Strain identifier

BacDive ID: 10580

Type strain: Yes

Species: Gordonia hirsuta

Strain Designation: K 718a

Strain history: CIP <- 1997, DSMZ <- S. Klatte: strain K 718a

NCBI tax ID(s): 1121927 (strain), 53427 (species)

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General

@ref: 11518

BacDive-ID: 10580

DSM-Number: 44140

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic

description: Gordonia hirsuta K 718a is an aerobe, mesophilic bacterium that was isolated from biofilter of an animal rendering plant.

NCBI tax id

NCBI tax idMatching level
53427species
1121927strain

strain history

@refhistory
11518<- S. Klatte, K 718a
67770DSM 44140 <-- S. Klatte K718a.
119912CIP <- 1997, DSMZ <- S. Klatte: strain K 718a

doi: 10.13145/bacdive10580.20230509.8.1

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 hirsuta
  • full scientific name: Gordonia hirsuta corrig. Klatte et al. 1996

  • synonyms

    • @ref: 20215
    • synonym: Gordona hirsuta

@ref: 11518

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Gordoniaceae

genus: Gordonia

species: Gordonia hirsuta

full scientific name: Gordonia hirsuta Klatte et al. 1996

strain designation: K 718a

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no94.682
69480100positive
119912nopositiverod-shaped

colony morphology

@refincubation periodmedium used
2000410-14 daysISP 2
2000410-14 daysISP 3
2000410-14 daysISP 4
2000410-14 daysISP 5
2000410-14 daysISP 6
2000410-14 daysISP 7
119912

multicellular morphology

@refforms multicellular complexmedium name
20004noISP 2
20004noISP 3
20004noISP 4
20004noISP 5
20004noISP 6
20004noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11518TRYPTICASE 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
20004ISP 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
20004ISP 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:
20004ISP 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
20004ISP 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
20004ISP 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
20004ISP 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
41474MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
119912CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
11518positivegrowth28mesophilic
41474positivegrowth30mesophilic
54293positivegrowth30-37mesophilic
67770positivegrowth28mesophilic
119912positivegrowth25-37mesophilic
119912nogrowth10psychrophilic
119912nogrowth41thermophilic
119912nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
54293aerobe
119912obligate aerobe

spore formation

@refspore formationconfidence
69481no96
69480no99.992

halophily

@refsaltgrowthtested relationconcentration
20004NaClpositivemaximum5 %
119912NaClpositivegrowth0-4 %
119912NaClnogrowth6 %
119912NaClnogrowth8 %
119912NaClnogrowth10 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2000417234glucose+
2000422599arabinose+
2000417992sucrose+
2000418222xylose+
2000417268myo-inositol+
2000429864mannitol+
2000428757fructose+
2000426546rhamnose+
2000416634raffinose+
2000462968cellulose+
68371Potassium 5-ketogluconate-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
6837132528turanose-builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol-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
6837117306maltose-builds acid from
6837117057cellobiose-builds acid from
683714853esculin-builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
6837159640N-acetylglucosamine-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837112936D-galactose-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837116988D-ribose-builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate+assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis
11991216947citrate-carbon source
1199124853esculin-hydrolysis
119912606565hippurate-hydrolysis
11991217632nitrate+reduction
11991216301nitrite-reduction

antibiotic resistance

  • @ref: 119912
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno
11991235581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin+
6836835581indole-
11991215688acetoin-
11991217234glucose-

enzymes

@refvalueactivityec
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
119912oxidase-
119912beta-galactosidase+3.2.1.23
119912alcohol dehydrogenase-1.1.1.1
119912gelatinase-
119912amylase-
119912DNase-
119912caseinase-3.4.21.50
119912catalase+1.11.1.6
119912tween esterase+
119912gamma-glutamyltransferase+2.3.2.2
119912lecithinase-
119912lipase-
119912lysine decarboxylase-4.1.1.18
119912ornithine decarboxylase-4.1.1.17
119912phenylalanine ammonia-lyase-4.3.1.24
119912protease-
119912tryptophan deaminase-
119912urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase lipase (C 8)+
68382leucine arylamidase+3.4.11.1
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 zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
20004+-+-+++--++---+----
119912+++++-+--++---+-----

