streptomyces, Nocardia, Streptosporangium and Mycobacterium chlorophenolicumyesDistilled water make up to (1000.000 ml);Agar (20.000 g);Glucose (4.000g);Yeast extract (4.000 g);Malt extract (10.000 g)
118998CIP Medium 116yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=116

culture temp

@refgrowthtypetemperaturerange
12095positivegrowth28mesophilic
20125positiveoptimum28mesophilic
31693positivegrowth30mesophilic
31693positiveoptimum30mesophilic
37519positivegrowth30mesophilic
60051positivegrowth37mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepH
31693positivegrowth7
31693positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31693aerobe
60051microaerophile
118998obligate aerobe

spore formation

@refspore formationconfidence
31693yes
69481yes100
69480no99.925

observation

@refobservation
31693aggregates in chains
67770quinones: MK-9(H8), MK-9(H6)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3169316449alanine+carbon source
3169335391aspartate+carbon source
3169316947citrate+carbon source
31693506227N-acetylglucosamine+carbon source
3169330031succinate+carbon source
3169317992sucrose+carbon source
11899817632nitrate-reduction
11899816301nitrite-reduction
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

metabolite production

  • @ref: 118998
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
31693cytochrome oxidase+1.9.3.1
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
118998oxidase-
118998catalase+1.11.1.6
118998urease+3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase lipase (C 8)+
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
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
20125--+/-+--+-+----------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
20125+++++----++-+-++---
118998+-+------++-+-+++---

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
12095human sputumJapanJPNAsia
60051Human sputum,74-yr-old man,kidney dysfunctionJapanJPNAsia
67770Sputum of a 74-year-old Japanese male patient with kidney dysfunction
118998Human, SputumJapanJPNAsia

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Host Body Product#Fluids#Sputum

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
12095yes, in single cases1Risk group (German classification)
201252
1189981Risk group (French classification)

Sequence information

16S sequences

  • @ref: 12095
  • description: Gordonia effusa gene for 16S rRNA, partial sequence, strain: IFM 10200
  • accession: AB162799
  • length: 1509
  • database: ena
  • NCBI tax ID: 263908

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Gordonia effusa NBRC 1004321077974.3wgspatric1077974
66792Gordonia effusa NBRC 1004322523231038draftimg1077974
67770Gordonia effusa NBRC 100432GCA_000241305contigncbi1077974

GC content

  • @ref: 67770
  • GC-content: 62.5
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno95.481yes
flagellatedno98.235yes
gram-positiveyes91.208yes
anaerobicno99.479yes
aerobicyes89.367no
halophileno94.209no
spore-formingno76.593yes
thermophileno99.478no
glucose-utilyes88.967no
glucose-fermentno92.311no

External links

@ref: 12095

culture collection no.: CCUG 53882, CIP 109345, DSM 44810, IFM 10200, JCM 12130, NBRC 100432

straininfo link

  • @ref: 79884
  • straininfo: 297194

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16902014Gordonia araii sp. nov. and Gordonia effusa sp. nov., isolated from patients in Japan.Kageyama A, Iida S, Yazawa K, Kudo T, Suzuki SI, Koga T, Saito H, Inagawa H, Wada A, Kroppenstedt RM, Mikami YInt J Syst Evol Microbiol10.1099/ijs.0.64067-02006Aged, Base Composition, Corynebacterium/chemistry/*classification/physiology, Corynebacterium Infections/complications/microbiology, DNA, Bacterial/chemistry/genetics, Humans, Japan, Kidney Diseases/complications, Male, Middle Aged, Molecular Sequence Data, Phenotype, Pneumonia, Bacterial/microbiology, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Homology, Nucleic Acid, Species Specificity, Sputum/microbiologyPathogenicity
Phylogeny33709899Gordonia asplenii sp. nov., isolated from humic soil on bird's nest fern (Asplenium nidus L.).Suriyachadkun C, Ngaemthao W, Pujchakarn T, Chunhametha SInt J Syst Evol Microbiol10.1099/ijsem.0.0047462021

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
12095Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44810)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44810
20125Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44810.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
31693Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2797028776041
37519Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7076
60051Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 53882)https://www.ccug.se/strain?id=53882
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updates33211880Nucleic Acids Res. 49: D498-D508 2020
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
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
79884Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID297194.1StrainInfo: A central database for resolving microbial strain identifiers
118998Curators of the CIPCollection of Institut Pasteur (CIP 109345)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109345