Strain identifier

BacDive ID: 11513

Type strain: Yes

Species: Paenibacillus ehimensis

Strain Designation: EAG-5, EGA 5

Strain history: CIP <- 1996, IFO <- T. Takata, Coll. Agr. Ehime Univ., Japan: strain EGA 5

NCBI tax ID(s): 1220562 (strain), 79264 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 4162

BacDive-ID: 11513

DSM-Number: 11029

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, spore-forming, mesophilic, motile

description: Paenibacillus ehimensis EAG-5 is a facultative anaerobe, spore-forming, mesophilic bacterium that was isolated from garden soil.

NCBI tax id

NCBI tax idMatching level
1220562strain
79264species

strain history

@refhistory
4162<- IFO <- R. Takata, Ehime University, Japan
67770NBRC 15659 <-- IFO 15659 <-- R. Takata EAG-5.
119000CIP <- 1996, IFO <- T. Takata, Coll. Agr. Ehime Univ., Japan: strain EGA 5

doi: 10.13145/bacdive11513.20230509.8.1

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 ehimensis
  • full scientific name: Paenibacillus ehimensis (Kuroshima et al. 1996) Lee et al. 2004

  • synonyms

    • @ref: 20215
    • synonym: Bacillus ehimensis

@ref: 4162

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Paenibacillaceae

genus: Paenibacillus

species: Paenibacillus ehimensis

full scientific name: Paenibacillus ehimensis (Kuroshima et al. 1996) Lee et al. 2004

strain designation: EAG-5, EGA 5

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes95.212
69480100positive
119000yespositiverod-shaped

colony morphology

  • @ref: 119000
  • hemolysis ability: 1

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4162NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1; with strain-specific modifications) Composition: Soil extract 500.0 g/l Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
38522MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
119000CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
4162positivegrowth30mesophilic
38522positivegrowth30mesophilic
67770positivegrowth30mesophilic
119000positivegrowth22-37
119000nogrowth10psychrophilic
119000nogrowth45thermophilic
119000nogrowth55thermophilic

culture pH

  • @ref: 119000
  • ability: positive
  • type: growth
  • pH: 6

Physiology and metabolism

oxygen tolerance

  • @ref: 119000
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
69481yes100
69480yes100
119000yes

halophily

@refsaltgrowthtested relationconcentration
119000NaClpositivegrowth0-2 %
119000NaClnogrowth4 %
119000NaClnogrowth6 %
119000NaClnogrowth8 %
119000NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: MK-7

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
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
68371raffinose+builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose+builds acid from27082
68371sucrose+builds acid from17992
68371melibiose+builds acid from28053
68371maltose+builds acid from17306
68371N-acetylglucosamine+builds acid from59640
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
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
119000citrate-carbon source16947
119000esculin+hydrolysis4853
119000hippurate+hydrolysis606565
119000nitrate+reduction17632
119000nitrite-reduction16301
119000nitrate+respiration17632

metabolite production

  • @ref: 119000
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11900015688acetoin-
11900017234glucose-

enzymes

@refvalueactivityec
119000oxidase+
119000beta-galactosidase+3.2.1.23
119000alcohol dehydrogenase-1.1.1.1
119000gelatinase+
119000DNase-
119000caseinase-3.4.21.50
119000catalase+1.11.1.6
119000tween esterase-
119000gamma-glutamyltransferase-2.3.2.2
119000lecithinase+
119000lipase-
119000lysine decarboxylase-4.1.1.18
119000ornithine decarboxylase-4.1.1.17
119000urease-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
119000-++++------+++------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
119000+/---+/-++---++++-------+/-++/-+/-+/-+/-+/-++/-+++--+++-++------+/---

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119000+++++-+++++++++++++++++-+++----++++++----+------++---------++--------------+---++---+---++++++--++-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
4162garden soilMatsuyama, Ehime PrefectureJapanJPNAsia
67770Garden soil in MatsuyamaEhime Pref.JapanJPNAsia
119000Environment, SoilMatsuyamaJapanJPNAsia1993

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Engineered#Agriculture#Garden

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
41621Risk group (German classification)
1190001Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Bacillus ehimensis gene for 16S ribosomal RNAAB0211841513ena79264
20218Bacillus ehimensis strain KCTC3748 16S ribosomal RNA gene, partial sequenceAY1166651452ena79264
20218Paenibacillus ehimensis gene for 16S rRNA, partial sequence, strain: NBRC 15659AB6809371487ena79264

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Paenibacillus ehimensis NBRC 156591220562.3wgspatric1220562
67770Paenibacillus ehimensis NBRC 15659GCA_004000785contigncbi1220562

GC content

  • @ref: 4162
  • GC-content: 54.9
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileyes88.654no
gram-positiveno55.535no
anaerobicno98.437no
aerobicyes81.569no
halophileno95.35no
spore-formingyes94.792no
glucose-utilyes89.401no
flagellatedyes79.262no
thermophileno99.033yes
glucose-fermentno88.216no

External links

@ref: 4162

culture collection no.: DSM 11029, IFO 15659, NBRC 15659, JCM 12161, CCM 4526, CIP 104913, KCTC 3748, LMG 18048, NRRL B-23118

straininfo link

  • @ref: 80745
  • straininfo: 10546

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15143044Transfer of Bacillus ehimensis and Bacillus chitinolyticus to the genus Paenibacillus with emended descriptions of Paenibacillus ehimensis comb. nov. and Paenibacillus chitinolyticus comb. nov.Lee JS, Pyun YR, Bae KSInt J Syst Evol Microbiol10.1099/ijs.0.02765-02004Bacillus/*classification/genetics/metabolism, Bacteria/*classification/genetics/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Species SpecificityMetabolism
Phylogeny15545429Paenibacillus elgii sp. nov., with broad antimicrobial activity.Kim DS, Bae CY, Jeon JJ, Chun SJ, Oh HW, Hong SG, Baek KS, Moon EY, Bae KSInt J Syst Evol Microbiol10.1099/ijs.0.02414-02004Anaerobiosis, Anti-Bacterial Agents/*biosynthesis, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Fatty Acids/analysis/isolation & purification, Genes, rRNA, Gram-Positive Endospore-Forming Bacteria/*classification/cytology/isolation & purification/physiology, Molecular Sequence Data, Perilla frutescens/*microbiology, Phylogeny, Plant Roots/microbiology, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, TemperatureEnzymology
Enzymology16232486Purification and gene cloning of a chitosanase from Bacillus ehimensis EAG1.Akiyama K, Fujita T, Kuroshima K, Sakane T, Yokota A, Takata RJ Biosci Bioeng10.1016/s1389-1723(99)80050-41999
Phylogeny20543152Paenibacillus tianmuensis sp. nov., isolated from soil.Wu X, Fang H, Qian C, Wen Y, Shen X, Li O, Gao HInt J Syst Evol Microbiol10.1099/ijs.0.024109-02010China, DNA, Bacterial/genetics, Fatty Acids/metabolism, Molecular Sequence Data, Paenibacillus/*classification/genetics/*isolation & purification/metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil MicrobiologyMetabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4162Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11029)https://www.dsmz.de/collection/catalogue/details/culture/DSM-11029
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
38522Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16874
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
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
80745Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID10546.1StrainInfo: A central database for resolving microbial strain identifiers
119000Curators of the CIPCollection of Institut Pasteur (CIP 104913)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104913