Strain identifier

BacDive ID: 10578

Type strain: Yes

Species: Gordonia aichiensis

Strain Designation: E9028, N934

Strain history: CIP <- 1994, JCM, Rhodococcus aichiensis <- M. Tsukamura: strain E9028

NCBI tax ID(s): 1220583 (strain), 36820 (species)

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General

@ref: 11314

BacDive-ID: 10578

DSM-Number: 43978

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

description: Gordonia aichiensis E9028 is an obligate aerobe, mesophilic, Gram-positive bacterium that was isolated from sputum.

NCBI tax id

NCBI tax idMatching level
36820species
1220583strain

strain history

@refhistory
11314<- M. Goodfellow, N934 <- M. Tsukamura E 9028 (=62001)
67770M. Tsukamura E9028 (=62001).
116166CIP <- 1994, JCM, Rhodococcus aichiensis <- M. Tsukamura: strain E9028

doi: 10.13145/bacdive10578.20250331.9.3

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 aichiensis
  • full scientific name: Gordonia aichiensis corrig. (Tsukamura 1983) Klatte et al. 1994

  • synonyms

    @refsynonym
    20215Rhodococcus aichiensis
    20215Rhodococcus aichiense
    20215Gordona aichiensis

@ref: 11314

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Gordoniaceae

genus: Gordonia

species: Gordonia aichiensis

full scientific name: Gordonia aichiensis (Tsukamura 1983) Klatte et al. 1994

strain designation: E9028, N934

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
116166positiverod-shapedno
125438no93.6
125438positive90.002
125439positive93.9

colony morphology

@refcolony colorincubation periodmedium used
19990Deep orange (2011)10-14 daysISP 2
19990Pastel orange (2003)10-14 daysISP 3
19990Pastel orange (2003)10-14 daysISP 4
19990Deep orange (2011)10-14 daysISP 5
19990Beige (1001)10-14 daysISP 6
19990Deep orange (2011)10-14 daysISP 7
116166

multicellular morphology

@refforms multicellular complexmedium name
19990noISP 2
19990noISP 3
19990noISP 4
19990noISP 5
19990noISP 6
19990noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11314GYM 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
19990ISP 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
19990ISP 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:
19990ISP 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
19990ISP 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
19990ISP 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
19990ISP 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
40675MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
116166CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperature
19990positiveoptimum37
11314positivegrowth28
40675positivegrowth30
67770positivegrowth28
116166positivegrowth10-41
116166nogrowth45

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
116166obligate aerobe
125438aerobe91.517
125439obligate aerobe96.7

halophily

@refsaltgrowthtested relationconcentration
19990NaClpositivegrowth0 %
116166NaClpositivegrowth0-8 %
116166NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: MK-9(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1999017234glucose+
1999022599arabinose-
1999017992sucrose+
1999018222xylose-
1999017268myo-inositol-
1999029864mannitol+
1999028757fructose+
1999026546rhamnose-
1999016634raffinose-
1999062968cellulose-
11616616947citrate-carbon source
1161664853esculin-hydrolysis
116166606565hippurate-hydrolysis
11616617632nitrate+reduction
11616616301nitrite-reduction
11616617632nitrate-respiration
68371Potassium 5-ketogluconate-builds acid from
6837127613amygdalin-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837165327D-xylose-builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose-builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117306maltose-builds acid from
6837117057cellobiose-builds acid from
6837117814salicin-builds acid from
683714853esculin-builds acid from
6837118305arbutin-builds acid from
6837159640N-acetylglucosamine+builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose-builds acid from
6837112936D-galactose-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
11616635581indoleno
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-testindole test
11616615688acetoin-
11616617234glucose-
6836815688acetoin+
6836835581indole-

