Strain identifier

BacDive ID: 11122

Type strain: Yes

Species: Nocardioides panacihumi

Strain history: CIP <- 2007, KCTC <- S.T. Lee, KAIST, Daejon, Korea: strain Gsoil 616

NCBI tax ID(s): 400774 (species)

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General

@ref: 7643

BacDive-ID: 11122

DSM-Number: 18660

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

description: Nocardioides panacihumi DSM 18660 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from soil, ginseng field.

NCBI tax id

  • NCBI tax id: 400774
  • Matching level: species

strain history

@refhistory
7643<- S.-T. Lee <- W.-T. Im; Gsoil 616
67770KCTC 19187 <-- S.-T. Lee Gsoil 616.
67771<- ST Lee, KAIST
121524CIP <- 2007, KCTC <- S.T. Lee, KAIST, Daejon, Korea: strain Gsoil 616

doi: 10.13145/bacdive11122.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Propionibacteriales
  • family: Nocardioidaceae
  • genus: Nocardioides
  • species: Nocardioides panacihumi
  • full scientific name: Nocardioides panacihumi An et al. 2007

@ref: 7643

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardioidaceae

genus: Nocardioides

species: Nocardioides panacihumi

full scientific name: Nocardioides panacihumi An et al. 2007

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
32010positive0.7-1.2 µm0.3-0.5 µmrod-shapedno
67771positive
121524positiveoval-shapedno

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7643R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
37831MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromatiyesDistilled water make up to (1000.000 ml);R2A agar (18.200 g)
7643TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
121524CIP Medium 566yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566

culture temp

@refgrowthtypetemperaturerange
7643positivegrowth28mesophilic
19769positiveoptimum28mesophilic
32010positivegrowth15-30
32010positiveoptimum30mesophilic
37831positivegrowth30mesophilic
67770positivegrowth28mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepH
32010positivegrowth5.0-8.0
32010positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
32010aerobe
67771aerobe

spore formation

  • @ref: 32010
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
32010NaClpositivegrowth0-1 %
32010NaClpositiveoptimum0.5 %

murein

  • @ref: 7643
  • murein short key: A41.01
  • type: A3gamma LL-Dpm-Gly

observation

  • @ref: 67770
  • observation: quinones: MK-8(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
32010161933-hydroxybenzoate+carbon source
32010370543-hydroxybutyrate+carbon source
32010178794-hydroxybenzoate+carbon source
3201030089acetate+carbon source
3201016449alanine+carbon source
3201024265gluconate+carbon source
3201028087glycogen+carbon source
3201017306maltose+carbon source
3201018401phenylacetate+carbon source
3201026271proline+carbon source
3201017272propionate+carbon source
3201026546rhamnose+carbon source
3201017814salicin+carbon source
3201031011valerate+carbon source
320104853esculin+hydrolysis
3201017632nitrate+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
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose-builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837118305arbutin-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
6837117266L-sorbose-builds acid from
6837116024D-mannose-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
12152417632nitrate+reduction
12152416301nitrite-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

  • @ref: 121524
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
32010acid phosphatase+3.1.3.2
32010alkaline phosphatase+3.1.3.1
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
121524oxidase-
121524catalase+1.11.1.6
121524urease-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
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
68382alpha-fucosidase-3.2.1.51

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
19769------+-+----------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
19769-++-++---++---++---
121524-++-++-+-+----++++--

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
121524----------+/-+/---+/--------+/--+/-+/-+/-+/---+/----+/-----+/----------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7643soil, ginseng fieldPocheon provinceRepublic of KoreaKORAsia
67770Soil of a ginseng fieldPocheon ProvinceRepublic of KoreaKORAsia
67771From soil, ginseng fieldRepublic of KoreaKORAsia
121524Environment, Soil, ginseng fieldPocheonRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture#Field
#Environmental#Terrestrial#Soil
#Host#Plants#Herbaceous plants (Grass,Crops)

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
76431Risk group (German classification)
197691Risk group (German classification)
1215241Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7643
  • description: Nocardioides panacihumi gene for 16S rRNA, partial sequence
  • accession: AB271053
  • length: 1457
  • database: ena
  • NCBI tax ID: 400774

GC content

@refGC-contentmethod
764373
6777073high performance liquid chromatography (HPLC)

External links

@ref: 7643

culture collection no.: DSM 18660, KCTC 19187, Gsoil 616, JCM 15309, CIP 109747

straininfo link

  • @ref: 80371
  • straininfo: 292499

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17766888Nocardioides panacihumi sp. nov., isolated from soil of a ginseng field.An DS, Im WT, Lee ST, Yoon MHInt J Syst Evol Microbiol10.1099/ijs.0.64806-02007Actinomycetales/*classification/genetics/*isolation & purification/physiology, Aerobiosis, Bacterial Typing Techniques, Base Composition, Carbohydrate Metabolism, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA, Korea, Molecular Sequence Data, Panax, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, *Soil Microbiology, Vitamin K 2/analysisGenetics
Phylogeny19622661Nocardioides terrae sp. nov., isolated from forest soil.Zhang JY, Liu XY, Liu SJInt J Syst Evol Microbiol10.1099/ijs.0.010785-02009Actinomycetales/classification/genetics/*isolation & purification/metabolism, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Molecular Sequence Data, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Trees/*microbiologyMetabolism
Phylogeny24670898Nocardioides opuntiae sp. nov., isolated from soil of a cactus.Lee SD, Seong CNInt J Syst Evol Microbiol10.1099/ijs.0.060400-02014Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Cactaceae/*microbiology, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny33470927Nocardioides cynanchi sp. nov., isolated from soil of rhizosphere of Cynanchum wilfordii.Suh MK, Lee KC, Kim JS, Han KI, Kim HS, Eom MK, Shin YK, Lee JSInt J Syst Evol Microbiol10.1099/ijsem.0.0046402021Bacterial Typing Techniques, Base Composition, Cynanchum/*microbiology, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nocardioides/*classification/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7643Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18660)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18660
19769Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM18660.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
32010Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2826428776041
37831Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7524
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68371Automatically annotated from API 50CH acid
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
80371Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID292499.1StrainInfo: A central database for resolving microbial strain identifiers
121524Curators of the CIPCollection of Institut Pasteur (CIP 109747)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109747