Strain identifier

BacDive ID: 10598

Type strain: Yes

Species: Gordonia polyisoprenivorans

Strain Designation: Kd2

Strain history: CIP <- 1999, DSMZ <- A. Steinbüchel: strain Kd2

NCBI tax ID(s): 1077976 (strain), 84595 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 11655

BacDive-ID: 10598

DSM-Number: 44302

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

description: Gordonia polyisoprenivorans Kd2 is an obligate aerobe, mesophilic, Gram-positive bacterium that was isolated from fouling tire water on a farmers's field.

NCBI tax id

NCBI tax idMatching level
84595species
1077976strain

strain history

@refhistory
11655<- A. Steinbüchel, Kd2
67770DSM 44302 <-- A. Steinbüchel Kd2.
121928CIP <- 1999, DSMZ <- A. Steinbüchel: strain Kd2

doi: 10.13145/bacdive10598.20230509.8.1

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 polyisoprenivorans
  • full scientific name: Gordonia polyisoprenivorans Linos et al. 1999

@ref: 11655

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Gordoniaceae

genus: Gordonia

species: Gordonia polyisoprenivorans

full scientific name: Gordonia polyisoprenivorans Linos et al. 1999 emend. Nouioui et al. 2018

strain designation: Kd2

type strain: yes

Morphology

cell morphology

  • @ref: 121928
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 121928

multimedia

  • @ref: 11655
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_44302.jpg
  • caption: Medium 535 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11655TRYPTICASE 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
35926MEDIUM 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)
121928CIP Medium 116yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=116

culture temp

@refgrowthtypetemperaturerange
11655positivegrowth28mesophilic
35926positivegrowth30mesophilic
67770positivegrowth28mesophilic
121928positivegrowth25-30mesophilic
121928nogrowth10psychrophilic
121928nogrowth37mesophilic
121928nogrowth41thermophilic
121928nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 121928
  • oxygen tolerance: obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
121928NaClpositivegrowth0-2 %
121928NaClnogrowth6 %
121928NaClnogrowth8 %
121928NaClnogrowth10 %

observation

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

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose-builds acid from17306
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371esculin-builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-sorbose-builds acid from17266
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose-builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
68369decanoate-assimilation27689
68369gluconate+assimilation24265
68369N-acetylglucosamine+assimilation59640
68369D-mannitol+assimilation16899
68369gelatin-hydrolysis5291
68369esculin-hydrolysis4853
68369urea-hydrolysis16199
68369arginine-hydrolysis29016
68369D-glucose-fermentation17634
68369tryptophan-energy source27897
68369nitrate-reduction17632
121928citrate-carbon source16947
121928esculin-hydrolysis4853
121928hippurate-hydrolysis606565
121928nitrate-reduction17632
121928nitrite-reduction16301
121928nitrate-respiration17632

antibiotic resistance

  • @ref: 121928
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
12192835581indoleno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-testmethylred-test
6836935581indole-
12192815688acetoin-
12192817234glucose-

enzymes

@refvalueactivityec
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
121928oxidase-
121928beta-galactosidase-3.2.1.23
121928alcohol dehydrogenase-1.1.1.1
121928gelatinase-
121928amylase-
121928DNase-
121928caseinase-3.4.21.50
121928catalase+1.11.1.6
121928tween esterase+
121928gamma-glutamyltransferase-2.3.2.2
121928lecithinase-
121928lipase-
121928lysine decarboxylase-4.1.1.18
121928ornithine decarboxylase-4.1.1.17
121928phenylalanine ammonia-lyase-4.3.1.24
121928protease-
121928tryptophan deaminase-
121928urease+3.5.1.5
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
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 zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
11655--+/-+/-------++/----+----
121928-+++++----++---+----

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
11655--------+/-+/-+/-+++/-+-+/-+/-++

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
121928----------+/-+/-+/--+/-------+/---------+/-------------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121928+++++--+---------------+--++----++++++--+--+---------+-----++++++--++++-++++-+------+-+-++++-++-++-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
11655fouling tire water on a farmers's fieldNorthrhine-Westfalia, MünsterGermanyDEUEurope
67770Foul water inside a deteriorated automobile tyre on a farmer's fieldMünsterGermanyDEUEurope
121928Environment, Fouling tire water on a farmer's field

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture#Field
#Environmental#Aquatic

taxonmaps

  • @ref: 69479
  • File name: preview.99_1136.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_85;97_90;98_890;99_1136&stattab=map
  • Last taxonomy: Gordonia
  • 16S sequence: HM195279
  • Sequence Identity:
  • Total samples: 1645
  • soil counts: 57
  • aquatic counts: 521
  • animal counts: 885
  • plant counts: 182

