Strain identifier

BacDive ID: 11603

Type strain: Yes

Species: Paenibacillus ginsengarvi

Strain history: CIP <- 2008, DSMZ <- B.Y Kim <- W.T. Im, KAIST, Daejon, Korea: strain Gsoil 139

NCBI tax ID(s): 400777 (species)

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General

@ref: 7654

BacDive-ID: 11603

DSM-Number: 18677

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

description: Paenibacillus ginsengarvi DSM 18677 is an aerobe, spore-forming, Gram-positive bacterium that was isolated from soil, ginseng field.

NCBI tax id

  • NCBI tax id: 400777
  • Matching level: species

strain history

@refhistory
7654<- Byung-Yong Kim <- Wan-Taek Im, Gsoil 139
67771<- ST Lee, KAIST
119623CIP <- 2008, DSMZ <- B.Y Kim <- W.T. Im, KAIST, Daejon, Korea: strain Gsoil 139

doi: 10.13145/bacdive11603.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Paenibacillaceae
  • genus: Paenibacillus
  • species: Paenibacillus ginsengarvi
  • full scientific name: Paenibacillus ginsengarvi Yoon et al. 2007

@ref: 7654

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Paenibacillaceae

genus: Paenibacillus

species: Paenibacillus ginsengarvi

full scientific name: Paenibacillus ginsengarvi Yoon et al. 2007

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
32065positive1.5-3.0 µm0.3-0.5 µmrod-shapedno
67771rod-shapedno
67771positive
119623positiverod-shapedno

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7654CASO AGAR (MERCK 105458) (DSMZ Medium 220)yeshttps://mediadive.dsmz.de/medium/220Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water
37843MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
119623CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperature
7654positivegrowth30
32065positivegrowth18-45
32065positiveoptimum37
37843positivegrowth30
67771positivegrowth37

culture pH

@refabilitytypepHPH range
32065positivegrowth5.0-8.5alkaliphile
32065positiveoptimum6.75

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
32065aerobe
67771aerobe
119623obligate aerobe

spore formation

@refspore formationtype of sporeconfidence
32065yes
67771yesspore
69480yes90.653

halophily

  • @ref: 32065
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: <2 %

observation

  • @ref: 67771
  • observation: quinones: MK-7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3206522599arabinose+carbon source
3206517057cellobiose+carbon source
3206524265gluconate+carbon source
3206517234glucose+carbon source
3206517754glycerol+carbon source
3206517306maltose+carbon source
3206528053melibiose+carbon source
3206516634raffinose+carbon source
3206533942ribose+carbon source
3206517814salicin+carbon source
3206517992sucrose+carbon source
3206527082trehalose+carbon source
3206518222xylose+carbon source
68371Potassium 2-ketogluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-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
6837117814salicin-builds acid from
683714853esculin+builds acid from
6837127613amygdalin-builds acid from
6837159640N-acetylglucosamine-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
6837117634D-glucose+builds acid from
6837112936D-galactose-builds acid from
6837174863methyl beta-D-xylopyranoside+builds acid from
6837165328L-xylose-builds acid from
6837130849L-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
11962317632nitrate-reduction
11962316301nitrite-reduction

metabolite production

  • @ref: 119623
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
32065catalase+1.11.1.6
32065cytochrome oxidase+1.9.3.1
119623oxidase+
119623catalase+1.11.1.6
119623urease-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
119623-----+----++-+--+---

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
119623--+/--+/-+/--+/-+-++/-+/-------+/-+/---+/-+-+/-+-+++--+---++---+/---+/--+/-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7654soil, ginseng fieldDaejonRepublic of KoreaKORAsia
67771From soil, ginseng fieldRepublic of KoreaKORAsia
119623Environment, Soil, ginseng fieldDaejeonRepublic of KoreaKORAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_42205.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15358;96_11382;97_24245;98_30672;99_42205&stattab=map
  • Last taxonomy: Paenibacillus ginsengarvi subclade
  • 16S sequence: AB271057
  • Sequence Identity:
  • Total samples: 270
  • soil counts: 202
  • aquatic counts: 28
  • animal counts: 26
  • plant counts: 14

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
76541Risk group (German classification)
1196231Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7654
  • description: Paenibacillus ginsengarvi gene for 16S rRNA, partial sequence
  • accession: AB271057
  • length: 1469
  • database: nuccore
  • NCBI tax ID: 400777

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Paenibacillus ginsengarvi KCTC 13059GCA_003626695scaffoldncbi400777
66792Paenibacillus ginsengarvi strain KCTC 13059400777.3wgspatric400777
66792Paenibacillus ginsengarvi KCTC 130592904143049draftimg400777

GC content

  • @ref: 7654
  • GC-content: 48.1

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69480gram-positivegram-positivePositive reaction to Gram-stainingyes63.739yes
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no92.166no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes71.157yes
69480spore-formingspore-formingAbility to form endo- or exosporesyes90.653yes
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno92.839yes
69480flagellatedmotile2+Ability to perform flagellated movementyes83.733no

External links

@ref: 7654

culture collection no.: DSM 18677, CIP 109800, KCTC 13059, Gsoil 139

straininfo link

  • @ref: 80829
  • straininfo: 292472

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17684262Paenibacillus ginsengarvi sp. nov., isolated from soil from ginseng cultivation.Yoon MH, Ten LN, Im WTInt J Syst Evol Microbiol10.1099/ijs.0.64906-02007DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Gram-Positive Endospore-Forming Bacteria/classification/genetics/*isolation & purification, Korea, Molecular Sequence Data, Panax/*microbiology, RNA, Ribosomal, 16S/genetics, *Soil MicrobiologyGenetics
Phylogeny25977281Paenibacillus oenotherae sp. nov. and Paenibacillus hemerocallicola sp. nov., isolated from the roots of herbaceous plants.Kim TS, Han JH, Joung Y, Kim SBInt J Syst Evol Microbiol10.1099/ijs.0.0003292015Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Hemerocallis/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Oenothera/*microbiology, Paenibacillus/*classification/genetics/isolation & purification, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny34559622Paenibacillus oceani sp. nov., isolated from surface seawater.Chen YF, Ye L, Huang HQ, Jiang MG, Hu YH, Sun DM, Mo KLInt J Syst Evol Microbiol10.1099/ijsem.0.0050242021Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, *Fatty Acids/chemistry, *Paenibacillus/genetics, Phospholipids, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater, Sequence Analysis, DNATranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
7654Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18677)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18677
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
32065Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2831228776041
37843Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7584
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 updates33211880Nucleic Acids Res. 49: D498-D508 2020
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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)
80829Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID292472.1StrainInfo: A central database for resolving microbial strain identifiers
119623Curators of the CIPCollection of Institut Pasteur (CIP 109800)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109800