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382leucine arylamidase+3.4.11.1
68382trypsin-3.4.21.4
68382lipase (C 14)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
116166oxidase-
116166beta-galactosidase+3.2.1.23
116166alcohol dehydrogenase-1.1.1.1
116166gelatinase-
116166amylase-
116166DNase-
116166caseinase-3.4.21.50
116166catalase+1.11.1.6
116166tween esterase+
116166gamma-glutamyltransferase+2.3.2.2
116166lecithinase-
116166lysine decarboxylase-4.1.1.18
116166ornithine decarboxylase-4.1.1.17
116166phenylalanine ammonia-lyase-4.3.1.24
116166tryptophan deaminase-
116166urease+3.5.1.5
68382beta-glucosidase+3.2.1.21
68382esterase lipase (C 8)+
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

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
19990+++++++--+++--++---
116166+++++----++---++----

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19990------+--+-

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
116166+/----+/------+/-+/----------+--------+/---------+/----------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
116166++-++--+---+------++-----------+---+-----------------+-------++++-------++-+-+------++--+-++----+--

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
11314sputum
67770Human sputa
116166Human, SputumJapanJPNAsia

isolation source categories

  • Cat1: #Host Body Product
  • Cat2: #Fluids
  • Cat3: #Sputum

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: X80633
  • 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
113142Risk group (German classification)
199902German classification
1161661Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Gordonia aichiensis clone C1 16S ribosomal RNA gene, partial sequenceAY262332505nuccore36820
20218G.aichiensis 16S rRNA gene (ATCC 33611T)X819251320nuccore36820
20218Gordonia aichiensis 16S rRNA gene, strain DSM43978TX806331469nuccore36820

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Gordonia aichiensis NBRC 1082231220583.3wgspatric1220583
66792Gordonia aichiensis NBRC 1082232523231036draftimg1220583
67770Gordonia aichiensis NBRC 108223GCA_000332975contigncbi1220583

GC content

@refGC-contentmethod
6777065.4thermal denaturation, midpoint method (Tm)
6777065.9thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe96.7
125439BacteriaNetgram_stainReaction to gram-stainingpositive93.9
125439BacteriaNetmotilityAbility to perform movementno60.2
125439BacteriaNetspore_formationAbility to form endo- or exosporesno88.9
125438gram-positivegram-positivePositive reaction to Gram-stainingyes90.002no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no97.348yes
125438spore-formingspore-formingAbility to form endo- or exosporesno60.516no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes91.517yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno96yes
125438motile2+flagellatedAbility to perform flagellated movementno93.6no

External links

@ref: 11314

culture collection no.: DSM 43978, ATCC 33611, JCM 6046, CIP 104184, IFO 16046, KCTC 9808, NBRC 108223, NBRC 16046, NRRL B-16934, PCM 2573

straininfo link

  • @ref: 79853
  • straininfo: 44965

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny6763136Numerical analysis of the taxonomy of Nocardiae and Rhodococci.Tsukamura MMicrobiol Immunol10.1111/j.1348-0421.1982.tb00260.x1982Actinomycetales/*classification/growth & development, Drug Resistance, Microbial, Humans, Lung Diseases/etiology, Nocardia/*classification/drug effects/growth & development, Nocardia Infections/complications/microbiology, Nocardia asteroides/growth & developmentPathogenicity
Phylogeny7981103Transfer of Rhodococcus aichiensis Tsukamura 1982 and Nocardia amarae Lechevalier and Lechevalier 1974 to the genus Gordona as Gordona aichiensis comb. nov. and Gordona amarae comb. nov.Klatte S, Rainey FA, Kroppenstedt RMInt J Syst Bacteriol10.1099/00207713-44-4-7691994Base Sequence, Molecular Sequence Data, Nocardia/*classification/genetics/growth & development, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodococcus/*classification/genetics/growth & developmentGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11314Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 43978)https://www.dsmz.de/collection/catalogue/details/culture/DSM-43978
19990Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM43978.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
40675Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16064
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/
68368Automatically annotated from API 20E
68371Automatically annotated from API 50CH acid
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
79853Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID44965.1StrainInfo: A central database for resolving microbial strain identifiers
116166Curators of the CIPCollection of Institut Pasteur (CIP 104184)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104184
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1