Strain identifier

BacDive ID: 10617

Type strain: Yes

Species: Gordonia shandongensis

Strain Designation: SD29

Strain history: CIP <- 2007, JCM <- 2006, Y. Huang, Chinese Acad. Sciences, Beijing, China: strain SD29

NCBI tax ID(s): 1121928 (strain), 376351 (species)

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General

@ref: 12336

BacDive-ID: 10617

DSM-Number: 45094

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

description: Gordonia shandongensis SD29 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from farmland soil.

NCBI tax id

NCBI tax idMatching level
1121928strain
376351species

strain history

@refhistory
12336<- JCM <- Y. Huang; SD29
67770Y. Huang SD29.
122581CIP <- 2007, JCM <- 2006, Y. Huang, Chinese Acad. Sciences, Beijing, China: strain SD29

doi: 10.13145/bacdive10617.20230509.8.1

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 shandongensis
  • full scientific name: Gordonia shandongensis Luo et al. 2007

@ref: 12336

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Gordoniaceae

genus: Gordonia

species: Gordonia shandongensis

full scientific name: Gordonia shandongensis Luo et al. 2007 emend. Nouioui et al. 2018

strain designation: SD29

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
31855positiverod-shapedno
69480no96.601
69480positive100
122581positiverod-shapedno

multimedia

  • @ref: 12336
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_45094.jpg
  • caption: Medium 65 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12336GYM 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
12336TRYPTICASE 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
33307MEDIUM 112 - for JanibacteryesDistilled water make up to (1000.000 ml);Magnesium sulphate heptahydrate (1.000 g);Agar (20.000 g);Yeast extract (5.000 g);Peptone (10.000 g);Tween 80 (50.000 mg);Glycerol (2.000 g);Malt extract (5.000 g);Beef extract (2.000 g);Casamino acids (5.000 g);Ca
122581CIP Medium 112yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=112

culture temp

@refgrowthtypetemperaturerange
12336positivegrowth28mesophilic
31855positivegrowth20-37
31855positiveoptimum28.5mesophilic
33307positivegrowth30mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
31855positivegrowth5.5-9.0alkaliphile
31855positiveoptimum7.3

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31855aerobe
122581obligate aerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.991

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3185522599arabinose+carbon source
3185517057cellobiose+carbon source
3185526271proline+carbon source
318554853esculin+hydrolysis
3185517632nitrate+reduction
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
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose-builds acid from
6837117992sucrose-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
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
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose-builds acid from
6837115824D-fructose-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
6837117754glycerol-builds acid from
12258117632nitrate-reduction
12258116301nitrite-reduction

metabolite production

  • @ref: 122581
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
31855urease+3.5.1.5
122581oxidase-
122581catalase+1.11.1.6
122581urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
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-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
122581-++++++---++---+----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
122581----------+/---------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
12336farmland soilShandong ProvinceChinaCHNAsia
67770Farmland soilShandong ProvinceChinaCHNAsia
122581Environment, SoilChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Engineered#Agriculture#Field

taxonmaps

  • @ref: 69479
  • File name: preview.99_6555.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_3107;97_3808;98_4839;99_6555&stattab=map
  • Last taxonomy: Gordonia shandongensis subclade
  • 16S sequence: DQ420167
  • Sequence Identity:
  • Total samples: 356
  • soil counts: 45
  • aquatic counts: 58
  • animal counts: 242
  • plant counts: 11

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
123361Risk group (German classification)
1225811Risk group (French classification)

Sequence information

16S sequences

  • @ref: 12336
  • description: Gordonia shandongensis strain SD29 16S ribosomal RNA gene, partial sequence
  • accession: DQ420167
  • length: 1398
  • database: ena
  • NCBI tax ID: 376351

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Gordonia shandongensis DSM 450941121928.3wgspatric1121928
66792Gordonia shandongensis DSM 450942524614582draftimg1121928
67770Gordonia shandongensis DSM 45094GCA_000423025scaffoldncbi1121928

GC content

  • @ref: 67770
  • GC-content: 69.3
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes77no
motileno95.57yes
flagellatedno98.04yes
gram-positiveyes92.35no
anaerobicno99.084yes
halophileno78.749no
spore-formingno89.31no
thermophileno96.088yes
glucose-utilyes87.853no
aerobicyes88.643yes
glucose-fermentno86.151no

External links

@ref: 12336

culture collection no.: DSM 45094, CGMCC 4.3492, JCM 13907, CIP 109551

straininfo link

  • @ref: 79889
  • straininfo: 297195

literature

  • topic: Phylogeny
  • Pubmed-ID: 17329793
  • title: Gordonia shandongensis sp. nov., isolated from soil in China.
  • authors: Luo H, Gu Q, Xie J, Hu C, Liu Z, Huang Y
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.64536-0
  • year: 2007
  • mesh: China, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Gordonia Bacterium/chemistry/*classification/genetics/isolation & purification, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
12336Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45094)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45094
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
31855Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2811928776041
33307Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7307
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/
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)
79889Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID297195.1StrainInfo: A central database for resolving microbial strain identifiers
122581Curators of the CIPCollection of Institut Pasteur (CIP 109551)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109551