Strain identifier

BacDive ID: 1269

Type strain: Yes

Species: Ectobacillus panaciterrae

Strain history: CIP <- 2007, CCUG <- 2006, KCTC <- S.T. Lee, KAIST

NCBI tax ID(s): 1121093 (strain), 363872 (species)

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General

@ref: 7887

BacDive-ID: 1269

DSM-Number: 19096

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

description: Ectobacillus panaciterrae DSM 19096 is an aerobe, spore-forming, rod-shaped bacterium that was isolated from soil, ginseng field.

NCBI tax id

NCBI tax idMatching level
1121093strain
363872species

strain history

@refhistory
7887<- CCUG <- S.-T. Lee, Gsoil 1517
67771<- ST Lee, KAIST
121527CIP <- 2007, CCUG <- 2006, KCTC <- S.T. Lee, KAIST

doi: 10.13145/bacdive1269.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Bacillaceae
  • genus: Ectobacillus
  • species: Ectobacillus panaciterrae
  • full scientific name: Ectobacillus panaciterrae (Ten et al. 2006) Gupta et al. 2020

  • synonyms

    • @ref: 20215
    • synonym: Bacillus panaciterrae

@ref: 7887

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Bacillaceae

genus: Ectobacillus

species: Ectobacillus panaciterrae

full scientific name: Ectobacillus panaciterrae (Ten et al. 2006) Gupta et al. 2020

type strain: yes

Morphology

cell morphology

@refcell shapemotilitygram stain
67771rod-shapedno
67771positive
121527rod-shapednopositive

multimedia

  • @ref: 7887
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_19096.jpg
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7887R2A 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
37314MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
121527CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperature
7887positivegrowth30
37314positivegrowth30
67771positivegrowth30

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
67771aerobe
121527facultative anaerobe

spore formation

@reftype of sporespore formationconfidence
67771endosporeyes
69481yes100

observation

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

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 2-ketogluconate-builds acid from
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose+builds acid from27082
68371sucrose+builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose-builds acid from17306
68371cellobiose-builds acid from17057
68371salicin+builds acid from17814
68371esculin+builds acid from4853
68371arbutin+builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine+builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol+builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose-builds acid from16024
68371D-fructose+builds acid from15824
68371D-glucose+builds acid from17634
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose-builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
121527nitrate+reduction17632
121527nitrite-reduction16301

metabolite production

  • @ref: 121527
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase+3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase-
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin+3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase+3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)-
68382esterase (C 4)+
68382alkaline phosphatase-3.1.3.1
121527oxidase+
121527catalase+1.11.1.6
121527urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
121527--+--+-+-++----++---

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
121527----------++-----+---+-+++----++--+/------------+/--+/-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7887soil, ginseng fieldPocheon ProvinceRepublic of KoreaKORAsia
59560Soil,ginseng fieldPocheonRepublic of KoreaKORAsia
67771From soil of ginseng fieldRepublic of KoreaKORAsia
121527Environment, Soil, ginseng fieldPocheonRepublic 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_124756.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_14079;97_39867;98_83831;99_124756&stattab=map
  • Last taxonomy: Bacillus panaciterrae subclade
  • 16S sequence: AB245380
  • Sequence Identity:
  • Total samples: 442
  • soil counts: 275
  • aquatic counts: 33
  • animal counts: 112
  • plant counts: 22

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
78871Risk group (German classification)
1215271Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7887
  • description: Bacillus panaciterrae gene for 16S rRNA, partial sequence, strain: Gsoil 1517
  • accession: AB245380
  • length: 1476
  • database: nuccore
  • NCBI tax ID: 363872

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Ectobacillus panaciterrae DSM 19096GCA_000430785scaffoldncbi1121093
66792Bacillus panaciterrae DSM 190961121093.3wgspatric1121093
66792Bacillus panaciterrae DSM 190962524614636draftimg1121093

GC content

  • @ref: 7887
  • GC-content: 47.8

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesyes100no
69480gram-positivegram-positivePositive reaction to Gram-stainingyes77.718yes
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no92.368no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes60.733no
69480spore-formingspore-formingAbility to form endo- or exosporesyes87.977no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno96.68no
69480flagellatedmotile2+Ability to perform flagellated movementno66.717yes

External links

@ref: 7887

culture collection no.: DSM 19096, CCUG 52470, Gsoil 1517, KCTC 13929, LMG 23408, CIP 109496

straininfo link

  • @ref: 70925
  • straininfo: 289787

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17158988Bacillus panaciterrae sp. nov., isolated from soil of a ginseng field.Ten LN, Baek SH, Im WT, Liu QM, Aslam Z, Lee STInt J Syst Evol Microbiol10.1099/ijs.0.64403-02006Agriculture, Bacillus/chemistry/*classification/genetics/isolation & purification, Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Molecular Sequence Data, Panax/*growth & development, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil MicrobiologyGenetics
Phylogeny25505346Bacillus polymachus sp. nov., with a broad range of antibacterial activity, isolated from forest topsoil samples by using a modified culture method.Nguyen TM, Kim JInt J Syst Evol Microbiol10.1099/ijs.0.070326-02014Anti-Bacterial Agents/chemistry, Bacillus/chemistry/*classification/genetics/isolation & purification, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Forests, Molecular Sequence Data, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny31125305Bacillus antri sp. nov., isolated from cave soil.Rao MPN, Dong ZY, Zhang H, Niu XK, Zhang K, Fang BZ, Xiao M, Kang YQ, Li WJInt J Syst Evol Microbiol10.1099/ijsem.0.0034732019Bacillus/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, Caves/*microbiology, Cell Wall/chemistry, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Glycolipids/chemistry, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phosphatidylethanolamines, Phosphatidylglycerols/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny34346001Ectobacillus aegiceratis sp. nov., a novel bacterium isolated from branch of Aegiceras corniculatum.Chen XH, Yan XR, Huang ZH, Chen MS, Tuo LAntonie Van Leeuwenhoek10.1007/s10482-021-01622-72021Bacterial Typing Techniques, China, DNA, Bacterial/genetics, Fatty Acids/analysis, *Phospholipids/analysis, Phylogeny, *Primulaceae, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome

Reference

@idauthorscataloguedoi/urltitle
7887Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19096)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19096
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
37314Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7246
59560Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 52470)https://www.ccug.se/strain?id=52470
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)
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)
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
70925Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID289787.1StrainInfo: A central database for resolving microbial strain identifiers
121527Curators of the CIPCollection of Institut Pasteur (CIP 109496)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109496