Strain identifier

BacDive ID: 10613

Type strain: Yes

Species: Gordonia araii

Strain history: Y. Mikami IFM 10211.

NCBI tax ID(s): 1073574 (strain), 263909 (species)

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General

@ref: 12096

BacDive-ID: 10613

DSM-Number: 44811

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

description: Gordonia araii DSM 44811 is an aerobe, spore-forming, mesophilic human pathogen that was isolated from human sputum.

NCBI tax id

NCBI tax idMatching level
263909species
1073574strain

strain history

@refhistory
12096<- Y. Mikami, IFM
67770Y. Mikami IFM 10211.

doi: 10.13145/bacdive10613.20230509.8.1

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

@ref: 12096

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Gordoniaceae

genus: Gordonia

species: Gordonia araii

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

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31693positive0.5-1.1 µm0.3-0.5 µmrod-shapedno
69480no97.459
69480positive100

colony morphology

@refcolony colorincubation periodmedium used
19875Beige10-14 daysISP 2
19875Beige10-14 daysISP 3
1987510-14 daysISP 4
1987510-14 daysISP 5
1987510-14 daysISP 6
1987510-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
19875noISP 2
19875noISP 3
19875noISP 4
19875noISP 5
19875noISP 6
19875noISP 7

pigmentation

  • @ref: 31693
  • production: yes

multimedia

  • @ref: 12096
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_44811.jpg
  • caption: Medium 215 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12096BHI MEDIUM (DSMZ Medium 215)yeshttps://mediadive.dsmz.de/medium/215Name: BHI MEDIUM (DSMZ Medium 215) Composition: Brain heart infusion 37.0 g/l Distilled water
12096TRYPTICASE 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
19875ISP 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
19875ISP 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:
19875ISP 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
19875ISP 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
19875ISP 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
19875ISP 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
12096positivegrowth28mesophilic
19875positiveoptimum28mesophilic
31693positivegrowth30mesophilic
31693positiveoptimum30mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepH
31693positivegrowth7
31693positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 31693
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
31693yes
69481yes100
69480no99.973

observation

@refobservation
31693aggregates in chains
67770quinones: MK-9(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3169317234glucose+carbon source
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
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
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

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
19875-+-+--+-+----------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
19875+++-+-+--++-+-++---

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
12096human sputumJapanJPNAsia
60052Human sputum,48-yr-old male,pneumoniaJapanJPNAsia
67770Sputum of a 48-year-old male Japanese patient with bacterial pneumonia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_110.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_85;97_90;98_99;99_110&stattab=map
  • Last taxonomy: Gordonia
  • 16S sequence: KF410341
  • Sequence Identity:
  • Total samples: 373
  • soil counts: 33
  • aquatic counts: 131
  • animal counts: 198
  • plant counts: 11

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
12096yes, in single cases1Risk group (German classification)
198752Risk group

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Gordonia araii strain DSM 44811 16S ribosomal RNA gene, partial sequenceKF4103411365ena263909
12096Gordonia araii gene for 16S rRNA, partial sequence, strain: IFM 10211AB1628001499ena1073574

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Gordonia araii NBRC 100433 IFM 10211GCA_013004535contigncbi1073574
66792Gordonia araii NBRC 1004331073574.3wgspatric1073574
66792Gordonia araii NBRC 100433 strain IFM 102111073574.5wgspatric1073574
66792Gordonia araii NBRC 1004332519899569draftimg1073574
67770Gordonia araii NBRC 100433GCA_000241265contigncbi1073574

GC content

  • @ref: 67770
  • GC-content: 68
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno95.093yes
flagellatedno98.375yes
gram-positiveyes90.239yes
anaerobicno99.376no
aerobicyes90.828yes
halophileno89.031no
spore-formingno84.142yes
thermophileno97.747yes
glucose-utilyes86.405no
glucose-fermentno89.503no

External links

@ref: 12096

culture collection no.: DSM 44811, IFM 10211, JCM 12131, NBRC 100433, CCUG 53883, CIP 109346

straininfo link

  • @ref: 79886
  • straininfo: 297191

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
Phylogeny19567568Gordonia kroppenstedtii sp. nov., a phenol-degrading actinomycete isolated from a polluted stream.Kim KK, Lee KC, Klenk HP, Oh HM, Lee JSInt J Syst Evol Microbiol10.1099/ijs.0.005322-02009Actinobacteria/*classification/genetics/isolation & purification/*metabolism, Aerobiosis, Bacterial Typing Techniques, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Korea, Locomotion, Molecular Sequence Data, Phenol/*metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, Rivers/*microbiology, Sequence Analysis, DNA, *Water Pollution, ChemicalMetabolism
Phylogeny32427091Gordonia crocea sp. nov. and Gordonia spumicola sp. nov. isolated from sludge of a wastewater treatment plant.Tamura T, Saito S, Hamada M, Kang Y, Hoshino Y, Gonoi T, Mikami Y, Yaguchi TInt J Syst Evol Microbiol10.1099/ijsem.0.0042252020Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gordonia Bacterium/*classification/isolation & purification, Japan, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, Vitamin K 2/analogs & derivatives/chemistry, Waste Water/*microbiologyTranscriptome
Genetics33664146Complete and Circularized Bacterial Genome Sequence of Gordonia sp. Strain X0973.Gulvik CA, Batra D, Rowe LA, Sheth M, Nobles S, Lee JS, McQuiston JR, Lasker BAMicrobiol Resour Announc10.1128/MRA.01479-202021

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
12096Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44811)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44811
19875Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44811.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
31693Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604127970
60052Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 53883)https://www.ccug.se/strain?id=53883
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 updatesNucleic Acids Res. 49: D498-D508 202033211880
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
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
79886Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID297191.1StrainInfo: A central database for resolving microbial strain identifiers