Strain identifier

BacDive ID: 10601

Type strain: Yes

Species: Gordonia amicalis

Strain Designation: IEGM

Strain history: CIP <- 2005, DSMZ <- M. Goodfellow, Newcastle Univ., Newcastle, UK: strain IEGM

NCBI tax ID(s): 1220574 (strain), 89053 (species)

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General

@ref: 11788

BacDive-ID: 10601

DSM-Number: 44461

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

description: Gordonia amicalis IEGM is an aerobe, mesophilic, Gram-positive bacterium that was isolated from garden soil.

NCBI tax id

NCBI tax idMatching level
1220574strain
89053species

strain history

@refhistory
11788<- M. Goodfellow, Univ. Newcastle; IEGM
67770DSM 44461 <-- M. Goodfellow strain IEGM.
67771<- SB Kim <- DSM <- <- M. Goodfellow, Univ. Newcastle, IEGM
116329CIP <- 2005, DSMZ <- M. Goodfellow, Newcastle Univ., Newcastle, UK: strain IEGM

doi: 10.13145/bacdive10601.20230509.8.1

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 amicalis
  • full scientific name: Gordonia amicalis Kim et al. 2000

@ref: 11788

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Gordoniaceae

genus: Gordonia

species: Gordonia amicalis

full scientific name: Gordonia amicalis Kim et al. 2000 emend. Nouioui et al. 2018

strain designation: IEGM

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
67771positive
69480positive100
116329positiverod-shapedno

colony morphology

@refcolony colorincubation periodmedium used
19669Salmon orange10-14 daysISP 2
19669Salmon orange10-14 daysISP 3
19669Salmon orange10-14 daysISP 4
19669Salmon orange10-14 daysISP 5
19669Salmon orange10-14 daysISP 6
19669Salmon orange10-14 daysISP 7
116329

multicellular morphology

@refforms multicellular complexmedium name
19669noISP 2
19669noISP 3
19669noISP 4
19669noISP 5
19669noISP 6
19669noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11788TRYPTICASE 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
11788BHI MEDIUM WITH ADDITIONAL GLUCOSE (DSMZ Medium 215b)yeshttps://mediadive.dsmz.de/medium/215bName: BHI MEDIUM WITH ADDITIONAL GLUCOSE (DSMZ Medium 215b) Composition: Brain heart infusion 37.0 g/l Glucose 5.0 g/l Distilled water
19669ISP 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
19669ISP 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:
19669ISP 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
19669ISP 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
19669ISP 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
19669ISP 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
38324MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
116329CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
19669positiveoptimum28mesophilic
11788positivegrowth28mesophilic
38324positivegrowth30mesophilic
58343positivegrowth28mesophilic
67770positivegrowth28mesophilic
67771positivegrowth28mesophilic
116329positivegrowth10-37
116329nogrowth41thermophilic
116329nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
58343aerobe
67771aerobe
116329obligate aerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.925

halophily

  • @ref: 116329
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-10 %

observation

@refobservation
67770quinones: MK-9(H2), MK-8(H2)
67771quinones: MK-9(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1966917234glucose+
1966922599arabinose-
1966917992sucrose+
1966918222xylose-
1966917268myo-inositol-
1966929864mannitol+
1966928757fructose+
1966926546rhamnose-
1966916634raffinose-
1966962968cellulose-
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate+assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis
11632916947citrate-carbon source
1163294853esculin-hydrolysis
116329606565hippurate-hydrolysis
11632917632nitrate-reduction
11632916301nitrite-reduction
11632917632nitrate-respiration
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

@refChebi-IDmetaboliteproduction
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno
11632935581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin-
6836835581indole-
11632915688acetoin-
11632917234glucose-

enzymes

@refvalueactivityec
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
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
116329oxidase-
116329beta-galactosidase+3.2.1.23
116329alcohol dehydrogenase-1.1.1.1
116329gelatinase-
116329amylase-
116329DNase-
116329caseinase-3.4.21.50
116329catalase+1.11.1.6
116329tween esterase-
116329gamma-glutamyltransferase-2.3.2.2
116329lecithinase-
116329lipase-
116329lysine decarboxylase-4.1.1.18
116329ornithine decarboxylase-4.1.1.17
116329phenylalanine ammonia-lyase-4.3.1.24
116329tryptophan deaminase-
116329urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
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-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
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
19669--++--+------------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
19669+-+++++--++---+----
116329+++++++--++-+-++----