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
116551Risk group (German classification)
1219281Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Gordonia polyisoprenivorans strain W7924 16S ribosomal RNA gene, partial sequenceHM1952791445ena84595
11655Gordonia polyisoprenivorans 16S rRNA geneY183101457ena84595

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Gordonia polyisoprenivorans NBRC 163201077976.3wgspatric1077976
66792Gordonia polyisoprenivorans NBRC 16320 = JCM 106751077976.8wgspatric1077976
66792Gordonia polyisoprenivorans Kd22734481953draftimg1077976
66792Gordonia polyisoprenivorans Kd22523231043draftimg1077976
67770Gordonia polyisoprenivorans NBRC 16320 = JCM 10675GCA_000241325contigncbi1077976
67770Gordonia polyisoprenivorans ATCC BAA-14GCA_012396285contigncbi84595
66792Gordonia polyisoprenivorans NBRC 16320 = JCM 10675GCA_001313585contigncbi1077976

GC content

  • @ref: 67770
  • GC-content: 66.9
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno94.143no
flagellatedno98.56no
gram-positiveyes84.863no
anaerobicno99.241no
aerobicyes87.405no
halophileno93.642no
spore-formingno75.481no
thermophileno99.026yes
glucose-utilyes90.834no
glucose-fermentno90.85yes

External links

@ref: 11655

culture collection no.: DSM 44302, ATCC BAA 14, IFO 16320, JCM 10675, NBRC 16320, CIP 106350, IFM 10351, KCTC 9953, NCIMB 13616

straininfo link

  • @ref: 79873
  • straininfo: 44255

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny10555361Gordonia polyisoprenivorans sp. nov., a rubber-degrading actinomycete isolated from an automobile tyre.Linos A, Steinbuchel A, Sproer C, Kroppenstedt RMInt J Syst Bacteriol10.1099/00207713-49-4-17851999Actinomycetales/chemistry/*classification/isolation & purification/*metabolism, *Automobiles, Bacterial Typing Techniques, Biodegradation, Environmental, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Molecular Sequence Data, Mycolic Acids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Rubber/*metabolismMetabolism
Phylogeny11750816Taxonomic characterization of two rubber degrading bacteria belonging to the species Gordonia polyisoprenivorans and analysis of hyper variable regions of 16S rDNA sequences.Arenskotter M, Baumeister D, Berekaa MM, Potter G, Kroppenstedt RM, Linos A, Steinbuchel AFEMS Microbiol Lett10.1111/j.1574-6968.2001.tb10961.x2001Actinomycetales/chemistry/*classification/genetics, Base Sequence, Chromatography, High Pressure Liquid, Fatty Acids/analysis, Molecular Sequence Data, RNA, Bacterial/*genetics, RNA, Ribosomal, 16S/analysis/*genetics, Rubber/*metabolism, Sequence Alignment, Species Specificity, Vitamin K 2/analysisGenetics
Phylogeny30932808Gordonia oryzae sp. nov., isolated from rice plant stems (Oryza sativa L.).Muangham S, Lipun K, Thamchaipenet A, Matsumoto A, Duangmal KInt J Syst Evol Microbiol10.1099/ijsem.0.0033682019Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Gordonia Bacterium/*classification/isolation & purification, Nucleic Acid Hybridization, Oryza/*microbiology, Phospholipids/chemistry, *Phylogeny, Pigmentation, Plant Stems/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Thailand, Vitamin K 2/chemistryTranscriptome
Phylogeny30994431Gordonia sediminis sp. nov., an actinomycete isolated from mangrove sediment.Sangkanu S, Suriyachadkun C, Phongpaichit SInt J Syst Evol Microbiol10.1099/ijsem.0.0033992019Actinobacteria/genetics, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Gordonia Bacterium/*classification/isolation & purification, Mycolic Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhizophoraceae/*microbiology, Sequence Analysis, DNA, Thailand, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny32667871Gordonia mangrovi sp. nov., a novel actinobacterium isolated from mangrove soil in Hainan.Xie Y, Zhou S, Xu Y, Wu W, Xia W, Zhang R, Huang D, Huang XInt J Syst Evol Microbiol10.1099/ijsem.0.0043102020Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Gordonia Bacterium/*classification/isolation & purification, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11655Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44302)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44302
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
35926Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18471
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/
68369Automatically annotated from API 20NE
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
79873Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID44255.1StrainInfo: A central database for resolving microbial strain identifiers
121928Curators of the CIPCollection of Institut Pasteur (CIP 106350)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106350