Strain identifier

BacDive ID: 10614

Type strain: Yes

Species: Gordonia soli

Strain Designation: CC-AB07

Strain history: CIP <- 2007, DSMZ <- A.L. Jones, Newcastle Univ., Newcastle, UK <- F.T. Shen, Newcastle Univ., Newcastle, UK: strain CC-AB07

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 12227

BacDive-ID: 10614

DSM-Number: 44995

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

description: Gordonia soli CC-AB07 is an obligate aerobe, mesophilic, Gram-positive bacterium that was isolated from soil.

NCBI tax id

NCBI tax idMatching level
320799species
1223545strain

strain history

@refhistory
12227<- A. L. Jones <- F.-T. Shen; CC-AB07
67770IFM 10767 <-- DSM 44995 <-- A. L. Jones <-- F.-T. Shen CC-AB07.
122658CIP <- 2007, DSMZ <- A.L. Jones, Newcastle Univ., Newcastle, UK <- F.T. Shen, Newcastle Univ., Newcastle, UK: strain CC-AB07

doi: 10.13145/bacdive10614.20230509.8.1

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 soli
  • full scientific name: Gordonia soli Shen et al. 2006

@ref: 12227

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Gordoniaceae

genus: Gordonia

species: Gordonia soli

full scientific name: Gordonia soli Shen et al. 2006

strain designation: CC-AB07

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480positive100
122658positiverod-shapedno

colony morphology

@refcolony colorincubation periodmedium used
19900Brown beige10-14 daysISP 2
19900Beige10-14 daysISP 3
1990010-14 daysISP 4
1990010-14 daysISP 5
19900Beige10-14 daysISP 6
1990010-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
19900noISP 2
19900noISP 3
19900noISP 4
19900noISP 5
19900noISP 6
19900noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12227TRYPTICASE 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
19900ISP 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
19900ISP 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:
19900ISP 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
19900ISP 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
19900ISP 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
19900ISP 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
37303MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
122658CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
12227positivegrowth28mesophilic
19900positiveoptimum28mesophilic
37303positivegrowth30mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 122658
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no95
69480no99.064

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836925115malate+assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol+assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose-assimilation
683695291gelatin-hydrolysis
683694853esculin+hydrolysis
6836916199urea+hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction
12265817632nitrate-reduction
12265816301nitrite-reduction
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
6836935581indoleno
12265835581indoleno

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

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
68369gelatinase-
68369beta-glucosidase+3.2.1.21
68369urease+3.5.1.5
68369arginine dihydrolase-3.5.3.6
122658oxidase-
122658catalase+1.11.1.6
122658urease+3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382lipase (C 14)-
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+
68382beta-galactosidase-3.2.1.23
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
19900---+--+--+---------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
19900+-+-+----+++--++---
12227++/-+/-------++---++/-----
122658+++-+----++---+-----

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
12227----++-----+-----+++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
12227soilcampus of National Chung Hsing UniversityTaiwanTWNAsia
67770Soil from the campus of National Chung Hsing Univ.TaichungTaiwanTWNAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_5512.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_85;97_90;98_890;99_5512&stattab=map
  • Last taxonomy: Gordonia soli
  • 16S sequence: AY995560
  • Sequence Identity:
  • Total samples: 218
  • soil counts: 21
  • aquatic counts: 84
  • animal counts: 92
  • plant counts: 21

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
122271Risk group (German classification)
199001Risk group (German classification)
1226581Risk group (French classification)

Sequence information

16S sequences

  • @ref: 12227
  • description: Gordonia soli strain CC-AB07 16S ribosomal RNA gene, partial sequence
  • accession: AY995560
  • length: 1485
  • database: ena
  • NCBI tax ID: 320799

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Gordonia soli NBRC 1082431223545.3wgspatric1223545
66792Gordonia soli NBRC 1082432523231047draftimg1223545
67770Gordonia soli NBRC 108243GCA_000334455contigncbi1223545

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno95no
motileno94.958no
gram-positiveyes87.465no
anaerobicno99.277no
aerobicyes87.645no
halophileno88.733no
spore-formingno82.744no
glucose-utilyes85.424yes
flagellatedno98.206no
thermophileno99.218no
glucose-fermentno88.468yes

External links

@ref: 12227

culture collection no.: DSM 44995, BCRC 16810, CIP 109465, JCM 14298, IFM 10767, NBRC 108243

straininfo link

  • @ref: 79887
  • straininfo: 297196

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17082398Gordonia soli sp. nov., a novel actinomycete isolated from soil.Shen FT, Goodfellow M, Jones AL, Chen YP, Arun AB, Lai WA, Rekha PD, Young CCInt J Syst Evol Microbiol10.1099/ijs.0.64492-02006Bacterial Typing Techniques, Cell Wall/chemistry, DNA Gyrase/genetics, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Enzymes/metabolism, Fatty Acids/analysis, Genes, rRNA, Gordonia Bacterium/chemistry/*classification/*isolation & purification/physiology, Molecular Sequence Data, Muramic Acids/analysis, Phylogeny, Quinones/analysis/chemistry, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, *Soil MicrobiologyEnzymology
Phylogeny19643878Gordonia hankookensis sp. nov., isolated from soil.Park S, Kang SJ, Kim W, Yoon JHInt J Syst Evol Microbiol10.1099/ijs.0.011585-02009DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Gordonia Bacterium/*classification/genetics/*isolation & purification/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil MicrobiologyMetabolism

Reference

@idauthorscataloguedoi/urltitle
12227Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44995)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44995
19900Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44995.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
37303Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7211
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
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
79887Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID297196.1StrainInfo: A central database for resolving microbial strain identifiers
122658Curators of the CIPCollection of Institut Pasteur (CIP 109465)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109465