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
20004----+----+-

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
119912+/----------+/-+/-+/----+/---------+/---+/--+/------+/-------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119912-+------+-----------------------+---------------------+--------------------+-----------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
11518biofilter of an animal rendering plantLower saxonyGermanyDEUEurope
54293Biofilter of an animal rendering plant
67770Wet-ground filter material (fiber bark compost) from a large scale biofilter
119912Biofilter of an animal rendering plantGermanyDEUEurope1989

isolation source categories

Cat1Cat2Cat3
#Engineered#Bioremediation#Biofilter
#Engineered#Industrial#Plant (Factory)

taxonmaps

  • @ref: 69479
  • File name: preview.99_5321.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_2575;97_3155;98_3965;99_5321&stattab=map
  • Last taxonomy: Gordonia hirsuta subclade
  • 16S sequence: X93485
  • Sequence Identity:
  • Total samples: 1006
  • soil counts: 81
  • aquatic counts: 649
  • animal counts: 269
  • plant counts: 7

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
115181Risk group (German classification)
200041German classification
1199121Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: G.hirsuta 16S rRNA gene
  • accession: X93485
  • length: 1461
  • database: ena
  • NCBI tax ID: 1121927

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Gordonia hirsuta DSM 44140 = NBRC 160561121927.3wgspatric1121927
66792Gordonia hirsuta K718a, DSM 441402563367079draftimg1121927
66792Gordonia hirsuta K718a, DSM 441402526164525draftimg1121927
67770Gordonia hirsuta DSM 44140 = NBRC 16056GCA_000420685contigncbi1121927
67770Gordonia hirsuta DSM 44140 = NBRC 16056GCA_000333015contigncbi1121927

GC content

  • @ref: 11518
  • GC-content: 69
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno96no
motileno96.16no
flagellatedno98.679no
gram-positiveyes92.468no
anaerobicno99.301yes
halophileno83.807no
spore-formingno92.678no
thermophileno98.062yes
glucose-utilyes89.608no
aerobicyes89.97no
glucose-fermentno82.781no

External links

@ref: 11518

culture collection no.: CCUG 38498, DSM 44140, CIP 105097, JCM 10105, ATCC 700255, CECT 7018, IFO 16056, KCTC 9816, NBRC 16056, PCM 2574

straininfo link

  • @ref: 79855
  • straininfo: 45417

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny22228669Gordonia caeni sp. nov., isolated from sludge of a sewage disposal plant.Srinivasan S, Park G, Yang H, Hwang S, Bae Y, Jung YA, Kim MK, Lee MInt J Syst Evol Microbiol10.1099/ijs.0.029736-02012Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Gordonia Bacterium/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/analysis, *Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Sewage/*microbiologyGenetics
Phylogeny22389287Gordonia phosphorivorans sp. nov., isolated from a wastewater bioreactor with phosphorus removal.Kampfer P, Martin K, Dott WInt J Syst Evol Microbiol10.1099/ijs.0.037093-02012Bacterial Typing Techniques, Base Composition, Bioreactors/*microbiology, DNA, Bacterial/genetics, Fatty Acids/analysis, Gordonia Bacterium/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/analysis, Phosphorus/*metabolism, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/analysis, Waste Water/microbiologyGenetics
Phylogeny22427452Gordonia alkaliphila sp. nov., an actinomycete isolated from tidal flat sediment.Cha JH, Cha CJInt J Syst Evol Microbiol10.1099/ijs.0.039289-02012Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Geologic Sediments/*microbiology, Gordonia Bacterium/*classification/genetics/isolation & purification, Molecular Sequence Data, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/analysisGenetics
Phylogeny25052399Gordonia iterans sp. nov., isolated from a patient with pneumonia.Kang YQ, Ming H, Gonoi T, Chen Y, Cao Y, Wang YY, Cheng J, Koga T, Mikami Y, Li WJInt J Syst Evol Microbiol10.1099/ijs.0.063438-02014Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Gordonia Bacterium/*classification/genetics/isolation & purification, Humans, Japan, Male, Middle Aged, Molecular Sequence Data, Mycolic Acids/chemistry, Nucleic Acid Hybridization, *Phylogeny, Pneumonia, Bacterial/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sputum/*microbiology, Vitamin K 2/analogs & derivatives/chemistryPathogenicity

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11518Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44140)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44140
20004Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44140.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
41474Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17078
54293Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 38498)https://www.ccug.se/strain?id=38498
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/
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
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
79855Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID45417.1StrainInfo: A central database for resolving microbial strain identifiers
119912Curators of the CIPCollection of Institut Pasteur (CIP 105097)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105097