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19669----+------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
116329++-+---+----------------------------------------++-----+-----------------------++-------+-------++-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
11788garden soilPermRussiaRUSEurope
58343Soil,garden soil,permRussiaRUS
67770Garden soilPermRussiaRUS
67771From garden soilRussiaRUS
116329Environment, Garden soilRussian FederationRUSEurope

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Engineered#Agriculture#Garden

taxonmaps

  • @ref: 69479
  • File name: preview.99_2949.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_85;97_90;98_746;99_2949&stattab=map
  • Last taxonomy: Gordonia amicalis
  • 16S sequence: AF101418
  • Sequence Identity:
  • Total samples: 1000
  • soil counts: 524
  • aquatic counts: 146
  • animal counts: 316
  • plant counts: 14

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
117881Risk group (German classification)
196691Risk group (German classification)
1163291Risk group (French classification)

Sequence information

16S sequences

  • @ref: 11788
  • description: Gordonia amicalis 16S ribosomal RNA gene, partial sequence
  • accession: AF101418
  • length: 1513
  • database: ena
  • NCBI tax ID: 89053

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Gordonia amicalis NBRC 100051 = JCM 11271GCA_001313725contigncbi1220574
66792Gordonia amicalis NBRC 100051 = JCM 112711220574.5wgspatric1220574
66792Gordonia amicalis NBRC 100051 = JCM 112711220574.3wgspatric1220574
66792Gordonia amicalis strain DSM 4446189053.6wgspatric89053
66792Gordonia amicalis IEGM2734481960draftimg1220574
66792Gordonia amicalis IEGM2523231037draftimg1220574
67770Gordonia amicalis NBRC 100051 = JCM 11271GCA_000332995contigncbi1220574
67770Gordonia amicalis DSM 44461GCA_012395955contigncbi89053

GC content

@refGC-contentmethod
1178864.2high performance liquid chromatography (HPLC)
6777067.4genome sequence analysis
6777164.0

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno86no
motileno93.921no
gram-positiveyes87.866no
anaerobicno99.303no
aerobicyes94.245yes
halophileno83.062no
spore-formingno94.8no
thermophileno99.52yes
glucose-utilyes91.132yes
flagellatedno98.864no
glucose-fermentno92.888yes

External links

@ref: 11788

culture collection no.: DSM 44461, CIP 108824, KCTC 9940, CCUG 48822, JCM 11271, KCTC 9899, NBRC 100051, BCRC 16387, IFM 10353

straininfo link

  • @ref: 79875
  • straininfo: 362269

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny11155977Gordonia amicalis sp. nov., a novel dibenzothiophene-desulphurizing actinomycete.Kim SB, Brown R, Oldfield C, Gilbert SC, Iliarionov S, Goodfellow MInt J Syst Evol Microbiol10.1099/00207713-50-6-20312000Actinomycetales/chemistry/*classification/genetics/isolation & purification, DNA, Ribosomal/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil Microbiology, Sulfur/*metabolism, Thiophenes/*metabolismGenetics
Phylogeny13130028Gordonia sihwensis sp. nov., a novel nitrate-reducing bacterium isolated from a wastewater-treatment bioreactor.Kim KK, Lee CS, Kroppenstedt RM, Stackebrandt E, Lee STInt J Syst Evol Microbiol10.1099/ijs.0.02224-02003Bioreactors, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Gordonia Bacterium/classification/genetics/*isolation & purification/*metabolism, Korea, Molecular Sequence Data, Mycolic Acids/analysis, Nitrates/metabolism, Oxidation-Reduction, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Waste Disposal, FluidMetabolism

Reference

@idauthorscataloguedoi/urltitle
11788Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44461)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44461
19669Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44461.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
38324Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6496
58343Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 48822)https://www.ccug.se/strain?id=48822
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/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68368Automatically annotated from API 20E
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)
79875Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID362269.1StrainInfo: A central database for resolving microbial strain identifiers
116329Curators of the CIPCollection of Institut Pasteur (CIP 108824)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108824